From c28cf8abef7afe64bbc97f1ac7c1f063ba55968e Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Mon, 7 Jun 2021 20:13:57 +0200
Subject: [PATCH 001/852] Copy over code for fetchngs.

At first, this pipeline was called nf-core/fetchfastq. After initial release we found that this name was already taken by another bioinformatics tool. We took the decision to rename to nf-core/fetchngs.

In this commit I am taking the released code with the new pipeline name and putting it into a single commit.
---
 .github/CONTRIBUTING.md                |   4 +-
 .github/workflows/awsfulltest.yml      |   8 +-
 .github/workflows/awstest.yml          |   5 -
 .github/workflows/ci.yml               |  34 ++++-
 .nf-core-lint.yaml                     |  13 ++
 CHANGELOG.md                           |  25 +++-
 CITATIONS.md                           |  16 ++-
 README.md                              |  30 ++---
 assets/schema_input.json               |  36 +-----
 assets/sendmail_template.txt           |  25 ----
 bin/sra_ids_to_runinfo.py              | 170 +++++++++++++++++++++++++
 bin/sra_runinfo_to_ftp.py              | 107 ++++++++++++++++
 conf/base.config                       |   7 -
 conf/modules.config                    |  22 +++-
 conf/test.config                       |   7 +-
 conf/test_full.config                  |   7 +-
 docs/output.md                         |  50 ++------
 docs/usage.md                          |  58 +++------
 lib/NfcoreSchema.groovy                |   3 +-
 lib/NfcoreTemplate.groovy              |  26 +---
 lib/WorkflowFetchngs.groovy            |  57 +++------
 lib/WorkflowMain.groovy                |  22 +---
 main.nf                                |   8 --
 modules/local/sra_fastq_ftp.nf         |  50 ++++++++
 modules/local/sra_ids_to_runinfo.nf    |  36 ++++++
 modules/local/sra_merge_samplesheet.nf |  31 +++++
 modules/local/sra_runinfo_to_ftp.nf    |  30 +++++
 modules/local/sra_to_samplesheet.nf    |  54 ++++++++
 nextflow.config                        |  25 +---
 nextflow_schema.json                   |  84 +++---------
 workflows/fetchngs.nf                  | 159 +++++++++++------------
 31 files changed, 748 insertions(+), 461 deletions(-)
 create mode 100644 .nf-core-lint.yaml
 create mode 100755 bin/sra_ids_to_runinfo.py
 create mode 100755 bin/sra_runinfo_to_ftp.py
 create mode 100644 modules/local/sra_fastq_ftp.nf
 create mode 100644 modules/local/sra_ids_to_runinfo.nf
 create mode 100644 modules/local/sra_merge_samplesheet.nf
 create mode 100644 modules/local/sra_runinfo_to_ftp.nf
 create mode 100644 modules/local/sra_to_samplesheet.nf

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 4d6668f2..981e9187 100755
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -75,9 +75,7 @@ If you wish to contribute a new step, please use the following coding standards:
 8. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`.
 9. Do local tests that the new code works properly and as expected.
 10. Add a new test command in `.github/workflow/ci.yml`.
-11. If applicable add a [MultiQC](https://https://multiqc.info/) module.
-12. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order.
-13. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
+11. Add any descriptions of output files to `docs/output.md`.
 
 ### Default values
 
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index f69a0703..bd653ac5 100755
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -8,7 +8,6 @@ on:
     types: [published]
   workflow_dispatch:
 
-
 env:
   AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
   AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
@@ -17,7 +16,6 @@ env:
   AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
   AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
 
-
 jobs:
   run-awstest:
     name: Run AWS full tests
@@ -32,14 +30,10 @@ jobs:
       - name: Install awscli
         run: conda install -c conda-forge awscli
       - name: Start AWS batch job
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
-        # Then specify `-profile test_full` instead of `-profile test` on the AWS batch command
         run: |
           aws batch submit-job \
             --region eu-west-1 \
             --job-name nf-core-fetchngs \
             --job-queue $AWS_JOB_QUEUE \
             --job-definition $AWS_JOB_DEFINITION \
-            --container-overrides '{"command": ["nf-core/fetchngs", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/fetchngs/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/fetchngs/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+            --container-overrides '{"command": ["nf-core/fetchngs", "-r '"${GITHUB_SHA}"' -profile test_full --outdir s3://'"${AWS_S3_BUCKET}"'/fetchngs/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/fetchngs/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index 67ec91a9..79805554 100755
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -6,7 +6,6 @@ name: nf-core AWS test
 on:
   workflow_dispatch:
 
-
 env:
   AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
   AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
@@ -15,7 +14,6 @@ env:
   AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
   AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
 
-
 jobs:
   run-awstest:
     name: Run AWS tests
@@ -30,9 +28,6 @@ jobs:
       - name: Install awscli
         run: conda install -c conda-forge awscli
       - name: Start AWS batch job
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
         run: |
           aws batch submit-job \
           --region eu-west-1 \
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c01e1fce..d149562c 100755
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -23,7 +23,7 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['21.04.0', '']
+        nxf_ver: ["21.04.0", ""]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -36,8 +36,34 @@ jobs:
           sudo mv nextflow /usr/local/bin/
 
       - name: Run pipeline with test data
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker
+
+  parameters:
+    name: Test workflow parameters
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}
+    runs-on: ubuntu-latest
+    env:
+      NXF_VER: ${{ matrix.nxf_ver }}
+      NXF_ANSI_LOG: false
+    strategy:
+      matrix:
+        parameters:
+          [
+            "--nf_core_pipeline rnaseq",
+            "--ena_metadata_fields run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5",
+            --skip_fastq_download,
+          ]
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+      - name: Run pipeline with various parameters
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }}
diff --git a/.nf-core-lint.yaml b/.nf-core-lint.yaml
new file mode 100644
index 00000000..d472f25c
--- /dev/null
+++ b/.nf-core-lint.yaml
@@ -0,0 +1,13 @@
+files_unchanged:
+  - .github/CONTRIBUTING.md
+  - .github/ISSUE_TEMPLATE/bug_report.md
+  - .github/PULL_REQUEST_TEMPLATE.md
+  - .github/workflows/linting.yml
+  - assets/sendmail_template.txt
+  - docs/README.md
+  - lib/NfcoreSchema.groovy
+  - .gitignore
+files_exist:
+  - .github/markdownlint.yml
+  - bin/markdown_to_html.py
+actions_awsfulltest: False
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 15c9b7d6..04618e30 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,14 +3,29 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.0dev - [date]
+## [[1.0](https://github.com/nf-core/fetchngs/releases/tag/1.0)] - 2021-06-08
 
 Initial release of nf-core/fetchngs, created with the [nf-core](https://nf-co.re/) template.
 
-### `Added`
+## Pipeline summary
 
-### `Fixed`
+Via a single file of ids, provided one-per-line the pipeline performs the following steps:
 
-### `Dependencies`
+1. Resolve database ids back to appropriate experiment-level ids and to be compatible with the [ENA API](https://ena-docs.readthedocs.io/en/latest/retrieval/programmatic-access.html)
+2. Fetch extensive id metadata including direct download links to FastQ files via ENA API
+3. Download FastQ files in parallel via `curl` and perform `md5sum` check
+4. Collate id metadata and paths to FastQ files in a single samplesheet
 
-### `Deprecated`
+## Supported database ids
+
+Currently, the following types of example identifiers are supported:
+
+| `SRA`        | `ENA`        | `GEO`      |
+|--------------|--------------|------------|
+| SRR11605097  | ERR4007730   | GSM4432381 |
+| SRX8171613   | ERX4009132   | GSE147507  |
+| SRS6531847   | ERS4399630   |            |
+| SAMN14689442 | SAMEA6638373 |            |
+| SRP256957    | ERP120836    |            |
+| SRA1068758   | ERA2420837   |            |
+| PRJNA625551  | PRJEB37513   |            |
diff --git a/CITATIONS.md b/CITATIONS.md
index 523339ee..00f85a25 100755
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -10,10 +10,20 @@
 
 ## Pipeline tools
 
-* [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+* [Python](http://www.python.org)
 
-* [MultiQC](https://www.ncbi.nlm.nih.gov/pubmed/27312411/)
-    > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
+* [Requests](https://docs.python-requests.org/)
+
+## Pipeline resources
+
+* [ENA](https://pubmed.ncbi.nlm.nih.gov/33175160/)
+    > Harrison PW, Ahamed A, Aslam R, Alako BTF, Burgin J, Buso N, Courtot M, Fan J, Gupta D, Haseeb M, Holt S, Ibrahim T, Ivanov E, Jayathilaka S, Kadhirvelu VB, Kumar M, Lopez R, Kay S, Leinonen R, Liu X, O'Cathail C, Pakseresht A, Park Y, Pesant S, Rahman N, Rajan J, Sokolov A, Vijayaraja S, Waheed Z, Zyoud A, Burdett T, Cochrane G. The European Nucleotide Archive in 2020. Nucleic Acids Res. 2021 Jan 8;49(D1):D82-D85. doi: 10.1093/nar/gkaa1028. PubMed PMID: 33175160; PubMed Central PMCID: PMC7778925.
+
+* [SRA](https://pubmed.ncbi.nlm.nih.gov/21062823/)
+    > Leinonen R, Sugawara H, Shumway M, International Nucleotide Sequence Database Collaboration. The sequence read archive. Nucleic Acids Res. 2011 Jan;39 (Database issue):D19-21. doi: 10.1093/nar/gkq1019. Epub 2010 Nov 9. PubMed PMID: 21062823; PubMed Central PMCID: PMC3013647.
+
+* [GEO](https://pubmed.ncbi.nlm.nih.gov/23193258/)
+    > Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A. NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5. doi: 10.1093/nar/gks1193. Epub 2012 Nov 27. PubMed PMID: 23193258; PubMed Central PMCID: PMC3531084.
 
 ## Software packaging/containerisation tools
 
diff --git a/README.md b/README.md
index 598d2567..54fa6ed2 100755
--- a/README.md
+++ b/README.md
@@ -16,20 +16,22 @@
 
 ## Introduction
 
-<!-- TODO nf-core: Write a 1-2 sentence summary of what data the pipeline is for and what it does -->
-**nf-core/fetchngs** is a bioinformatics best-practice analysis pipeline for Pipeline to fetch metadata and raw FastQ files from public databases.
+**nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from public databases. At present, the pipeline supports SRA / ENA / GEO ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)).
 
-The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
+The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.
 
-<!-- TODO nf-core: Add full-sized test dataset and amend the paragraph below if applicable -->
 On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/fetchngs/results).
 
 ## Pipeline summary
 
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
+Via a single file of ids, provided one-per-line (see [example input file](https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/public_database_ids.txt)) the pipeline performs the following steps:
 
-1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+1. Resolve database ids back to appropriate experiment-level ids and to be compatible with the [ENA API](https://ena-docs.readthedocs.io/en/latest/retrieval/programmatic-access.html)
+2. Fetch extensive id metadata including direct download links to FastQ files via ENA API
+3. Download FastQ files in parallel via `curl` and perform `md5sum` check
+4. Collate id metadata and paths to FastQ files in a single samplesheet
+
+The columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core.
 
 ## Quick Start
 
@@ -49,10 +51,8 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 4. Start running your own analysis!
 
-    <!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
-
     ```console
-    nextflow run nf-core/fetchngs -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input samplesheet.csv --genome GRCh37
+    nextflow run nf-core/fetchngs -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input ids.txt
     ```
 
 ## Documentation
@@ -61,11 +61,7 @@ The nf-core/fetchngs pipeline comes with documentation about the pipeline [usage
 
 ## Credits
 
-nf-core/fetchngs was originally written by Harshil Patel.
-
-We thank the following people for their extensive assistance in the development of this pipeline:
-
-<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
+nf-core/fetchngs was originally written by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [The Bioinformatics & Biostatistics Group](https://www.crick.ac.uk/research/science-technology-platforms/bioinformatics-and-biostatistics/) at [The Francis Crick Institute, London](https://www.crick.ac.uk/) and Jose Espinosa-Carrasco ([@JoseEspinosa](https://github.com/JoseEspinosa)) from [The Comparative Bioinformatics Group](https://www.crg.eu/en/cedric_notredame) at [The Centre for Genomic Regulation, Spain](https://www.crg.eu/).
 
 ## Contributions and Support
 
@@ -75,10 +71,8 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use  nf-core/fetchngs for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+If you use  nf-core/fetchngs for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX)
 
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
 You can cite the `nf-core` publication as follows:
diff --git a/assets/schema_input.json b/assets/schema_input.json
index a3eb1209..b4141272 100755
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -5,35 +5,11 @@
     "description": "Schema for the file provided with params.input",
     "type": "array",
     "items": {
-        "type": "object",
-        "properties": {
-            "sample": {
-                "type": "string",
-                "pattern": "^\\S+$",
-                "errorMessage": "Sample name must be provided and cannot contain spaces"
-            },
-            "fastq_1": {
-                "type": "string",
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
-                "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
-            },
-            "fastq_2": {
-                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
-                "anyOf": [
-                    {
-                        "type": "string",
-                        "pattern": "^\\S+\\.f(ast)?q\\.gz$"
-                    },
-                    {
-                        "type": "string",
-                        "maxLength": 0
-                    }
-                ]
-            }
-        },
-        "required": [
-            "sample",
-            "fastq_1"
-        ]
+        "type": "array",
+        "items": {
+            "type": "string",
+            "pattern": "^[SEPG][RAS][RXSMPAJXE][EN]?[AB]?\\d{4,9}$",
+            "errorMessage": "Please provide a valid SRA, GEO or ENA identifier"
+        }
     }
 }
diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt
index 5e636e55..0c0ebc2c 100755
--- a/assets/sendmail_template.txt
+++ b/assets/sendmail_template.txt
@@ -25,29 +25,4 @@ Content-Disposition: inline; filename="nf-core-fetchngs_logo.png"
     flatten().
     join( '\n' ) %>
 
-<%
-if (mqcFile){
-def mqcFileObj = new File("$mqcFile")
-if (mqcFileObj.length() < mqcMaxSize){
-out << """
---nfcoremimeboundary
-Content-Type: text/html; name=\"multiqc_report\"
-Content-Transfer-Encoding: base64
-Content-ID: <mqcreport>
-Content-Disposition: attachment; filename=\"${mqcFileObj.getName()}\"
-
-${mqcFileObj.
-    bytes.
-    encodeBase64().
-    toString().
-    tokenize( '\n' )*.
-    toList()*.
-    collate( 76 )*.
-    collect { it.join() }.
-    flatten().
-    join( '\n' )}
-"""
-}}
-%>
-
 --nfcoremimeboundary--
diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
new file mode 100755
index 00000000..f78eb31f
--- /dev/null
+++ b/bin/sra_ids_to_runinfo.py
@@ -0,0 +1,170 @@
+#!/usr/bin/env python
+
+import os
+import re
+import sys
+import csv
+import errno
+import requests
+import argparse
+
+## Example ids supported by this script
+SRA_IDS = ['PRJNA63463', 'SAMN00765663', 'SRA023522', 'SRP003255', 'SRR390278', 'SRS282569', 'SRX111814']
+ENA_IDS = ['ERA2421642', 'ERP120836', 'ERR674736', 'ERS4399631', 'ERX629702', 'PRJEB7743', 'SAMEA3121481']
+GEO_IDS = ['GSE18729', 'GSM465244']
+ID_REGEX = r'^[A-Z]+'
+PREFIX_LIST = sorted(list(set([re.search(ID_REGEX,x).group() for x in SRA_IDS + ENA_IDS + GEO_IDS])))
+
+## List of meta fields fetched from the ENA API - can be overriden by --ena_metadata_fields
+## Full list of accepted fields can be obtained here: https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run
+ENA_METADATA_FIELDS = [
+    'accession', 'run_accession', 'experiment_accession', 'sample_accession', 'secondary_sample_accession', 'study_accession', 'secondary_study_accession', 'parent_study', 'submission_accession',
+    'run_alias', 'experiment_alias', 'sample_alias', 'study_alias',
+    'library_layout', 'library_selection', 'library_source', 'library_strategy', 'library_name',
+    'instrument_model', 'instrument_platform',
+    'base_count', 'read_count',
+    'tax_id', 'scientific_name',
+    'sample_title', 'experiment_title', 'study_title',
+    'description', 'sample_description',
+    'fastq_md5', 'fastq_bytes', 'fastq_ftp', 'fastq_galaxy', 'fastq_aspera'
+]
+
+def parse_args(args=None):
+    Description = 'Download and create a run information metadata file from SRA/ENA/GEO identifiers.'
+    Epilog = 'Example usage: python fetch_sra_runinfo.py <FILE_IN> <FILE_OUT>'
+
+    parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
+    parser.add_argument('FILE_IN', help="File containing database identifiers, one per line.")
+    parser.add_argument('FILE_OUT', help="Output file in tab-delimited format.")
+    parser.add_argument('-ef', '--ena_metadata_fields', type=str, dest="ENA_METADATA_FIELDS", default='', help="Comma-separated list of ENA metadata fields to fetch. (default: {}).".format(','.join(ENA_METADATA_FIELDS)))
+    return parser.parse_args(args)
+
+def validate_csv_param(param, valid_vals, param_desc):
+    valid_list = []
+    if param:
+        user_vals = param.split(',')
+        intersect = [i for i in user_vals if i in valid_vals]
+        if len(intersect) == len(user_vals):
+            valid_list = intersect
+        else:
+            print("ERROR: Please provide a valid value for {}!\nProvided values = {}\nAccepted values = {}".format(param_desc,param,','.join(valid_vals)))
+            sys.exit(1)
+    return valid_list
+
+def make_dir(path):
+    if not len(path) == 0:
+        try:
+            os.makedirs(path)
+        except OSError as exception:
+            if exception.errno != errno.EEXIST:
+                raise
+
+def fetch_url(url, encoding='utf-8'):
+    try:
+        r = requests.get(url)
+    except requests.exceptions.RequestException as e:
+        raise SystemExit(e)
+    if r.status_code != 200:
+        print("ERROR: Connection failed\nError code '{}'".format(r.status_code))
+        sys.exit(1)
+    return r.content.decode(encoding).splitlines()
+
+def id_to_srx(db_id):
+    ids = []
+    url = 'https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&db=sra&rettype=runinfo&term={}'.format(db_id)
+    for row in csv.DictReader(fetch_url(url), delimiter=','):
+        ids.append(row['Experiment'])
+    return ids
+
+def id_to_erx(db_id):
+    ids = []
+    fields = ['run_accession', 'experiment_accession']
+    url = 'http://www.ebi.ac.uk/ena/data/warehouse/filereport?accession={}&result=read_run&fields={}'.format(db_id,','.join(fields))
+    for row in csv.DictReader(fetch_url(url), delimiter='\t'):
+        ids.append(row['experiment_accession'])
+    return ids
+
+def gse_to_srx(db_id):
+    ids = []
+    url = 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={}&targ=gsm&view=data&form=text'.format(db_id)
+    gsm_ids = [x.split('=')[1].strip() for x in fetch_url(url) if x.find('GSM') != -1]
+    for gsm_id in gsm_ids:
+        ids += id_to_srx(gsm_id)
+    return ids
+
+def get_ena_fields():
+    fields = []
+    url = 'https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run'
+    for row in csv.DictReader(fetch_url(url), delimiter='\t'):
+        fields.append(row['columnId'])
+    return fields
+
+def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields=ENA_METADATA_FIELDS):
+    total_out = 0
+    seen_ids = []; run_ids = []
+    header = []
+    make_dir(os.path.dirname(file_out))
+    with open(file_in,"r") as fin, open(file_out,"w") as fout:
+        for line in fin:
+            db_id = line.strip()
+            match = re.search(ID_REGEX, db_id)
+            if match:
+                prefix = match.group()
+                if prefix in PREFIX_LIST:
+                    if not db_id in seen_ids:
+
+                        ids = [db_id]
+                        ## Resolve/expand these ids against GEO URL
+                        if prefix in ['GSE']:
+                            ids = gse_to_srx(db_id)
+
+                        ## Resolve/expand these ids against SRA URL
+                        elif prefix in ['GSM', 'PRJNA', 'SAMN', 'SRR']:
+                            ids = id_to_srx(db_id)
+
+                        ## Resolve/expand these ids against ENA URL
+                        elif prefix in ['ERR']:
+                            ids = id_to_erx(db_id)
+
+                        ## Resolve/expand to get run identifier from ENA and write to file
+                        for id in ids:
+                            url = 'http://www.ebi.ac.uk/ena/data/warehouse/filereport?accession={}&result=read_run&fields={}'.format(id,','.join(ena_metadata_fields))
+                            csv_dict = csv.DictReader(fetch_url(url), delimiter='\t')
+                            for row in csv_dict:
+                                run_id = row['run_accession']
+                                if not run_id in run_ids:
+                                    if total_out == 0:
+                                        header = row.keys()
+                                        fout.write('{}\n'.format('\t'.join(header)))
+                                    else:
+                                        if header != row.keys():
+                                            print("ERROR: Metadata columns do not match for id {}!\nLine: '{}'".format(run_id,line.strip()))
+                                            sys.exit(1)
+                                    fout.write('{}\n'.format('\t'.join([row[x] for x in header])))
+                                    total_out += 1
+                                    run_ids.append(run_id)
+                        seen_ids.append(db_id)
+
+                        if not ids:
+                            print("ERROR: No matches found for database id {}!\nLine: '{}'".format(db_id,line.strip()))
+                            sys.exit(1)
+
+                else:
+                    id_str = ', '.join([x + "*" for x in PREFIX_LIST])
+                    print("ERROR: Please provide a valid database id starting with {}!\nLine: '{}'".format(id_str,line.strip()))
+                    sys.exit(1)
+            else:
+                id_str = ', '.join([x + "*" for x in PREFIX_LIST])
+                print("ERROR: Please provide a valid database id starting with {}!\nLine: '{}'".format(id_str,line.strip()))
+                sys.exit(1)
+
+def main(args=None):
+    args = parse_args(args)
+    ena_metadata_fields = args.ENA_METADATA_FIELDS
+    if not args.ENA_METADATA_FIELDS:
+        ena_metadata_fields = ','.join(ENA_METADATA_FIELDS)
+    ena_metadata_fields = validate_csv_param(ena_metadata_fields, valid_vals=get_ena_fields(), param_desc='--ena_metadata_fields')
+    fetch_sra_runinfo(args.FILE_IN, args.FILE_OUT, ena_metadata_fields)
+
+if __name__ == '__main__':
+    sys.exit(main())
diff --git a/bin/sra_runinfo_to_ftp.py b/bin/sra_runinfo_to_ftp.py
new file mode 100755
index 00000000..a6f02136
--- /dev/null
+++ b/bin/sra_runinfo_to_ftp.py
@@ -0,0 +1,107 @@
+#!/usr/bin/env python
+
+import os
+import sys
+import errno
+import argparse
+import collections
+
+def parse_args(args=None):
+    Description = "Create samplesheet with FTP download links and md5ums from sample information obtained via 'sra_ids_to_runinfo.py' script."
+    Epilog = 'Example usage: python sra_runinfo_to_ftp.py <FILES_IN> <FILE_OUT>'
+
+    parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
+    parser.add_argument('FILES_IN', help="Comma-separated list of metadata file created from 'sra_ids_to_runinfo.py' script.")
+    parser.add_argument('FILE_OUT', help="Output file containing paths to download FastQ files along with their associated md5sums.")
+    return parser.parse_args(args)
+
+def make_dir(path):
+    if not len(path) == 0:
+        try:
+            os.makedirs(path)
+        except OSError as exception:
+            if exception.errno != errno.EEXIST:
+                raise
+
+def parse_sra_runinfo(file_in):
+    runinfo_dict = {}
+    with open(file_in, "r") as fin:
+        header = fin.readline().strip().split('\t')
+        for line in fin:
+            line_dict   = dict(zip(header,line.strip().split('\t')))
+            line_dict   = collections.OrderedDict(list(line_dict.items()))
+            run_id      = line_dict['run_accession']
+            exp_id      = line_dict['experiment_accession']
+            library     = line_dict['library_layout']
+            fastq_files = line_dict['fastq_ftp']
+            fastq_md5   = line_dict['fastq_md5']
+
+            db_id = exp_id
+            sample_dict = collections.OrderedDict()
+            if library == 'SINGLE':
+                sample_dict = collections.OrderedDict([('fastq_1',''), ('fastq_2',''), ('md5_1',''), ('md5_2',''), ('single_end','true')])
+                if fastq_files:
+                    sample_dict['fastq_1']  = fastq_files
+                    sample_dict['md5_1']    = fastq_md5
+                else:
+                    ## In some instances FTP links don't exist for FastQ files
+                    ## These have to be downloaded via fastq-dump / fasterq-dump / parallel-fastq-dump via the run id
+                    db_id = run_id
+
+            elif library == 'PAIRED':
+                sample_dict = collections.OrderedDict([('fastq_1',''), ('fastq_2',''), ('md5_1',''), ('md5_2',''), ('single_end','false')])
+                if fastq_files:
+                    fq_files = fastq_files.split(';')[-2:]
+                    fq_md5   = fastq_md5.split(';')[-2:]
+                    if len(fq_files) == 2:
+                        if fq_files[0].find('_1.fastq.gz') != -1 and fq_files[1].find('_2.fastq.gz') != -1:
+                            sample_dict['fastq_1'] = fq_files[0]
+                            sample_dict['fastq_2'] = fq_files[1]
+                            sample_dict['md5_1']   = fq_md5[0]
+                            sample_dict['md5_2']   = fq_md5[1]
+                        else:
+                            print("Invalid FastQ files found for database id:'{}'!.".format(run_id))
+                    else:
+                        print("Invalid number of FastQ files ({}) found for paired-end database id:'{}'!.".format(len(fq_files), run_id))
+                else:
+                    db_id = run_id
+
+            if sample_dict:
+                sample_dict.update(line_dict)
+                if db_id not in runinfo_dict:
+                    runinfo_dict[db_id] = [sample_dict]
+                else:
+                    if sample_dict in runinfo_dict[db_id]:
+                        print("Input run info file contains duplicate rows!\nLine: '{}'".format(line))
+                    else:
+                        runinfo_dict[db_id].append(sample_dict)
+
+    return runinfo_dict
+
+def sra_runinfo_to_ftp(files_in, file_out):
+    samplesheet_dict = {}
+    for file_in in files_in:
+        runinfo_dict = parse_sra_runinfo(file_in)
+        for db_id in runinfo_dict.keys():
+            if db_id not in samplesheet_dict:
+                samplesheet_dict[db_id] = runinfo_dict[db_id]
+            else:
+                print("Duplicate sample identifier found!\nID: '{}'".format(db_id))
+
+    ## Write samplesheet with paths to FastQ files and md5 sums
+    if samplesheet_dict:
+        out_dir = os.path.dirname(file_out)
+        make_dir(out_dir)
+        with open(file_out, "w") as fout:
+            header = ['id'] + list(samplesheet_dict[list(samplesheet_dict.keys())[0]][0].keys())
+            fout.write("\t".join(header) + "\n")
+            for db_id in sorted(samplesheet_dict.keys()):
+                for idx,val in enumerate(samplesheet_dict[db_id]):
+                    fout.write('\t'.join(["{}_T{}".format(db_id,idx+1)] + [val[x] for x in header[1:]]) + '\n')
+
+def main(args=None):
+    args = parse_args(args)
+    sra_runinfo_to_ftp([x.strip() for x in args.FILES_IN.split(',')], args.FILE_OUT)
+
+if __name__ == '__main__':
+    sys.exit(main())
diff --git a/conf/base.config b/conf/base.config
index a4d68207..bfff487a 100755
--- a/conf/base.config
+++ b/conf/base.config
@@ -10,7 +10,6 @@
 
 process {
 
-    // TODO nf-core: Check the defaults for all processes
     cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
     memory = { check_max( 6.GB * task.attempt, 'memory' ) }
     time   = { check_max( 4.h  * task.attempt, 'time'   ) }
@@ -20,12 +19,6 @@ process {
     maxErrors     = '-1'
 
     // Process-specific resource requirements
-    // NOTE - Please try and re-use the labels below as much as possible.
-    //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
-    //        If possible, it would be nice to keep the same label naming convention when
-    //        adding in your local modules too.
-    // TODO nf-core: Customise requirements for specific processes.
-    // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_low {
         cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
         memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
diff --git a/conf/modules.config b/conf/modules.config
index 0b1bfdec..4059a911 100755
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -22,11 +22,25 @@
 
 params {
     modules {
-        'fastqc' {
-            args = "--quiet"
+        'sra_ids_to_runinfo' {
+            publish_dir     = 'metadata'
+            publish_files   = false
         }
-        'multiqc' {
-            args = ""
+        'sra_runinfo_to_ftp' {
+            publish_dir     = 'metadata'
+            publish_files   = ['tsv':'']
+        }
+        'sra_fastq_ftp' {
+            publish_dir     = 'fastq'
+            publish_files   = ['fastq.gz':'', 'md5':'md5']
+            args            = '-C - --max-time 1200'
+        }
+        'sra_to_samplesheet' {
+            publish_dir     = 'samplesheet'
+            publish_files   = false
+        }
+        'sra_merge_samplesheet' {
+            publish_dir     = 'samplesheet'
         }
     }
 }
diff --git a/conf/test.config b/conf/test.config
index 8fadc49c..ee909409 100755
--- a/conf/test.config
+++ b/conf/test.config
@@ -20,10 +20,5 @@ params {
     max_time   = 6.h
 
     // Input data
-    // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
-    // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
-
-    // Genome references
-    genome = 'R64-1-1'
+    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/public_database_ids.txt'
 }
diff --git a/conf/test_full.config b/conf/test_full.config
index 759deae1..a5aea2dc 100755
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -15,10 +15,5 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
-    // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
-
-    // Genome references
-    genome = 'R64-1-1'
+    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/public_database_ids.txt'
 }
diff --git a/docs/output.md b/docs/output.md
index fa3c1cd8..f2cc20a5 100755
--- a/docs/output.md
+++ b/docs/output.md
@@ -2,56 +2,33 @@
 
 ## Introduction
 
-This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.
-
-The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.
-
-<!-- TODO nf-core: Write this documentation describing your workflow's output -->
+This document describes the output produced by the pipeline. The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.
 
 ## Pipeline overview
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
-* [FastQC](#fastqc) - Raw read QC
-* [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
+* [FastQ download](#fastq-download) - Download FastQ files via SRA / ENA / GEO ids
 * [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
-### FastQC
+### FastQ download
 
 <details markdown="1">
 <summary>Output files</summary>
 
-* `fastqc/`
-    * `*_fastqc.html`: FastQC report containing quality metrics.
-    * `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
+* `fastq/`
+    * `*.fastq.gz`: Paired-end/single-end reads downloaded from the ENA / SRA.
+* `fastq/md5/`
+    * `*.md5`: Files containing `md5` sum for FastQ files downloaded from the ENA / SRA.
+* `samplesheet/`
+    * `samplesheet.csv`: Auto-created samplesheet with collated metadata and paths to downloaded FastQ files.
+* `metadata/`
+    * `*.runinfo_ftp.tsv`: Re-formatted metadata file downloaded from the ENA
+    * `*.runinfo.tsv`: Original metadata file downloaded from the ENA
 
 </details>
 
-[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
-
-![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png)
-
-![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png)
-
-![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png)
-
-> **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
-
-### MultiQC
-
-<details markdown="1">
-<summary>Output files</summary>
-
-* `multiqc/`
-    * `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
-    * `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
-    * `multiqc_plots/`: directory containing static images from the report in various formats.
-
-</details>
-
-[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
-
-Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
+Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introduction) for a list of supported public repository identifiers and how to provide them to the pipeline. The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5sums. If download links exist, the files will be downloaded in parallel by FTP otherwise they will NOT be downloaded. This is intentional because the tools such as `parallel-fastq-dump`, `fasterq-dump`, `prefetch` etc require pre-existing configuration files in the users home directory which makes automation tricky across different platforms and containerisation.
 
 ### Pipeline information
 
@@ -61,7 +38,6 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
 * `pipeline_info/`
     * Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
     * Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.csv`.
-    * Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
 
 </details>
 
diff --git a/docs/usage.md b/docs/usage.md
index e75b575e..68c1422d 100755
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -6,58 +6,40 @@
 
 ## Introduction
 
-<!-- TODO nf-core: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website. -->
+The pipeline has been set-up to automatically download and process the raw FastQ files from public repositories. Identifiers can be provided in a file, one-per-line via the `--input` parameter. Currently, the following types of example identifiers are supported:
 
-## Samplesheet input
+| `SRA`        | `ENA`        | `GEO`      |
+|--------------|--------------|------------|
+| SRR11605097  | ERR4007730   | GSM4432381 |
+| SRX8171613   | ERX4009132   | GSE147507  |
+| SRS6531847   | ERS4399630   |            |
+| SAMN14689442 | SAMEA6638373 |            |
+| SRP256957    | ERP120836    |            |
+| SRA1068758   | ERA2420837   |            |
+| PRJNA625551  | PRJEB37513   |            |
 
-You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below.
+If `SRR`/`ERR` run ids are provided then these will be resolved back to their appropriate `SRX`/`ERX` ids to be able to merge multiple runs from the same experiment. This is conceptually the same as merging multiple libraries sequenced from the same sample.
 
-```bash
---input '[path to samplesheet file]'
-```
-
-### Multiple runs of the same sample
-
-The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes:
-
-```bash
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
-CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz
-CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz
-```
-
-### Full samplesheet
+The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5 sums. If download links exist, the files will be downloaded in parallel by FTP otherwise they will NOT be downloaded. This is intentional because tools such as `parallel-fastq-dump`, `fasterq-dump`, `prefetch` etc require pre-existing configuration files in the users home directory which makes automation tricky across different platforms and containerisation. We may add this functionality in later releases.
 
-The pipeline will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 3 columns to match those defined in the table below.
+As a bonus, the columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core. It is highly recommended that you double-check that all of the identifiers you defined using `--input` are represented in the samplesheet. Also, public databases don't reliably hold information such as strandedness information so you may need to amend these entries too if for example your samplesheet was created by providing `--nf_core_pipeline rnaseq`.
 
-A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice.
+All of the sample metadata obtained from the ENA will be appended as additional columns to help you manually curate the samplesheet before you run the pipeline. You can customise the metadata fields that are appended to the samplesheet via the `--ena_metadata_fields` parameter. The default list of fields used by the pipeline can be found at the top of the [`bin/sra_ids_to_runinfo.py`](https://github.com/nf-core/fetchngs/blob/master/bin/sra_ids_to_runinfo.py) script within the pipeline repo. However, this pipeline requires a minimal set of fields to download FastQ files i.e. `'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'`. A comprehensive list of accepted metadata fields can be obtained from the [ENA API](https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run]).
 
-```bash
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
-CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz
-CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz
-TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz,
-TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz,
-TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz,
-TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,
-```
+If you have a GEO accession (found in the data availability section of published papers) you can directly download a text file containing the appropriate SRA ids to pass to the pipeline:
 
-| Column         | Description                                                                                                                 |
-|----------------|-----------------------------------------------------------------------------------------------------------------------------|
-| `sample`       | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample.               |
-| `fastq_1`      | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".  |
-| `fastq_2`      | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".  |
+* Search for your GEO accession on [GEO](https://www.ncbi.nlm.nih.gov/geo)
+* Click `SRA Run Selector` at the bottom of the GEO accession page
+* Select the desired samples in the `SRA Run Selector` and then download the `Accession List`
 
-An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
+This downloads a text file called `SRR_Acc_List.txt` which can be directly provided to the pipeline e.g. `--public_data_ids SRR_Acc_List.txt`.
 
 ## Running the pipeline
 
 The typical command for running the pipeline is as follows:
 
 ```bash
-nextflow run nf-core/fetchngs --input samplesheet.csv --genome GRCh37 -profile docker
+nextflow run nf-core/fetchngs --input ids.txt -profile docker
 ```
 
 This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy
index 16986434..8d6920dd 100755
--- a/lib/NfcoreSchema.groovy
+++ b/lib/NfcoreSchema.groovy
@@ -121,7 +121,8 @@ class NfcoreSchema {
             def params_ignore = params.schema_ignore_params.split(',') + 'schema_ignore_params'
             def expectedParamsLowerCase = expectedParams.collect{ it.replace("-", "").toLowerCase() }
             def specifiedParamLowerCase = specifiedParam.replace("-", "").toLowerCase()
-            if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !expectedParamsLowerCase.contains(specifiedParamLowerCase)) {
+            def isCamelCaseBug = (specifiedParam.contains("-") && !expectedParams.contains(specifiedParam) && expectedParamsLowerCase.contains(specifiedParamLowerCase))
+            if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !isCamelCaseBug) {
                 // Temporarily remove camelCase/camel-case params #1035
                 def unexpectedParamsLowerCase = unexpectedParams.collect{ it.replace("-", "").toLowerCase()}
                 if (!unexpectedParamsLowerCase.contains(specifiedParamLowerCase)){
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
index b6e689ec..b8fd59ab 100755
--- a/lib/NfcoreTemplate.groovy
+++ b/lib/NfcoreTemplate.groovy
@@ -42,7 +42,7 @@ class NfcoreTemplate {
     //
     // Construct and send completion email
     //
-    public static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[]) {
+    public static void email(workflow, params, summary_params, projectDir, log) {
 
         // Set up the e-mail variables
         def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
@@ -80,24 +80,6 @@ class NfcoreTemplate {
         email_fields['projectDir']   = workflow.projectDir
         email_fields['summary']      = summary << misc_fields
 
-        // On success try attach the multiqc report
-        def mqc_report = null
-        try {
-            if (workflow.success) {
-                mqc_report = multiqc_report.getVal()
-                if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
-                    if (mqc_report.size() > 1) {
-                        log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
-                    }
-                    mqc_report = mqc_report[0]
-                }
-            }
-        } catch (all) {
-            if (multiqc_report) {
-                log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
-            }
-        }
-
         // Check if we are only sending emails on failure
         def email_address = params.email
         if (!params.email && params.email_on_fail && !workflow.success) {
@@ -116,8 +98,7 @@ class NfcoreTemplate {
         def email_html    = html_template.toString()
 
         // Render the sendmail template
-        def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit
-        def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
+        def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir" ]
         def sf                     = new File("$projectDir/assets/sendmail_template.txt")
         def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
         def sendmail_html          = sendmail_template.toString()
@@ -133,9 +114,6 @@ class NfcoreTemplate {
             } catch (all) {
                 // Catch failures and try with plaintext
                 def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
-                if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
-                    mail_cmd += [ '-A', mqc_report ]
-                }
                 mail_cmd.execute() << email_html
                 log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
             }
diff --git a/lib/WorkflowFetchngs.groovy b/lib/WorkflowFetchngs.groovy
index bd9b9ebe..ccff938b 100755
--- a/lib/WorkflowFetchngs.groovy
+++ b/lib/WorkflowFetchngs.groovy
@@ -7,53 +7,26 @@ class WorkflowFetchngs {
     //
     // Check and validate parameters
     //
-    public static void initialise(params, log) {
-        genomeExistsError(params, log)
-
-        if (!params.fasta) {
-            log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
+    public static void initialise(params, log, valid_params) {
+        // Check minimal ENA fields are provided to download FastQ files
+        def ena_metadata_fields = params.ena_metadata_fields ? params.ena_metadata_fields.split(',').collect{ it.trim().toLowerCase() } : valid_params['ena_metadata_fields']
+        if (!ena_metadata_fields.containsAll(valid_params['ena_metadata_fields'])) {
+            log.error "Invalid option: '${params.ena_metadata_fields}'. Minimally required fields for '--ena_metadata_fields': '${valid_params['ena_metadata_fields'].join(',')}'"
             System.exit(1)
         }
     }
 
     //
-    // Get workflow summary for MultiQC
+    // Print a warning after pipeline has completed
     //
-    public static String paramsSummaryMultiqc(workflow, summary) {
-        String summary_section = ''
-        for (group in summary.keySet()) {
-            def group_params = summary.get(group)  // This gets the parameters of that particular group
-            if (group_params) {
-                summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
-                summary_section += "    <dl class=\"dl-horizontal\">\n"
-                for (param in group_params.keySet()) {
-                    summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
-                }
-                summary_section += "    </dl>\n"
-            }
-        }
-
-        String yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
-        yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
-        yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
-        yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
-        yaml_file_text        += "plot_type: 'html'\n"
-        yaml_file_text        += "data: |\n"
-        yaml_file_text        += "${summary_section}"
-        return yaml_file_text
-    }
-
-    //
-    // Exit pipeline if incorrect --genome key provided
-    //
-    private static void genomeExistsError(params, log) {
-        if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
-            log.error "=============================================================================\n" +
-                "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
-                "  Currently, the available genome keys are:\n" +
-                "  ${params.genomes.keySet().join(", ")}\n" +
-                "==================================================================================="
-            System.exit(1)
-        }
+    public static void curateSamplesheetWarn(log) {
+        log.warn "=============================================================================\n" +
+            "  Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" +
+            "  Public databases don't reliably hold information such as strandedness\n" +
+            "  information, controls etc\n\n" +
+            "  All of the sample metadata obtained from the ENA has been appended\n" +
+            "  as additional columns to help you manually curate the samplesheet before\n" +
+            "  running nf-core/other pipelines.\n" +
+            "==================================================================================="
     }
 }
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index e8304ec2..a15e60d8 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -9,9 +9,8 @@ class WorkflowMain {
     //
     public static String citation(workflow) {
         return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-            // TODO nf-core: Add Zenodo DOI for pipeline after first release
-            //"* The pipeline\n" +
-            //"  https://doi.org/10.5281/zenodo.XXXXXXX\n\n" +
+            "* The pipeline\n" +
+            "  https://doi.org/10.5281/zenodo.XXXXXXX\n\n" +
             "* The nf-core framework\n" +
             "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
             "* Software dependencies\n" +
@@ -22,7 +21,7 @@ class WorkflowMain {
     // Print help to screen if required
     //
     public static String help(workflow, params, log) {
-        def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
+        def command = "nextflow run ${workflow.manifest.name} --input ids.txt -profile docker"
         def help_string = ''
         help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs)
         help_string += NfcoreSchema.paramsHelp(workflow, params, command)
@@ -74,21 +73,8 @@ class WorkflowMain {
 
         // Check input has been provided
         if (!params.input) {
-            log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'"
+            log.error "Please provide an input samplesheet to the pipeline e.g. '--input ids.txt'"
             System.exit(1)
         }
     }
-
-    //
-    // Get attribute from genome config file e.g. fasta
-    //
-    public static String getGenomeAttribute(params, attribute) {
-        def val = ''
-        if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
-            if (params.genomes[ params.genome ].containsKey(attribute)) {
-                val = params.genomes[ params.genome ][ attribute ]
-            }
-        }
-        return val
-    }
 }
diff --git a/main.nf b/main.nf
index 56291035..f28f690f 100755
--- a/main.nf
+++ b/main.nf
@@ -11,14 +11,6 @@
 
 nextflow.enable.dsl = 2
 
-/*
-========================================================================================
-    GENOME PARAMETER VALUES
-========================================================================================
-*/
-
-params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
-
 /*
 ========================================================================================
     VALIDATE & PRINT PARAMETER SUMMARY
diff --git a/modules/local/sra_fastq_ftp.nf b/modules/local/sra_fastq_ftp.nf
new file mode 100644
index 00000000..126c0647
--- /dev/null
+++ b/modules/local/sra_fastq_ftp.nf
@@ -0,0 +1,50 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process SRA_FASTQ_FTP {
+    tag "$meta.id"
+    label 'process_medium'
+    label 'error_retry'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
+    } else {
+        container "biocontainers/biocontainers:v1.2.0_cv1"
+    }
+
+    input:
+    tuple val(meta), val(fastq)
+
+    output:
+    tuple val(meta), path("*fastq.gz"), emit: fastq
+    tuple val(meta), path("*md5")     , emit: md5
+
+    script:
+    if (meta.single_end) {
+        """
+        bash -c 'until curl $options.args -L ${fastq[0]} -o ${meta.id}.fastq.gz; do sleep 1; done';
+
+        echo "${meta.md5_1} ${meta.id}.fastq.gz" > ${meta.id}.fastq.gz.md5
+        md5sum -c ${meta.id}.fastq.gz.md5
+        """
+    } else {
+        """
+        bash -c 'until curl $options.args -L ${fastq[0]} -o ${meta.id}_1.fastq.gz; do sleep 1; done';
+
+        echo "${meta.md5_1} ${meta.id}_1.fastq.gz" > ${meta.id}_1.fastq.gz.md5
+        md5sum -c ${meta.id}_1.fastq.gz.md5
+
+        bash -c 'until curl $options.args -L ${fastq[1]} -o ${meta.id}_2.fastq.gz; do sleep 1; done';
+
+        echo "${meta.md5_2} ${meta.id}_2.fastq.gz" > ${meta.id}_2.fastq.gz.md5
+        md5sum -c ${meta.id}_2.fastq.gz.md5
+        """
+    }
+}
diff --git a/modules/local/sra_ids_to_runinfo.nf b/modules/local/sra_ids_to_runinfo.nf
new file mode 100644
index 00000000..d5b9705c
--- /dev/null
+++ b/modules/local/sra_ids_to_runinfo.nf
@@ -0,0 +1,36 @@
+// Import generic module functions
+include { saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+
+process SRA_IDS_TO_RUNINFO {
+    tag "$id"
+    label 'error_retry'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+
+    conda (params.enable_conda ? "conda-forge::requests=2.24.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/requests:2.24.0"
+    } else {
+        container "quay.io/biocontainers/requests:2.24.0"
+    }
+
+    input:
+    val id
+    val fields
+
+    output:
+    path "*.tsv", emit: tsv
+
+    script:
+    def metadata_fields = fields ? "--ena_metadata_fields ${fields}" : ''
+    """
+    echo $id > id.txt
+    sra_ids_to_runinfo.py \\
+        id.txt \\
+        ${id}.runinfo.tsv \\
+        $metadata_fields
+    """
+}
diff --git a/modules/local/sra_merge_samplesheet.nf b/modules/local/sra_merge_samplesheet.nf
new file mode 100644
index 00000000..423be634
--- /dev/null
+++ b/modules/local/sra_merge_samplesheet.nf
@@ -0,0 +1,31 @@
+// Import generic module functions
+include { saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+
+process SRA_MERGE_SAMPLESHEET {
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
+    } else {
+        container "biocontainers/biocontainers:v1.2.0_cv1"
+    }
+
+    input:
+    path ('samplesheets/*')
+
+    output:
+    path "*csv", emit: csv
+
+    script:
+    """
+    head -n 1 `ls ./samplesheets/* | head -n 1` > samplesheet.csv
+    for fileid in `ls ./samplesheets/*`; do
+        awk 'NR>1' \$fileid >> samplesheet.csv
+    done
+    """
+}
diff --git a/modules/local/sra_runinfo_to_ftp.nf b/modules/local/sra_runinfo_to_ftp.nf
new file mode 100644
index 00000000..1418bf34
--- /dev/null
+++ b/modules/local/sra_runinfo_to_ftp.nf
@@ -0,0 +1,30 @@
+// Import generic module functions
+include { saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+
+process SRA_RUNINFO_TO_FTP {
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+
+    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
+    } else {
+        container "quay.io/biocontainers/python:3.8.3"
+    }
+
+    input:
+    path runinfo
+
+    output:
+    path "*.tsv", emit: tsv
+
+    script:
+    """
+    sra_runinfo_to_ftp.py \\
+        ${runinfo.join(',')} \\
+        ${runinfo.toString().tokenize(".")[0]}.runinfo_ftp.tsv
+    """
+}
diff --git a/modules/local/sra_to_samplesheet.nf b/modules/local/sra_to_samplesheet.nf
new file mode 100644
index 00000000..a30e0f5e
--- /dev/null
+++ b/modules/local/sra_to_samplesheet.nf
@@ -0,0 +1,54 @@
+// Import generic module functions
+include { saveFiles; getSoftwareName } from './functions'
+
+params.options     = [:]
+params.results_dir = ''
+
+process SRA_TO_SAMPLESHEET {
+    tag "$meta.id"
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    memory 100.MB
+
+    input:
+    tuple val(meta), path(fastq)
+    val   pipeline
+
+    output:
+    tuple val(meta), path("*csv"), emit: csv
+
+    exec:
+    //  Remove custom keys needed to download the data
+    def meta_map = meta.clone()
+    meta_map.remove("id")
+    meta_map.remove("fastq_1")
+    meta_map.remove("fastq_2")
+    meta_map.remove("md5_1")
+    meta_map.remove("md5_2")
+    meta_map.remove("single_end")
+
+    // Add relevant fields to the beginning of the map
+    pipeline_map = [
+        sample  : "${meta.id.split('_')[0..-2].join('_')}",
+        fastq_1 : "${params.outdir}/${params.results_dir}/${fastq[0]}",
+        fastq_2 : meta.single_end ? '' : "${params.outdir}/${params.results_dir}/${fastq[1]}"
+    ]
+
+    // Add nf-core pipeline specific entries
+    if (pipeline) {
+        if (pipeline == 'rnaseq') {
+            pipeline_map << [ strandedness: 'unstranded' ]
+        }
+    }
+    pipeline_map << meta_map
+
+    // Create a samplesheet
+    csv  = pipeline_map.keySet().collect{ '"' + it + '"'}.join(",") + '\n'
+    csv += pipeline_map.values().collect{ '"' + it + '"'}.join(",")
+
+    // Write to file
+    def file = task.workDir.resolve("${meta.id}.samplesheet.csv")
+    file.text = csv
+}
diff --git a/nextflow.config b/nextflow.config
index 1b9e9ad4..94ddb47f 100755
--- a/nextflow.config
+++ b/nextflow.config
@@ -9,19 +9,11 @@
 // Global default params, used in configs
 params {
 
-    // TODO nf-core: Specify your pipeline's command line flags
     // Input options
     input                      = null
-
-    // References
-    genome                     = null
-    igenomes_base              = 's3://ngi-igenomes/igenomes/'
-    igenomes_ignore            = false
-
-    // MultiQC options
-    multiqc_config             = null
-    multiqc_title              = null
-    max_multiqc_email_size     = '25.MB'
+    nf_core_pipeline           = null
+    ena_metadata_fields        = null
+    skip_fastq_download        = false
 
     // Boilerplate options
     outdir                     = './results'
@@ -34,7 +26,7 @@ params {
     help                       = false
     validate_params            = true
     show_hidden_params         = false
-    schema_ignore_params       = 'genomes,modules'
+    schema_ignore_params       = 'modules,igenomes_base'
     enable_conda               = false
     singularity_pull_docker_container = false
 
@@ -68,13 +60,6 @@ try {
     System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
 }
 
-// Load igenomes.config if required
-if (!params.igenomes_ignore) {
-    includeConfig 'conf/igenomes.config'
-} else {
-    params.genomes = [:]
-}
-
 profiles {
     debug { process.beforeScript = 'echo $HOSTNAME' }
     conda {
@@ -161,7 +146,7 @@ manifest {
     description     = 'Pipeline to fetch metadata and raw FastQ files from public databases'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.04.0'
-    version         = '1.0dev'
+    version         = '1.0'
 }
 
 // Function to ensure that resource requirements don't go beyond
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 4b88f9e5..e5b24df1 100755
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -17,12 +17,27 @@
                 "input": {
                     "type": "string",
                     "format": "file-path",
-                    "mimetype": "text/csv",
-                    "pattern": "\\.csv$",
+                    "mimetype": "text/plain",
+                    "pattern": "\\.txt$",
                     "schema": "assets/schema_input.json",
-                    "description": "Path to comma-separated file containing information about the samples in the experiment.",
-                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/fetchngs/usage#samplesheet-input).",
-                    "fa_icon": "fas fa-file-csv"
+                    "fa_icon": "fas fa-file-excel",
+                    "description": "File containing SRA/ENA/GEO identifiers one per line to download their associated metadata and FastQ files."
+                },
+                "ena_metadata_fields": {
+                    "type": "string",
+                    "fa_icon": "fas fa-columns",
+                    "description": "Comma-separated list of ENA metadata fields to fetch before downloading data.",
+                    "help_text": "The default list of fields used by the pipeline can be found at the top of the [`bin/sra_ids_to_runinfo.py`](https://github.com/nf-core/fetchngs/blob/master/bin/sra_ids_to_runinfo.py) script within the pipeline repo. This pipeline requires a minimal set of fields to download FastQ files i.e. `'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'`. Full list of accepted metadata fields can be obtained from the [ENA API](https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run])."
+                },
+                "nf_core_pipeline": {
+                    "type": "string",
+                    "fa_icon": "fab fa-apple",
+                    "description": "Name of supported nf-core pipeline e.g.  'rnaseq'. A samplesheet for direct use with the pipeline will be created with the appropriate columns."
+                },
+                "skip_fastq_download": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-fast-forward",
+                    "description": "Only download metadata for public data database ids and don't download the FastQ files."
                 },
                 "outdir": {
                     "type": "string",
@@ -36,49 +51,6 @@
                     "fa_icon": "fas fa-envelope",
                     "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
                     "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
-                },
-                "multiqc_title": {
-                    "type": "string",
-                    "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
-                    "fa_icon": "fas fa-file-signature"
-                }
-            }
-        },
-        "reference_genome_options": {
-            "title": "Reference genome options",
-            "type": "object",
-            "fa_icon": "fas fa-dna",
-            "description": "Reference genome related files and options required for the workflow.",
-            "properties": {
-                "genome": {
-                    "type": "string",
-                    "description": "Name of iGenomes reference.",
-                    "fa_icon": "fas fa-book",
-                    "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
-                },
-                "fasta": {
-                    "type": "string",
-                    "format": "file-path",
-                    "mimetype": "text/plain",
-                    "pattern": "\\.fn?a(sta)?(\\.gz)?$",
-                    "description": "Path to FASTA genome file.",
-                    "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
-                    "fa_icon": "far fa-file-code"
-                },
-                "igenomes_base": {
-                    "type": "string",
-                    "format": "directory-path",
-                    "description": "Directory / URL base for iGenomes references.",
-                    "default": "s3://ngi-igenomes/igenomes",
-                    "fa_icon": "fas fa-cloud-download-alt",
-                    "hidden": true
-                },
-                "igenomes_ignore": {
-                    "type": "boolean",
-                    "description": "Do not load the iGenomes reference config.",
-                    "fa_icon": "fas fa-ban",
-                    "hidden": true,
-                    "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
                 }
             }
         },
@@ -214,25 +186,12 @@
                     "fa_icon": "fas fa-remove-format",
                     "hidden": true
                 },
-                "max_multiqc_email_size": {
-                    "type": "string",
-                    "description": "File size limit when attaching MultiQC reports to summary emails.",
-                    "default": "25.MB",
-                    "fa_icon": "fas fa-file-upload",
-                    "hidden": true
-                },
                 "monochrome_logs": {
                     "type": "boolean",
                     "description": "Do not use coloured log outputs.",
                     "fa_icon": "fas fa-palette",
                     "hidden": true
                 },
-                "multiqc_config": {
-                    "type": "string",
-                    "description": "Custom config file to supply to MultiQC.",
-                    "fa_icon": "fas fa-cog",
-                    "hidden": true
-                },
                 "tracedir": {
                     "type": "string",
                     "description": "Directory to keep pipeline Nextflow logs and reports.",
@@ -274,9 +233,6 @@
         {
             "$ref": "#/definitions/input_output_options"
         },
-        {
-            "$ref": "#/definitions/reference_genome_options"
-        },
         {
             "$ref": "#/definitions/institutional_config_options"
         },
diff --git a/workflows/fetchngs.nf b/workflows/fetchngs.nf
index 2541ff11..4ba08fb3 100755
--- a/workflows/fetchngs.nf
+++ b/workflows/fetchngs.nf
@@ -4,27 +4,26 @@
 ========================================================================================
 */
 
+def valid_params = [
+    ena_metadata_fields : ['run_accession', 'experiment_accession', 'library_layout', 'fastq_ftp', 'fastq_md5']
+]
+
 def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
 
 // Validate input parameters
-WorkflowFetchngs.initialise(params, log)
-
-// TODO nf-core: Add all file path parameters for the pipeline to the list below
-// Check input path parameters to see if they exist
-def checkPathParamList = [ params.input, params.multiqc_config, params.fasta ]
-for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
+WorkflowFetchngs.initialise(params, log, valid_params)
 
 // Check mandatory parameters
-if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
-
-/*
-========================================================================================
-    CONFIG FILES
-========================================================================================
-*/
-
-ch_multiqc_config        = file("$projectDir/assets/multiqc_config.yaml", checkIfExists: true)
-ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
+if (params.input) {
+    Channel
+        .from(file(params.input, checkIfExists: true))
+        .splitCsv(header:false, sep:'', strip:true)
+        .map { it[0] }
+        .unique()
+        .set { ch_ids }
+} else {
+    exit 1, 'Input file with public database ids not specified!'
+}
 
 /*
 ========================================================================================
@@ -35,30 +34,11 @@ ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multi
 // Don't overwrite global params.modules, create a copy instead and use that within the main script.
 def modules = params.modules.clone()
 
-//
-// MODULE: Local to the pipeline
-//
-include { GET_SOFTWARE_VERSIONS } from '../modules/local/get_software_versions' addParams( options: [publish_files : ['csv':'']] )
-
-//
-// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
-//
-include { INPUT_CHECK } from '../subworkflows/local/input_check' addParams( options: [:] )
-
-/*
-========================================================================================
-    IMPORT NF-CORE MODULES/SUBWORKFLOWS
-========================================================================================
-*/
-
-def multiqc_options   = modules['multiqc']
-multiqc_options.args += params.multiqc_title ? Utils.joinModuleArgs(["--title \"$params.multiqc_title\""]) : ''
-
-//
-// MODULE: Installed directly from nf-core/modules
-//
-include { FASTQC  } from '../modules/nf-core/software/fastqc/main'  addParams( options: modules['fastqc'] )
-include { MULTIQC } from '../modules/nf-core/software/multiqc/main' addParams( options: multiqc_options   )
+include { SRA_IDS_TO_RUNINFO    } from '../modules/local/sra_ids_to_runinfo'    addParams( options: modules['sra_ids_to_runinfo']    )
+include { SRA_RUNINFO_TO_FTP    } from '../modules/local/sra_runinfo_to_ftp'    addParams( options: modules['sra_runinfo_to_ftp']    )
+include { SRA_FASTQ_FTP         } from '../modules/local/sra_fastq_ftp'         addParams( options: modules['sra_fastq_ftp']         )
+include { SRA_TO_SAMPLESHEET    } from '../modules/local/sra_to_samplesheet'    addParams( options: modules['sra_to_samplesheet'], results_dir: modules['sra_fastq_ftp'].publish_dir )
+include { SRA_MERGE_SAMPLESHEET } from '../modules/local/sra_merge_samplesheet' addParams( options: modules['sra_merge_samplesheet'] )
 
 /*
 ========================================================================================
@@ -66,61 +46,67 @@ include { MULTIQC } from '../modules/nf-core/software/multiqc/main' addParams( o
 ========================================================================================
 */
 
-// Info required for completion email and summary
-def multiqc_report = []
-
 workflow FETCHNGS {
 
-    ch_software_versions = Channel.empty()
-
     //
-    // SUBWORKFLOW: Read in samplesheet, validate and stage input files
+    // MODULE: Get SRA run information for public database ids
     //
-    INPUT_CHECK (
-        ch_input
+    SRA_IDS_TO_RUNINFO (
+        ch_ids,
+        params.ena_metadata_fields ?: ''
     )
 
     //
-    // MODULE: Run FastQC
+    // MODULE: Parse SRA run information, create file containing FTP links and read into workflow as [ meta, [reads] ]
     //
-    FASTQC (
-        INPUT_CHECK.out.reads
+    SRA_RUNINFO_TO_FTP (
+        SRA_IDS_TO_RUNINFO.out.tsv
     )
-    ch_software_versions = ch_software_versions.mix(FASTQC.out.version.first().ifEmpty(null))
 
-    //
-    // MODULE: Pipeline reporting
-    //
-    ch_software_versions
-        .map { it -> if (it) [ it.baseName, it ] }
-        .groupTuple()
-        .map { it[1][0] }
-        .flatten()
-        .collect()
-        .set { ch_software_versions }
-
-    GET_SOFTWARE_VERSIONS (
-        ch_software_versions.map { it }.collect()
-    )
-
-    //
-    // MODULE: MultiQC
-    //
-    workflow_summary    = WorkflowFetchngs.paramsSummaryMultiqc(workflow, summary_params)
-    ch_workflow_summary = Channel.value(workflow_summary)
-
-    ch_multiqc_files = Channel.empty()
-    ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config))
-    ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([]))
-    ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
-    ch_multiqc_files = ch_multiqc_files.mix(GET_SOFTWARE_VERSIONS.out.yaml.collect())
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
-
-    MULTIQC (
-        ch_multiqc_files.collect()
-    )
-    multiqc_report       = MULTIQC.out.report.toList()
-    ch_software_versions = ch_software_versions.mix(MULTIQC.out.version.ifEmpty(null))
+    SRA_RUNINFO_TO_FTP
+        .out
+        .tsv
+        .splitCsv(header:true, sep:'\t')
+        .map {
+            meta ->
+                meta.single_end = meta.single_end.toBoolean()
+                [ meta, [ meta.fastq_1, meta.fastq_2 ] ]
+        }
+        .unique()
+        .set { ch_sra_reads }
+
+    if (!params.skip_fastq_download) {
+        //
+        // MODULE: If FTP link is provided in run information then download FastQ directly via FTP and validate with md5sums
+        //
+        SRA_FASTQ_FTP (
+            ch_sra_reads.map { meta, reads -> if (meta.fastq_1)  [ meta, reads ] }
+        )
+
+        //
+        // MODULE: Stage FastQ files downloaded by SRA together and auto-create a samplesheet
+        //
+        SRA_TO_SAMPLESHEET (
+            SRA_FASTQ_FTP.out.fastq,
+            params.nf_core_pipeline ?: ''
+        )
+
+        //
+        // MODULE: Create a merged samplesheet across all samples for the pipeline
+        //
+        SRA_MERGE_SAMPLESHEET (
+            SRA_TO_SAMPLESHEET.out.csv.collect{it[1]}
+        )
+
+        //
+        // If ids don't have a direct FTP download link write them to file for download outside of the pipeline
+        //
+        def no_ids_file = ["${params.outdir}", "${modules['sra_fastq_ftp'].publish_dir}", "IDS_NOT_DOWNLOADED.txt" ].join(File.separator)
+        ch_sra_reads
+            .map { meta, reads -> if (!meta.fastq_1) "${meta.id.split('_')[0..-2].join('_')}" }
+            .unique()
+            .collectFile(name: no_ids_file, sort: true, newLine: true)
+    }
 }
 
 /*
@@ -130,8 +116,9 @@ workflow FETCHNGS {
 */
 
 workflow.onComplete {
-    NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
+    NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)
     NfcoreTemplate.summary(workflow, params, log)
+    WorkflowFetchngs.curateSamplesheetWarn(log)
 }
 
 /*

From 7a7b57323519b37462588390ceceed2e9ae0e6ad Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 7 Jun 2021 21:56:22 +0100
Subject: [PATCH 002/852] Be explicit about Illumina mode of viralrecon

---
 README.md     | 4 ++--
 docs/usage.md | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 54fa6ed2..0eb5cbfb 100755
--- a/README.md
+++ b/README.md
@@ -31,7 +31,7 @@ Via a single file of ids, provided one-per-line (see [example input file](https:
 3. Download FastQ files in parallel via `curl` and perform `md5sum` check
 4. Collate id metadata and paths to FastQ files in a single samplesheet
 
-The columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core.
+The columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core.
 
 ## Quick Start
 
@@ -52,7 +52,7 @@ The columns in the auto-created samplesheet can be tailored to be accepted out-o
 4. Start running your own analysis!
 
     ```console
-    nextflow run nf-core/fetchngs -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input ids.txt
+    nextflow run nf-core/fetchngs --input ids.txt -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
     ```
 
 ## Documentation
diff --git a/docs/usage.md b/docs/usage.md
index 68c1422d..2852035b 100755
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -22,7 +22,7 @@ If `SRR`/`ERR` run ids are provided then these will be resolved back to their ap
 
 The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5 sums. If download links exist, the files will be downloaded in parallel by FTP otherwise they will NOT be downloaded. This is intentional because tools such as `parallel-fastq-dump`, `fasterq-dump`, `prefetch` etc require pre-existing configuration files in the users home directory which makes automation tricky across different platforms and containerisation. We may add this functionality in later releases.
 
-As a bonus, the columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core. It is highly recommended that you double-check that all of the identifiers you defined using `--input` are represented in the samplesheet. Also, public databases don't reliably hold information such as strandedness information so you may need to amend these entries too if for example your samplesheet was created by providing `--nf_core_pipeline rnaseq`.
+As a bonus, the columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core. It is highly recommended that you double-check that all of the identifiers you defined using `--input` are represented in the samplesheet. Also, public databases don't reliably hold information such as strandedness information so you may need to amend these entries too if for example your samplesheet was created by providing `--nf_core_pipeline rnaseq`.
 
 All of the sample metadata obtained from the ENA will be appended as additional columns to help you manually curate the samplesheet before you run the pipeline. You can customise the metadata fields that are appended to the samplesheet via the `--ena_metadata_fields` parameter. The default list of fields used by the pipeline can be found at the top of the [`bin/sra_ids_to_runinfo.py`](https://github.com/nf-core/fetchngs/blob/master/bin/sra_ids_to_runinfo.py) script within the pipeline repo. However, this pipeline requires a minimal set of fields to download FastQ files i.e. `'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'`. A comprehensive list of accepted metadata fields can be obtained from the [ENA API](https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run]).
 

From 9f0e7d60a9d663df8eb5558a45ab471db131346f Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 7 Jun 2021 22:38:55 +0100
Subject: [PATCH 003/852] Delete check_samplesheet.py

---
 bin/check_samplesheet.py | 148 ---------------------------------------
 1 file changed, 148 deletions(-)
 delete mode 100755 bin/check_samplesheet.py

diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
deleted file mode 100755
index 15ba80dc..00000000
--- a/bin/check_samplesheet.py
+++ /dev/null
@@ -1,148 +0,0 @@
-#!/usr/bin/env python
-
-# TODO nf-core: Update the script to check the samplesheet
-# This script is based on the example at: https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
-
-import os
-import sys
-import errno
-import argparse
-
-
-def parse_args(args=None):
-    Description = "Reformat nf-core/fetchngs samplesheet file and check its contents."
-    Epilog = "Example usage: python check_samplesheet.py <FILE_IN> <FILE_OUT>"
-
-    parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
-    parser.add_argument("FILE_IN", help="Input samplesheet file.")
-    parser.add_argument("FILE_OUT", help="Output file.")
-    return parser.parse_args(args)
-
-
-def make_dir(path):
-    if len(path) > 0:
-        try:
-            os.makedirs(path)
-        except OSError as exception:
-            if exception.errno != errno.EEXIST:
-                raise exception
-
-
-def print_error(error, context="Line", context_str=""):
-    error_str = "ERROR: Please check samplesheet -> {}".format(error)
-    if context != "" and context_str != "":
-        error_str = "ERROR: Please check samplesheet -> {}\n{}: '{}'".format(
-            error, context.strip(), context_str.strip()
-        )
-    print(error_str)
-    sys.exit(1)
-
-
-# TODO nf-core: Update the check_samplesheet function
-def check_samplesheet(file_in, file_out):
-    """
-    This function checks that the samplesheet follows the following structure:
-
-    sample,fastq_1,fastq_2
-    SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz
-    SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz
-    SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz,
-
-    For an example see:
-    https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
-    """
-
-    sample_mapping_dict = {}
-    with open(file_in, "r") as fin:
-
-        ## Check header
-        MIN_COLS = 2
-        # TODO nf-core: Update the column names for the input samplesheet
-        HEADER = ["sample", "fastq_1", "fastq_2"]
-        header = [x.strip('"') for x in fin.readline().strip().split(",")]
-        if header[: len(HEADER)] != HEADER:
-            print("ERROR: Please check samplesheet header -> {} != {}".format(",".join(header), ",".join(HEADER)))
-            sys.exit(1)
-
-        ## Check sample entries
-        for line in fin:
-            lspl = [x.strip().strip('"') for x in line.strip().split(",")]
-
-            # Check valid number of columns per row
-            if len(lspl) < len(HEADER):
-                print_error(
-                    "Invalid number of columns (minimum = {})!".format(len(HEADER)),
-                    "Line",
-                    line,
-                )
-            num_cols = len([x for x in lspl if x])
-            if num_cols < MIN_COLS:
-                print_error(
-                    "Invalid number of populated columns (minimum = {})!".format(MIN_COLS),
-                    "Line",
-                    line,
-                )
-
-            ## Check sample name entries
-            sample, fastq_1, fastq_2 = lspl[: len(HEADER)]
-            if sample:
-                if sample.find(" ") != -1:
-                    print_error("Sample entry contains spaces!", "Line", line)
-            else:
-                print_error("Sample entry has not been specified!", "Line", line)
-
-            ## Check FastQ file extension
-            for fastq in [fastq_1, fastq_2]:
-                if fastq:
-                    if fastq.find(" ") != -1:
-                        print_error("FastQ file contains spaces!", "Line", line)
-                    if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"):
-                        print_error(
-                            "FastQ file does not have extension '.fastq.gz' or '.fq.gz'!",
-                            "Line",
-                            line,
-                        )
-
-            ## Auto-detect paired-end/single-end
-            sample_info = []  ## [single_end, fastq_1, fastq_2]
-            if sample and fastq_1 and fastq_2:  ## Paired-end short reads
-                sample_info = ["0", fastq_1, fastq_2]
-            elif sample and fastq_1 and not fastq_2:  ## Single-end short reads
-                sample_info = ["1", fastq_1, fastq_2]
-            else:
-                print_error("Invalid combination of columns provided!", "Line", line)
-
-            ## Create sample mapping dictionary = { sample: [ single_end, fastq_1, fastq_2 ] }
-            if sample not in sample_mapping_dict:
-                sample_mapping_dict[sample] = [sample_info]
-            else:
-                if sample_info in sample_mapping_dict[sample]:
-                    print_error("Samplesheet contains duplicate rows!", "Line", line)
-                else:
-                    sample_mapping_dict[sample].append(sample_info)
-
-    ## Write validated samplesheet with appropriate columns
-    if len(sample_mapping_dict) > 0:
-        out_dir = os.path.dirname(file_out)
-        make_dir(out_dir)
-        with open(file_out, "w") as fout:
-            fout.write(",".join(["sample", "single_end", "fastq_1", "fastq_2"]) + "\n")
-            for sample in sorted(sample_mapping_dict.keys()):
-
-                ## Check that multiple runs of the same sample are of the same datatype
-                if not all(x[0] == sample_mapping_dict[sample][0][0] for x in sample_mapping_dict[sample]):
-                    print_error("Multiple runs of a sample must be of the same datatype!", "Sample: {}".format(sample))
-
-                for idx, val in enumerate(sample_mapping_dict[sample]):
-                    fout.write(",".join(["{}_T{}".format(sample, idx + 1)] + val) + "\n")
-    else:
-        print_error("No entries to process!", "Samplesheet: {}".format(file_in))
-
-
-def main(args=None):
-    args = parse_args(args)
-    check_samplesheet(args.FILE_IN, args.FILE_OUT)
-
-
-if __name__ == "__main__":
-    sys.exit(main())

From 1081387eefbe7654d00c719a04e0f87e2b391054 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 7 Jun 2021 22:47:21 +0100
Subject: [PATCH 004/852] Delete files not required by pipeline

---
 assets/multiqc_config.yaml                    |  11 -
 assets/nf-core-fetchfastq_logo.png            | Bin 19699 -> 0 bytes
 assets/samplesheet.csv                        |   3 -
 conf/igenomes.config                          | 432 ------------------
 docs/images/mqc_fastqc_adapter.png            | Bin 23458 -> 0 bytes
 docs/images/mqc_fastqc_counts.png             | Bin 33918 -> 0 bytes
 docs/images/mqc_fastqc_quality.png            | Bin 55769 -> 0 bytes
 docs/images/nf-core-fetchfastq_logo.png       | Bin 37015 -> 0 bytes
 modules/nf-core/software/fastqc/functions.nf  |  68 ---
 modules/nf-core/software/fastqc/main.nf       |  47 --
 modules/nf-core/software/fastqc/meta.yml      |  51 ---
 modules/nf-core/software/multiqc/functions.nf |  68 ---
 modules/nf-core/software/multiqc/main.nf      |  35 --
 modules/nf-core/software/multiqc/meta.yml     |  39 --
 14 files changed, 754 deletions(-)
 delete mode 100755 assets/multiqc_config.yaml
 delete mode 100644 assets/nf-core-fetchfastq_logo.png
 delete mode 100755 assets/samplesheet.csv
 delete mode 100755 conf/igenomes.config
 delete mode 100755 docs/images/mqc_fastqc_adapter.png
 delete mode 100755 docs/images/mqc_fastqc_counts.png
 delete mode 100755 docs/images/mqc_fastqc_quality.png
 delete mode 100644 docs/images/nf-core-fetchfastq_logo.png
 delete mode 100755 modules/nf-core/software/fastqc/functions.nf
 delete mode 100755 modules/nf-core/software/fastqc/main.nf
 delete mode 100755 modules/nf-core/software/fastqc/meta.yml
 delete mode 100755 modules/nf-core/software/multiqc/functions.nf
 delete mode 100755 modules/nf-core/software/multiqc/main.nf
 delete mode 100755 modules/nf-core/software/multiqc/meta.yml

diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml
deleted file mode 100755
index 77679f83..00000000
--- a/assets/multiqc_config.yaml
+++ /dev/null
@@ -1,11 +0,0 @@
-report_comment: >
-    This report has been generated by the <a href="https://github.com/nf-core/fetchngs" target="_blank">nf-core/fetchngs</a>
-    analysis pipeline. For information about how to interpret these results, please see the
-    <a href="https://github.com/nf-core/fetchngs" target="_blank">documentation</a>.
-report_section_order:
-    software_versions:
-        order: -1000
-    nf-core-fetchngs-summary:
-        order: -1001
-
-export_plots: true
diff --git a/assets/nf-core-fetchfastq_logo.png b/assets/nf-core-fetchfastq_logo.png
deleted file mode 100644
index a725c75e44616c3b1bf7051c5dd2e18d525196e5..0000000000000000000000000000000000000000
GIT binary patch
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diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
deleted file mode 100755
index 5f653ab7..00000000
--- a/assets/samplesheet.csv
+++ /dev/null
@@ -1,3 +0,0 @@
-sample,fastq_1,fastq_2
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,
diff --git a/conf/igenomes.config b/conf/igenomes.config
deleted file mode 100755
index 855948de..00000000
--- a/conf/igenomes.config
+++ /dev/null
@@ -1,432 +0,0 @@
-/*
-========================================================================================
-    Nextflow config file for iGenomes paths
-========================================================================================
-    Defines reference genomes using iGenome paths.
-    Can be used by any config that customises the base path using:
-        $params.igenomes_base / --igenomes_base
-----------------------------------------------------------------------------------------
-*/
-
-params {
-    // illumina iGenomes reference file paths
-    genomes {
-        'GRCh37' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt"
-            mito_name   = "MT"
-            macs_gsize  = "2.7e9"
-            blacklist   = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed"
-        }
-        'GRCh38' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-            macs_gsize  = "2.7e9"
-            blacklist   = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
-        }
-        'GRCm38' {
-            fasta       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt"
-            mito_name   = "MT"
-            macs_gsize  = "1.87e9"
-            blacklist   = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed"
-        }
-        'TAIR10' {
-            fasta       = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt"
-            mito_name   = "Mt"
-        }
-        'EB2' {
-            fasta       = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt"
-        }
-        'UMD3.1' {
-            fasta       = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'WBcel235' {
-            fasta       = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed"
-            mito_name   = "MtDNA"
-            macs_gsize  = "9e7"
-        }
-        'CanFam3.1' {
-            fasta       = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'GRCz10' {
-            fasta       = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-        }
-        'BDGP6' {
-            fasta       = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed"
-            mito_name   = "M"
-            macs_gsize  = "1.2e8"
-        }
-        'EquCab2' {
-            fasta       = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'EB1' {
-            fasta       = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt"
-        }
-        'Galgal4' {
-            fasta       = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-        }
-        'Gm01' {
-            fasta       = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt"
-        }
-        'Mmul_1' {
-            fasta       = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'IRGSP-1.0' {
-            fasta       = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed"
-            mito_name   = "Mt"
-        }
-        'CHIMP2.1.4' {
-            fasta       = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'Rnor_5.0' {
-            fasta       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-        }
-        'Rnor_6.0' {
-            fasta       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-        }
-        'R64-1-1' {
-            fasta       = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-            macs_gsize  = "1.2e7"
-        }
-        'EF2' {
-            fasta       = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt"
-            mito_name   = "MT"
-            macs_gsize  = "1.21e7"
-        }
-        'Sbi1' {
-            fasta       = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt"
-        }
-        'Sscrofa10.2' {
-            fasta       = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'AGPv3' {
-            fasta       = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed"
-            mito_name   = "Mt"
-        }
-        'hg38' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-            macs_gsize  = "2.7e9"
-            blacklist   = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
-        }
-        'hg19' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt"
-            mito_name   = "chrM"
-            macs_gsize  = "2.7e9"
-            blacklist   = "${projectDir}/assets/blacklists/hg19-blacklist.bed"
-        }
-        'mm10' {
-            fasta       = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt"
-            mito_name   = "chrM"
-            macs_gsize  = "1.87e9"
-            blacklist   = "${projectDir}/assets/blacklists/mm10-blacklist.bed"
-        }
-        'bosTau8' {
-            fasta       = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-        }
-        'ce10' {
-            fasta       = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt"
-            mito_name   = "chrM"
-            macs_gsize  = "9e7"
-        }
-        'canFam3' {
-            fasta       = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-        'danRer10' {
-            fasta       = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-            macs_gsize  = "1.37e9"
-        }
-        'dm6' {
-            fasta       = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-            macs_gsize  = "1.2e8"
-        }
-        'equCab2' {
-            fasta       = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-        'galGal4' {
-            fasta       = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-        'panTro4' {
-            fasta       = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-        'rn6' {
-            fasta       = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-        }
-        'sacCer3' {
-            fasta       = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/"
-            readme      = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt"
-            mito_name   = "chrM"
-            macs_gsize  = "1.2e7"
-        }
-        'susScr3' {
-            fasta       = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/genome.fa"
-            bowtie2     = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-    }
-}
diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png
deleted file mode 100755
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diff --git a/modules/nf-core/software/fastqc/functions.nf b/modules/nf-core/software/fastqc/functions.nf
deleted file mode 100755
index da9da093..00000000
--- a/modules/nf-core/software/fastqc/functions.nf
+++ /dev/null
@@ -1,68 +0,0 @@
-//
-//  Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions  = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_meta) {
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-            for (key in key_list) {
-                if (args.meta && key instanceof String) {
-                    def path = key
-                    if (args.meta.containsKey(key)) {
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                    }
-                    path = path instanceof String ? path : ''
-                    path_list.add(path)
-                }
-            }
-        }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
-            }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
-        }
-    }
-}
diff --git a/modules/nf-core/software/fastqc/main.nf b/modules/nf-core/software/fastqc/main.nf
deleted file mode 100755
index 7ce76adf..00000000
--- a/modules/nf-core/software/fastqc/main.nf
+++ /dev/null
@@ -1,47 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
-process FASTQC {
-    tag "$meta.id"
-    label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
-
-    conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0"
-    } else {
-        container "quay.io/biocontainers/fastqc:0.11.9--0"
-    }
-
-    input:
-    tuple val(meta), path(reads)
-
-    output:
-    tuple val(meta), path("*.html"), emit: html
-    tuple val(meta), path("*.zip") , emit: zip
-    path  "*.version.txt"          , emit: version
-
-    script:
-    // Add soft-links to original FastQs for consistent naming in pipeline
-    def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
-    if (meta.single_end) {
-        """
-        [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
-        fastqc $options.args --threads $task.cpus ${prefix}.fastq.gz
-        fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt
-        """
-    } else {
-        """
-        [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
-        [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
-        fastqc $options.args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
-        fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt
-        """
-    }
-}
diff --git a/modules/nf-core/software/fastqc/meta.yml b/modules/nf-core/software/fastqc/meta.yml
deleted file mode 100755
index 8eb9953d..00000000
--- a/modules/nf-core/software/fastqc/meta.yml
+++ /dev/null
@@ -1,51 +0,0 @@
-name: fastqc
-description: Run FastQC on sequenced reads
-keywords:
-    - quality control
-    - qc
-    - adapters
-    - fastq
-tools:
-    - fastqc:
-        description: |
-            FastQC gives general quality metrics about your reads.
-            It provides information about the quality score distribution
-            across your reads, the per base sequence content (%A/C/G/T).
-            You get information about adapter contamination and other
-            overrepresented sequences.
-        homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
-        documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
-input:
-    - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-    - reads:
-        type: file
-        description: |
-            List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-            respectively.
-output:
-    - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-    - html:
-        type: file
-        description: FastQC report
-        pattern: "*_{fastqc.html}"
-    - zip:
-        type: file
-        description: FastQC report archive
-        pattern: "*_{fastqc.zip}"
-    - version:
-        type: file
-        description: File containing software version
-        pattern: "*.{version.txt}"
-authors:
-    - "@drpatelh"
-    - "@grst"
-    - "@ewels"
-    - "@FelixKrueger"
diff --git a/modules/nf-core/software/multiqc/functions.nf b/modules/nf-core/software/multiqc/functions.nf
deleted file mode 100755
index da9da093..00000000
--- a/modules/nf-core/software/multiqc/functions.nf
+++ /dev/null
@@ -1,68 +0,0 @@
-//
-//  Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions  = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_meta) {
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-            for (key in key_list) {
-                if (args.meta && key instanceof String) {
-                    def path = key
-                    if (args.meta.containsKey(key)) {
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                    }
-                    path = path instanceof String ? path : ''
-                    path_list.add(path)
-                }
-            }
-        }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
-            }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
-        }
-    }
-}
diff --git a/modules/nf-core/software/multiqc/main.nf b/modules/nf-core/software/multiqc/main.nf
deleted file mode 100755
index da780800..00000000
--- a/modules/nf-core/software/multiqc/main.nf
+++ /dev/null
@@ -1,35 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
-process MULTIQC {
-    label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
-
-    conda (params.enable_conda ? "bioconda::multiqc=1.10.1" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/multiqc:1.10.1--py_0"
-    } else {
-        container "quay.io/biocontainers/multiqc:1.10.1--py_0"
-    }
-
-    input:
-    path multiqc_files
-
-    output:
-    path "*multiqc_report.html", emit: report
-    path "*_data"              , emit: data
-    path "*_plots"             , optional:true, emit: plots
-    path "*.version.txt"       , emit: version
-
-    script:
-    def software = getSoftwareName(task.process)
-    """
-    multiqc -f $options.args .
-    multiqc --version | sed -e "s/multiqc, version //g" > ${software}.version.txt
-    """
-}
diff --git a/modules/nf-core/software/multiqc/meta.yml b/modules/nf-core/software/multiqc/meta.yml
deleted file mode 100755
index 532a8bb1..00000000
--- a/modules/nf-core/software/multiqc/meta.yml
+++ /dev/null
@@ -1,39 +0,0 @@
-name: MultiQC
-description: Aggregate results from bioinformatics analyses across many samples into a single report
-keywords:
-    - QC
-    - bioinformatics tools
-    - Beautiful stand-alone HTML report
-tools:
-    - multiqc:
-        description: |
-            MultiQC searches a given directory for analysis logs and compiles a HTML report.
-            It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
-        homepage: https://multiqc.info/
-        documentation: https://multiqc.info/docs/
-input:
-    - multiqc_files:
-        type: file
-        description: |
-            List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
-output:
-    - report:
-        type: file
-        description: MultiQC report file
-        pattern: "multiqc_report.html"
-    - data:
-        type: dir
-        description: MultiQC data dir
-        pattern: "multiqc_data"
-    - plots:
-        type: file
-        description: Plots created by MultiQC
-        pattern: "*_data"
-    - version:
-        type: file
-        description: File containing software version
-        pattern: "*.{version.txt}"
-authors:
-    - "@abhi18av"
-    - "@bunop"
-    - "@drpatelh"

From af973d4e877f7576656b13bf5998c1dab247bcda Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 7 Jun 2021 23:10:15 +0100
Subject: [PATCH 005/852] Remove samplesheet_check.nf module

---
 modules/local/samplesheet_check.nf | 31 ------------------------------
 1 file changed, 31 deletions(-)
 delete mode 100755 modules/local/samplesheet_check.nf

diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
deleted file mode 100755
index 77f58557..00000000
--- a/modules/local/samplesheet_check.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-// Import generic module functions
-include { saveFiles } from './functions'
-
-params.options = [:]
-
-process SAMPLESHEET_CHECK {
-    tag "$samplesheet"
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', meta:[:], publish_by_meta:[]) }
-
-    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
-    } else {
-        container "quay.io/biocontainers/python:3.8.3"
-    }
-
-    input:
-    path samplesheet
-
-    output:
-    path '*.csv'
-
-    script: // This script is bundled with the pipeline, in nf-core/fetchngs/bin/
-    """
-    check_samplesheet.py \\
-        $samplesheet \\
-        samplesheet.valid.csv
-    """
-}

From df21619d8aefb87f0d6fdd90922ab460d3cd0fc5 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 21 Jun 2021 14:08:19 +0100
Subject: [PATCH 006/852] Change container for sra_ids_to_runinfo.nf process

---
 CHANGELOG.md                        | 6 ++++++
 modules/local/sra_ids_to_runinfo.nf | 6 +++---
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 04618e30..4c4fae10 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,12 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[1.1](https://github.com/nf-core/fetchngs/releases/tag/1.1)] - 2021-06-22
+
+### Enhancements & fixes
+
+* [[#12](https://github.com/nf-core/fetchngs/issues/12)] - Error when using singularity - /etc/resolv.conf doesn't exist in container
+
 ## [[1.0](https://github.com/nf-core/fetchngs/releases/tag/1.0)] - 2021-06-08
 
 Initial release of nf-core/fetchngs, created with the [nf-core](https://nf-co.re/) template.
diff --git a/modules/local/sra_ids_to_runinfo.nf b/modules/local/sra_ids_to_runinfo.nf
index d5b9705c..b277197e 100644
--- a/modules/local/sra_ids_to_runinfo.nf
+++ b/modules/local/sra_ids_to_runinfo.nf
@@ -10,11 +10,11 @@ process SRA_IDS_TO_RUNINFO {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::requests=2.24.0" : null)
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/requests:2.24.0"
+        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
     } else {
-        container "quay.io/biocontainers/requests:2.24.0"
+        container "biocontainers/biocontainers:v1.2.0_cv1"
     }
 
     input:

From 6586c08da2dbb82fb1cdd04b27490372eb80be3c Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 21 Jun 2021 14:34:39 +0100
Subject: [PATCH 007/852] Updates relative to rnaseq

---
 bin/scrape_software_versions.py        |  4 ++--
 docs/output.md                         |  2 +-
 docs/usage.md                          |  8 ++++----
 main.nf                                | 10 +++++-----
 modules/local/get_software_versions.nf |  2 +-
 nextflow.config                        |  2 +-
 6 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py
index 71b81eff..a4e45493 100755
--- a/bin/scrape_software_versions.py
+++ b/bin/scrape_software_versions.py
@@ -30,7 +30,7 @@
     print("        <dt>{}</dt><dd><samp>{}</samp></dd>".format(k, v))
 print("    </dl>")
 
-# Write out regexes as csv file:
-with open("software_versions.csv", "w") as f:
+# Write out as tsv file:
+with open("software_versions.tsv", "w") as f:
     for k, v in sorted(results.items()):
         f.write("{}\t{}\n".format(k, v))
diff --git a/docs/output.md b/docs/output.md
index f2cc20a5..31653ad6 100755
--- a/docs/output.md
+++ b/docs/output.md
@@ -37,7 +37,7 @@ Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introductio
 
 * `pipeline_info/`
     * Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
-    * Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.csv`.
+    * Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.tsv`.
 
 </details>
 
diff --git a/docs/usage.md b/docs/usage.md
index 2852035b..0ca76395 100755
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -38,7 +38,7 @@ This downloads a text file called `SRR_Acc_List.txt` which can be directly provi
 
 The typical command for running the pipeline is as follows:
 
-```bash
+```console
 nextflow run nf-core/fetchngs --input ids.txt -profile docker
 ```
 
@@ -46,7 +46,7 @@ This will launch the pipeline with the `docker` configuration profile. See below
 
 Note that the pipeline will create the following files in your working directory:
 
-```bash
+```console
 work            # Directory containing the nextflow working files
 results         # Finished results (configurable, see below)
 .nextflow_log   # Log file from Nextflow
@@ -57,7 +57,7 @@ results         # Finished results (configurable, see below)
 
 When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
 
-```bash
+```console
 nextflow pull nf-core/fetchngs
 ```
 
@@ -221,6 +221,6 @@ Some HPC setups also allow you to run nextflow within a cluster job submitted yo
 In some cases, the Nextflow Java virtual machines can start to request a large amount of memory.
 We recommend adding the following line to your environment to limit this (typically in `~/.bashrc` or `~./bash_profile`):
 
-```bash
+```console
 NXF_OPTS='-Xms1g -Xmx4g'
 ```
diff --git a/main.nf b/main.nf
index f28f690f..475c87a8 100755
--- a/main.nf
+++ b/main.nf
@@ -25,12 +25,12 @@ WorkflowMain.initialise(workflow, params, log)
 ========================================================================================
 */
 
-workflow NFCORE_FETCHNGS {
+include { FETCHNGS } from './workflows/fetchngs'
 
-    //
-    // WORKFLOW: Run main nf-core/fetchngs analysis pipeline
-    //
-    include { FETCHNGS } from './workflows/fetchngs'
+//
+// WORKFLOW: Run main nf-core/fetchngs analysis pipeline
+//
+workflow NFCORE_FETCHNGS {
     FETCHNGS ()
 }
 
diff --git a/modules/local/get_software_versions.nf b/modules/local/get_software_versions.nf
index 5b6ad7ad..4d37bd6a 100755
--- a/modules/local/get_software_versions.nf
+++ b/modules/local/get_software_versions.nf
@@ -21,7 +21,7 @@ process GET_SOFTWARE_VERSIONS {
     path versions
 
     output:
-    path "software_versions.csv"     , emit: csv
+    path "software_versions.tsv"     , emit: tsv
     path 'software_versions_mqc.yaml', emit: yaml
 
     script: // This script is bundled with the pipeline, in nf-core/fetchngs/bin/
diff --git a/nextflow.config b/nextflow.config
index 94ddb47f..92b4c669 100755
--- a/nextflow.config
+++ b/nextflow.config
@@ -146,7 +146,7 @@ manifest {
     description     = 'Pipeline to fetch metadata and raw FastQ files from public databases'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.04.0'
-    version         = '1.0'
+    version         = '1.1'
 }
 
 // Function to ensure that resource requirements don't go beyond

From 34e32ec384d0d44be05e0a9610a8bea9a69aaa3a Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 21 Jun 2021 14:45:35 +0100
Subject: [PATCH 008/852] Actually get_software_versions

---
 modules/local/sra_runinfo_to_ftp.nf |  5 ++++-
 workflows/fetchngs.nf               | 19 +++++++++++++++++++
 2 files changed, 23 insertions(+), 1 deletion(-)

diff --git a/modules/local/sra_runinfo_to_ftp.nf b/modules/local/sra_runinfo_to_ftp.nf
index 1418bf34..b0421aea 100644
--- a/modules/local/sra_runinfo_to_ftp.nf
+++ b/modules/local/sra_runinfo_to_ftp.nf
@@ -19,12 +19,15 @@ process SRA_RUNINFO_TO_FTP {
     path runinfo
 
     output:
-    path "*.tsv", emit: tsv
+    path "*.tsv"         , emit: tsv
+    path  "*.version.txt", emit: version
 
     script:
     """
     sra_runinfo_to_ftp.py \\
         ${runinfo.join(',')} \\
         ${runinfo.toString().tokenize(".")[0]}.runinfo_ftp.tsv
+
+    python --version | sed -e "s/Python //g" > python.version.txt
     """
 }
diff --git a/workflows/fetchngs.nf b/workflows/fetchngs.nf
index 4ba08fb3..f03ae14a 100755
--- a/workflows/fetchngs.nf
+++ b/workflows/fetchngs.nf
@@ -39,6 +39,7 @@ include { SRA_RUNINFO_TO_FTP    } from '../modules/local/sra_runinfo_to_ftp'
 include { SRA_FASTQ_FTP         } from '../modules/local/sra_fastq_ftp'         addParams( options: modules['sra_fastq_ftp']         )
 include { SRA_TO_SAMPLESHEET    } from '../modules/local/sra_to_samplesheet'    addParams( options: modules['sra_to_samplesheet'], results_dir: modules['sra_fastq_ftp'].publish_dir )
 include { SRA_MERGE_SAMPLESHEET } from '../modules/local/sra_merge_samplesheet' addParams( options: modules['sra_merge_samplesheet'] )
+include { GET_SOFTWARE_VERSIONS } from '../modules/local/get_software_versions' addParams( options: [publish_files : ['tsv':'']]     )
 
 /*
 ========================================================================================
@@ -48,6 +49,8 @@ include { SRA_MERGE_SAMPLESHEET } from '../modules/local/sra_merge_samplesheet'
 
 workflow FETCHNGS {
 
+    ch_software_versions = Channel.empty()
+
     //
     // MODULE: Get SRA run information for public database ids
     //
@@ -74,6 +77,7 @@ workflow FETCHNGS {
         }
         .unique()
         .set { ch_sra_reads }
+    ch_software_versions = ch_software_versions.mix(SRA_RUNINFO_TO_FTP.out.version.first().ifEmpty(null))
 
     if (!params.skip_fastq_download) {
         //
@@ -107,6 +111,21 @@ workflow FETCHNGS {
             .unique()
             .collectFile(name: no_ids_file, sort: true, newLine: true)
     }
+
+    //
+    // MODULE: Pipeline reporting
+    //
+    ch_software_versions
+        .map { it -> if (it) [ it.baseName, it ] }
+        .groupTuple()
+        .map { it[1][0] }
+        .flatten()
+        .collect()
+        .set { ch_software_versions }
+
+    GET_SOFTWARE_VERSIONS (
+        ch_software_versions.map { it }.collect()
+    )
 }
 
 /*

From f0f21384a7742d9b2a87fc26f94d89977bec1057 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 21 Jun 2021 16:03:45 +0100
Subject: [PATCH 009/852] Add --sample_mapping_fields parameter

---
 CHANGELOG.md                           |  1 +
 docs/output.md                         |  7 +++++--
 modules/local/sra_merge_samplesheet.nf |  7 +++++++
 modules/local/sra_to_samplesheet.nf    | 29 +++++++++++++++++++++++---
 nextflow.config                        |  1 +
 nextflow_schema.json                   |  8 ++++++-
 workflows/fetchngs.nf                  |  6 ++++--
 7 files changed, 51 insertions(+), 8 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4c4fae10..66d1f812 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Enhancements & fixes
 
 * [[#12](https://github.com/nf-core/fetchngs/issues/12)] - Error when using singularity - /etc/resolv.conf doesn't exist in container
+* Added `--sample_mapping_fields` parameter to create a separate `mappings.tsv` with selected fields that can be used to rename samples in general and in [MultiQC](https://multiqc.info/docs/#bulk-sample-renaming)
 
 ## [[1.0](https://github.com/nf-core/fetchngs/releases/tag/1.0)] - 2021-06-08
 
diff --git a/docs/output.md b/docs/output.md
index 31653ad6..b501dbc2 100755
--- a/docs/output.md
+++ b/docs/output.md
@@ -22,12 +22,15 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
     * `*.md5`: Files containing `md5` sum for FastQ files downloaded from the ENA / SRA.
 * `samplesheet/`
     * `samplesheet.csv`: Auto-created samplesheet with collated metadata and paths to downloaded FastQ files.
+    * `mappings.tsv`: File with selected fields that can be used to rename samples in general and in [MultiQC](https://multiqc.info/docs/#bulk-sample-renaming); see [`--sample_mapping_fields`](https://nf-co.re/fetchngs/parameters#sample_mapping_fields) parameter to customise this behaviour.
 * `metadata/`
-    * `*.runinfo_ftp.tsv`: Re-formatted metadata file downloaded from the ENA
-    * `*.runinfo.tsv`: Original metadata file downloaded from the ENA
+    * `*.runinfo_ftp.tsv`: Re-formatted metadata file downloaded from the ENA.
+    * `*.runinfo.tsv`: Original metadata file downloaded from the ENA.
 
 </details>
 
+Added `--sample_mapping_fields` parameter to create a separate `mappings.tsv` with selected fields that can be used to rename samples in general and in [MultiQC](https://multiqc.info/docs/#bulk-sample-renaming)
+
 Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introduction) for a list of supported public repository identifiers and how to provide them to the pipeline. The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5sums. If download links exist, the files will be downloaded in parallel by FTP otherwise they will NOT be downloaded. This is intentional because the tools such as `parallel-fastq-dump`, `fasterq-dump`, `prefetch` etc require pre-existing configuration files in the users home directory which makes automation tricky across different platforms and containerisation.
 
 ### Pipeline information
diff --git a/modules/local/sra_merge_samplesheet.nf b/modules/local/sra_merge_samplesheet.nf
index 423be634..29b08783 100644
--- a/modules/local/sra_merge_samplesheet.nf
+++ b/modules/local/sra_merge_samplesheet.nf
@@ -17,9 +17,11 @@ process SRA_MERGE_SAMPLESHEET {
 
     input:
     path ('samplesheets/*')
+    path ('mappings/*')
 
     output:
     path "*csv", emit: csv
+    path "*tsv", emit: tsv
 
     script:
     """
@@ -27,5 +29,10 @@ process SRA_MERGE_SAMPLESHEET {
     for fileid in `ls ./samplesheets/*`; do
         awk 'NR>1' \$fileid >> samplesheet.csv
     done
+
+    head -n 1 `ls ./mappings/* | head -n 1` > mappings.tsv
+    for fileid in `ls ./mappings/*`; do
+        awk 'NR>1' \$fileid >> mappings.tsv
+    done
     """
 }
diff --git a/modules/local/sra_to_samplesheet.nf b/modules/local/sra_to_samplesheet.nf
index a30e0f5e..9eb8be05 100644
--- a/modules/local/sra_to_samplesheet.nf
+++ b/modules/local/sra_to_samplesheet.nf
@@ -15,11 +15,17 @@ process SRA_TO_SAMPLESHEET {
     input:
     tuple val(meta), path(fastq)
     val   pipeline
+    val   mapping_fields
 
     output:
     tuple val(meta), path("*csv"), emit: csv
+    tuple val(meta), path("*tsv"), emit: tsv
 
     exec:
+    //
+    // Create samplesheet containing metadata
+    //
+
     //  Remove custom keys needed to download the data
     def meta_map = meta.clone()
     meta_map.remove("id")
@@ -48,7 +54,24 @@ process SRA_TO_SAMPLESHEET {
     csv  = pipeline_map.keySet().collect{ '"' + it + '"'}.join(",") + '\n'
     csv += pipeline_map.values().collect{ '"' + it + '"'}.join(",")
 
-    // Write to file
-    def file = task.workDir.resolve("${meta.id}.samplesheet.csv")
-    file.text = csv
+    // Write samplesheet to file
+    def samplesheet_file = task.workDir.resolve("${meta.id}.samplesheet.csv")
+    samplesheet_file.text = csv
+
+    //
+    // Create sample id mappings file
+    //
+    mappings_map = pipeline_map.clone()
+    def fields = mapping_fields ? ['sample'] + mapping_fields.split(',').collect{ it.trim().toLowerCase() } : []
+    if ((mappings_map.keySet() + fields).unique().size() != mappings_map.keySet().size()) {
+        error("Invalid option for '--sample_mapping_fields': ${mapping_fields}.\nValid options: ${mappings_map.keySet().join(', ')}")
+    }
+
+    // Create mappings
+    tsv  = fields.join("\t") + '\n'
+    tsv += mappings_map.subMap(fields).values().join("\t")
+
+    // Write mappings to file
+    def mappings_file = task.workDir.resolve("${meta.id}.mappings.tsv")
+    mappings_file.text = tsv
 }
diff --git a/nextflow.config b/nextflow.config
index 92b4c669..5ac246e5 100755
--- a/nextflow.config
+++ b/nextflow.config
@@ -13,6 +13,7 @@ params {
     input                      = null
     nf_core_pipeline           = null
     ena_metadata_fields        = null
+    sample_mapping_fields      = 'run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description,description'
     skip_fastq_download        = false
 
     // Boilerplate options
diff --git a/nextflow_schema.json b/nextflow_schema.json
index e5b24df1..bf5961b4 100755
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -29,6 +29,12 @@
                     "description": "Comma-separated list of ENA metadata fields to fetch before downloading data.",
                     "help_text": "The default list of fields used by the pipeline can be found at the top of the [`bin/sra_ids_to_runinfo.py`](https://github.com/nf-core/fetchngs/blob/master/bin/sra_ids_to_runinfo.py) script within the pipeline repo. This pipeline requires a minimal set of fields to download FastQ files i.e. `'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'`. Full list of accepted metadata fields can be obtained from the [ENA API](https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run])."
                 },
+                "sample_mapping_fields": {
+                    "type": "string",
+                    "fa_icon": "fas fa-globe-americas",
+                    "description": "Comma-separated list of ENA metadata fields used to create mappings file for sample id mapping or renaming.",
+                    "default": "run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description,description"
+                },
                 "nf_core_pipeline": {
                     "type": "string",
                     "fa_icon": "fab fa-apple",
@@ -243,4 +249,4 @@
             "$ref": "#/definitions/generic_options"
         }
     ]
-}
+}
\ No newline at end of file
diff --git a/workflows/fetchngs.nf b/workflows/fetchngs.nf
index f03ae14a..d73cd374 100755
--- a/workflows/fetchngs.nf
+++ b/workflows/fetchngs.nf
@@ -92,14 +92,16 @@ workflow FETCHNGS {
         //
         SRA_TO_SAMPLESHEET (
             SRA_FASTQ_FTP.out.fastq,
-            params.nf_core_pipeline ?: ''
+            params.nf_core_pipeline ?: '',
+            params.sample_mapping_fields
         )
 
         //
         // MODULE: Create a merged samplesheet across all samples for the pipeline
         //
         SRA_MERGE_SAMPLESHEET (
-            SRA_TO_SAMPLESHEET.out.csv.collect{it[1]}
+            SRA_TO_SAMPLESHEET.out.csv.collect{it[1]},
+            SRA_TO_SAMPLESHEET.out.tsv.collect{it[1]}
         )
 
         //

From a13196432de534fb0c14aa067e2d5358ce9b5a26 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 21 Jun 2021 16:07:36 +0100
Subject: [PATCH 010/852] Fix ECLint

---
 nextflow_schema.json | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index bf5961b4..8bb27a97 100755
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -249,4 +249,5 @@
             "$ref": "#/definitions/generic_options"
         }
     ]
-}
\ No newline at end of file
+}
+

From 389d3d118dfbe50daf1a0ff3d0489680cd9425ba Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 21 Jun 2021 16:11:36 +0100
Subject: [PATCH 011/852] Tweak CI tests to deal with new parameter

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d149562c..26785ea1 100755
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -51,7 +51,7 @@ jobs:
         parameters:
           [
             "--nf_core_pipeline rnaseq",
-            "--ena_metadata_fields run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5",
+            "--ena_metadata_fields run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5 --sample_mapping_fields run_accession,library_layout",
             --skip_fastq_download,
           ]
     steps:

From 9ecb14857a44922a4ec661d952a8671301dfd873 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 21 Jun 2021 16:12:41 +0100
Subject: [PATCH 012/852] Tidy up docs

---
 docs/output.md | 2 --
 1 file changed, 2 deletions(-)

diff --git a/docs/output.md b/docs/output.md
index b501dbc2..e9918347 100755
--- a/docs/output.md
+++ b/docs/output.md
@@ -29,8 +29,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 </details>
 
-Added `--sample_mapping_fields` parameter to create a separate `mappings.tsv` with selected fields that can be used to rename samples in general and in [MultiQC](https://multiqc.info/docs/#bulk-sample-renaming)
-
 Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introduction) for a list of supported public repository identifiers and how to provide them to the pipeline. The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5sums. If download links exist, the files will be downloaded in parallel by FTP otherwise they will NOT be downloaded. This is intentional because the tools such as `parallel-fastq-dump`, `fasterq-dump`, `prefetch` etc require pre-existing configuration files in the users home directory which makes automation tricky across different platforms and containerisation.
 
 ### Pipeline information

From 957d89cf555def8130fa5534d1bbd9bfe2dec779 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 21 Jun 2021 18:03:18 +0100
Subject: [PATCH 013/852] Generate multiqc_config.yml for sample name mappings

---
 CHANGELOG.md                             |  2 +-
 bin/multiqc_mappings_config.py           | 14 ++++++++++
 conf/modules.config                      |  3 +++
 docs/output.md                           |  3 ++-
 modules/local/multiqc_mappings_config.nf | 33 ++++++++++++++++++++++++
 workflows/fetchngs.nf                    | 22 +++++++++++-----
 6 files changed, 69 insertions(+), 8 deletions(-)
 create mode 100755 bin/multiqc_mappings_config.py
 create mode 100644 modules/local/multiqc_mappings_config.nf

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 66d1f812..e707b208 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,7 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Enhancements & fixes
 
 * [[#12](https://github.com/nf-core/fetchngs/issues/12)] - Error when using singularity - /etc/resolv.conf doesn't exist in container
-* Added `--sample_mapping_fields` parameter to create a separate `mappings.tsv` with selected fields that can be used to rename samples in general and in [MultiQC](https://multiqc.info/docs/#bulk-sample-renaming)
+* Added `--sample_mapping_fields` parameter to create a separate `mappings.tsv` and `multiqc_config.yml` with selected fields that can be used to rename samples in general and in [MultiQC](https://multiqc.info/docs/#bulk-sample-renaming)
 
 ## [[1.0](https://github.com/nf-core/fetchngs/releases/tag/1.0)] - 2021-06-08
 
diff --git a/bin/multiqc_mappings_config.py b/bin/multiqc_mappings_config.py
new file mode 100755
index 00000000..5ee68e9b
--- /dev/null
+++ b/bin/multiqc_mappings_config.py
@@ -0,0 +1,14 @@
+#!/usr/bin/env python
+
+import sys
+
+with open(sys.argv[1], "r") as fin, open(sys.argv[2], "w") as fout:
+    header = fin.readline().split('\t')
+    config = "sample_names_rename_buttons:\n"
+    config += "\n".join(['  - ' + x for x in header])
+    config += "sample_names_rename:\n"
+    for line in fin:
+        lspl = ['"' + x + '"' for x in line.strip().split('\t')]
+        config += f"  - [{', '.join(lspl)}]\n"
+    fout.write(config)
+
diff --git a/conf/modules.config b/conf/modules.config
index 4059a911..3ae76b68 100755
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -42,5 +42,8 @@ params {
         'sra_merge_samplesheet' {
             publish_dir     = 'samplesheet'
         }
+        'multiqc_mappings_config' {
+            publish_dir     = 'samplesheet'
+        }
     }
 }
diff --git a/docs/output.md b/docs/output.md
index e9918347..0c2485aa 100755
--- a/docs/output.md
+++ b/docs/output.md
@@ -22,7 +22,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
     * `*.md5`: Files containing `md5` sum for FastQ files downloaded from the ENA / SRA.
 * `samplesheet/`
     * `samplesheet.csv`: Auto-created samplesheet with collated metadata and paths to downloaded FastQ files.
-    * `mappings.tsv`: File with selected fields that can be used to rename samples in general and in [MultiQC](https://multiqc.info/docs/#bulk-sample-renaming); see [`--sample_mapping_fields`](https://nf-co.re/fetchngs/parameters#sample_mapping_fields) parameter to customise this behaviour.
+    * `mappings.tsv`: File with selected fields that can be used to rename samples to more informative names; see [`--sample_mapping_fields`](https://nf-co.re/fetchngs/parameters#sample_mapping_fields) parameter to customise this behaviour.
+    * `multiqc_config.yml`: [MultiQC](https://multiqc.info/docs/#bulk-sample-renaming) config file that can be passed to most nf-core pipelines via the `--multiqc_config` parameter for bulk renaming of sample names from database ids;    [`--sample_mapping_fields`](https://nf-co.re/fetchngs/parameters#sample_mapping_fields) parameter to customise this behaviour
 * `metadata/`
     * `*.runinfo_ftp.tsv`: Re-formatted metadata file downloaded from the ENA.
     * `*.runinfo.tsv`: Original metadata file downloaded from the ENA.
diff --git a/modules/local/multiqc_mappings_config.nf b/modules/local/multiqc_mappings_config.nf
new file mode 100644
index 00000000..4d78e456
--- /dev/null
+++ b/modules/local/multiqc_mappings_config.nf
@@ -0,0 +1,33 @@
+// Import generic module functions
+include { saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+
+process MULTIQC_MAPPINGS_CONFIG {
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+
+    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
+    } else {
+        container "quay.io/biocontainers/python:3.8.3"
+    }
+
+    input:
+    path tsv
+
+    output:
+    path "*yml"         , emit: yml
+    path "*.version.txt", emit: version
+
+    script:
+    """
+    multiqc_mappings_config.py \\
+        $tsv \\
+        multiqc_config.yml
+    
+    python --version | sed -e "s/Python //g" > python.version.txt
+    """
+}
diff --git a/workflows/fetchngs.nf b/workflows/fetchngs.nf
index d73cd374..8d6c5218 100755
--- a/workflows/fetchngs.nf
+++ b/workflows/fetchngs.nf
@@ -34,12 +34,13 @@ if (params.input) {
 // Don't overwrite global params.modules, create a copy instead and use that within the main script.
 def modules = params.modules.clone()
 
-include { SRA_IDS_TO_RUNINFO    } from '../modules/local/sra_ids_to_runinfo'    addParams( options: modules['sra_ids_to_runinfo']    )
-include { SRA_RUNINFO_TO_FTP    } from '../modules/local/sra_runinfo_to_ftp'    addParams( options: modules['sra_runinfo_to_ftp']    )
-include { SRA_FASTQ_FTP         } from '../modules/local/sra_fastq_ftp'         addParams( options: modules['sra_fastq_ftp']         )
-include { SRA_TO_SAMPLESHEET    } from '../modules/local/sra_to_samplesheet'    addParams( options: modules['sra_to_samplesheet'], results_dir: modules['sra_fastq_ftp'].publish_dir )
-include { SRA_MERGE_SAMPLESHEET } from '../modules/local/sra_merge_samplesheet' addParams( options: modules['sra_merge_samplesheet'] )
-include { GET_SOFTWARE_VERSIONS } from '../modules/local/get_software_versions' addParams( options: [publish_files : ['tsv':'']]     )
+include { SRA_IDS_TO_RUNINFO      } from '../modules/local/sra_ids_to_runinfo'      addParams( options: modules['sra_ids_to_runinfo']      )
+include { SRA_RUNINFO_TO_FTP      } from '../modules/local/sra_runinfo_to_ftp'      addParams( options: modules['sra_runinfo_to_ftp']      )
+include { SRA_FASTQ_FTP           } from '../modules/local/sra_fastq_ftp'           addParams( options: modules['sra_fastq_ftp']           )
+include { SRA_TO_SAMPLESHEET      } from '../modules/local/sra_to_samplesheet'      addParams( options: modules['sra_to_samplesheet'], results_dir: modules['sra_fastq_ftp'].publish_dir )
+include { SRA_MERGE_SAMPLESHEET   } from '../modules/local/sra_merge_samplesheet'   addParams( options: modules['sra_merge_samplesheet']   )
+include { MULTIQC_MAPPINGS_CONFIG } from '../modules/local/multiqc_mappings_config' addParams( options: modules['multiqc_mappings_config'] )
+include { GET_SOFTWARE_VERSIONS   } from '../modules/local/get_software_versions'   addParams( options: [publish_files : ['tsv':'']]       )
 
 /*
 ========================================================================================
@@ -104,6 +105,15 @@ workflow FETCHNGS {
             SRA_TO_SAMPLESHEET.out.tsv.collect{it[1]}
         )
 
+        //
+        // MODULE: Create a MutiQC config file with sample name mappings
+        //
+        if (params.sample_mapping_fields) {
+            MULTIQC_MAPPINGS_CONFIG (
+                SRA_MERGE_SAMPLESHEET.out.tsv
+            )
+        }
+        
         //
         // If ids don't have a direct FTP download link write them to file for download outside of the pipeline
         //

From 3d25a0e38c318f58faa6dd71f963d0dd410f3ccd Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 21 Jun 2021 18:04:49 +0100
Subject: [PATCH 014/852] Fix ECLint

---
 modules/local/multiqc_mappings_config.nf | 2 +-
 workflows/fetchngs.nf                    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/multiqc_mappings_config.nf b/modules/local/multiqc_mappings_config.nf
index 4d78e456..9a4984e3 100644
--- a/modules/local/multiqc_mappings_config.nf
+++ b/modules/local/multiqc_mappings_config.nf
@@ -27,7 +27,7 @@ process MULTIQC_MAPPINGS_CONFIG {
     multiqc_mappings_config.py \\
         $tsv \\
         multiqc_config.yml
-    
+
     python --version | sed -e "s/Python //g" > python.version.txt
     """
 }
diff --git a/workflows/fetchngs.nf b/workflows/fetchngs.nf
index 8d6c5218..7d708927 100755
--- a/workflows/fetchngs.nf
+++ b/workflows/fetchngs.nf
@@ -113,7 +113,7 @@ workflow FETCHNGS {
                 SRA_MERGE_SAMPLESHEET.out.tsv
             )
         }
-        
+
         //
         // If ids don't have a direct FTP download link write them to file for download outside of the pipeline
         //

From 7a940d8569c3736920f33421dddfca8753e045c3 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 21 Jun 2021 18:33:26 +0100
Subject: [PATCH 015/852] Remove extra spaces

---
 docs/output.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/output.md b/docs/output.md
index 0c2485aa..d867898a 100755
--- a/docs/output.md
+++ b/docs/output.md
@@ -23,7 +23,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 * `samplesheet/`
     * `samplesheet.csv`: Auto-created samplesheet with collated metadata and paths to downloaded FastQ files.
     * `mappings.tsv`: File with selected fields that can be used to rename samples to more informative names; see [`--sample_mapping_fields`](https://nf-co.re/fetchngs/parameters#sample_mapping_fields) parameter to customise this behaviour.
-    * `multiqc_config.yml`: [MultiQC](https://multiqc.info/docs/#bulk-sample-renaming) config file that can be passed to most nf-core pipelines via the `--multiqc_config` parameter for bulk renaming of sample names from database ids;    [`--sample_mapping_fields`](https://nf-co.re/fetchngs/parameters#sample_mapping_fields) parameter to customise this behaviour
+    * `multiqc_config.yml`: [MultiQC](https://multiqc.info/docs/#bulk-sample-renaming) config file that can be passed to most nf-core pipelines via the `--multiqc_config` parameter for bulk renaming of sample names from database ids; [`--sample_mapping_fields`](https://nf-co.re/fetchngs/parameters#sample_mapping_fields) parameter to customise this behaviour.
 * `metadata/`
     * `*.runinfo_ftp.tsv`: Re-formatted metadata file downloaded from the ENA.
     * `*.runinfo.tsv`: Original metadata file downloaded from the ENA.

From 627b63238797efa48f76f6082bd9b9abea7b97b5 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 21 Jun 2021 21:19:00 +0100
Subject: [PATCH 016/852] Output csv for mappings file instead of tsv

---
 bin/multiqc_mappings_config.py           |  7 +++----
 docs/output.md                           |  2 +-
 modules/local/multiqc_mappings_config.nf |  4 ++--
 modules/local/sra_merge_samplesheet.nf   |  8 ++++----
 modules/local/sra_to_samplesheet.nf      | 18 +++++++++---------
 workflows/fetchngs.nf                    |  6 +++---
 6 files changed, 22 insertions(+), 23 deletions(-)

diff --git a/bin/multiqc_mappings_config.py b/bin/multiqc_mappings_config.py
index 5ee68e9b..a7fc92ba 100755
--- a/bin/multiqc_mappings_config.py
+++ b/bin/multiqc_mappings_config.py
@@ -3,12 +3,11 @@
 import sys
 
 with open(sys.argv[1], "r") as fin, open(sys.argv[2], "w") as fout:
-    header = fin.readline().split('\t')
+    header = fin.readline().split(',')
     config = "sample_names_rename_buttons:\n"
-    config += "\n".join(['  - ' + x for x in header])
+    config += "\n".join(['  - ' + x.strip('"') for x in header])
     config += "sample_names_rename:\n"
     for line in fin:
-        lspl = ['"' + x + '"' for x in line.strip().split('\t')]
-        config += f"  - [{', '.join(lspl)}]\n"
+        config += f"  - [{', '.join(line.strip().split(','))}]\n"
     fout.write(config)
 
diff --git a/docs/output.md b/docs/output.md
index d867898a..c0916e6d 100755
--- a/docs/output.md
+++ b/docs/output.md
@@ -22,7 +22,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
     * `*.md5`: Files containing `md5` sum for FastQ files downloaded from the ENA / SRA.
 * `samplesheet/`
     * `samplesheet.csv`: Auto-created samplesheet with collated metadata and paths to downloaded FastQ files.
-    * `mappings.tsv`: File with selected fields that can be used to rename samples to more informative names; see [`--sample_mapping_fields`](https://nf-co.re/fetchngs/parameters#sample_mapping_fields) parameter to customise this behaviour.
+    * `id_mappings.csv`: File with selected fields that can be used to rename samples to more informative names; see [`--sample_mapping_fields`](https://nf-co.re/fetchngs/parameters#sample_mapping_fields) parameter to customise this behaviour.
     * `multiqc_config.yml`: [MultiQC](https://multiqc.info/docs/#bulk-sample-renaming) config file that can be passed to most nf-core pipelines via the `--multiqc_config` parameter for bulk renaming of sample names from database ids; [`--sample_mapping_fields`](https://nf-co.re/fetchngs/parameters#sample_mapping_fields) parameter to customise this behaviour.
 * `metadata/`
     * `*.runinfo_ftp.tsv`: Re-formatted metadata file downloaded from the ENA.
diff --git a/modules/local/multiqc_mappings_config.nf b/modules/local/multiqc_mappings_config.nf
index 9a4984e3..63121b40 100644
--- a/modules/local/multiqc_mappings_config.nf
+++ b/modules/local/multiqc_mappings_config.nf
@@ -16,7 +16,7 @@ process MULTIQC_MAPPINGS_CONFIG {
     }
 
     input:
-    path tsv
+    path csv
 
     output:
     path "*yml"         , emit: yml
@@ -25,7 +25,7 @@ process MULTIQC_MAPPINGS_CONFIG {
     script:
     """
     multiqc_mappings_config.py \\
-        $tsv \\
+        $csv \\
         multiqc_config.yml
 
     python --version | sed -e "s/Python //g" > python.version.txt
diff --git a/modules/local/sra_merge_samplesheet.nf b/modules/local/sra_merge_samplesheet.nf
index 29b08783..e3c1314a 100644
--- a/modules/local/sra_merge_samplesheet.nf
+++ b/modules/local/sra_merge_samplesheet.nf
@@ -20,8 +20,8 @@ process SRA_MERGE_SAMPLESHEET {
     path ('mappings/*')
 
     output:
-    path "*csv", emit: csv
-    path "*tsv", emit: tsv
+    path "samplesheet.csv", emit: samplesheet
+    path "id_mappings.csv"   , emit: mappings
 
     script:
     """
@@ -30,9 +30,9 @@ process SRA_MERGE_SAMPLESHEET {
         awk 'NR>1' \$fileid >> samplesheet.csv
     done
 
-    head -n 1 `ls ./mappings/* | head -n 1` > mappings.tsv
+    head -n 1 `ls ./mappings/* | head -n 1` > id_mappings.csv
     for fileid in `ls ./mappings/*`; do
-        awk 'NR>1' \$fileid >> mappings.tsv
+        awk 'NR>1' \$fileid >> id_mappings.csv
     done
     """
 }
diff --git a/modules/local/sra_to_samplesheet.nf b/modules/local/sra_to_samplesheet.nf
index 9eb8be05..c4fc9af7 100644
--- a/modules/local/sra_to_samplesheet.nf
+++ b/modules/local/sra_to_samplesheet.nf
@@ -18,8 +18,8 @@ process SRA_TO_SAMPLESHEET {
     val   mapping_fields
 
     output:
-    tuple val(meta), path("*csv"), emit: csv
-    tuple val(meta), path("*tsv"), emit: tsv
+    tuple val(meta), path("*samplesheet.csv"), emit: samplesheet
+    tuple val(meta), path("*mappings.csv")   , emit: mappings
 
     exec:
     //
@@ -51,12 +51,12 @@ process SRA_TO_SAMPLESHEET {
     pipeline_map << meta_map
 
     // Create a samplesheet
-    csv  = pipeline_map.keySet().collect{ '"' + it + '"'}.join(",") + '\n'
-    csv += pipeline_map.values().collect{ '"' + it + '"'}.join(",")
+    samplesheet  = pipeline_map.keySet().collect{ '"' + it + '"'}.join(",") + '\n'
+    samplesheet += pipeline_map.values().collect{ '"' + it + '"'}.join(",")
 
     // Write samplesheet to file
     def samplesheet_file = task.workDir.resolve("${meta.id}.samplesheet.csv")
-    samplesheet_file.text = csv
+    samplesheet_file.text = samplesheet
 
     //
     // Create sample id mappings file
@@ -68,10 +68,10 @@ process SRA_TO_SAMPLESHEET {
     }
 
     // Create mappings
-    tsv  = fields.join("\t") + '\n'
-    tsv += mappings_map.subMap(fields).values().join("\t")
+    mappings  = fields.collect{ '"' + it + '"'}.join(",") + '\n'
+    mappings += mappings_map.subMap(fields).values().collect{ '"' + it + '"'}.join(",")
 
     // Write mappings to file
-    def mappings_file = task.workDir.resolve("${meta.id}.mappings.tsv")
-    mappings_file.text = tsv
+    def mappings_file = task.workDir.resolve("${meta.id}.mappings.csv")
+    mappings_file.text = mappings
 }
diff --git a/workflows/fetchngs.nf b/workflows/fetchngs.nf
index 7d708927..1602494f 100755
--- a/workflows/fetchngs.nf
+++ b/workflows/fetchngs.nf
@@ -101,8 +101,8 @@ workflow FETCHNGS {
         // MODULE: Create a merged samplesheet across all samples for the pipeline
         //
         SRA_MERGE_SAMPLESHEET (
-            SRA_TO_SAMPLESHEET.out.csv.collect{it[1]},
-            SRA_TO_SAMPLESHEET.out.tsv.collect{it[1]}
+            SRA_TO_SAMPLESHEET.out.samplesheet.collect{it[1]},
+            SRA_TO_SAMPLESHEET.out.mappings.collect{it[1]}
         )
 
         //
@@ -110,7 +110,7 @@ workflow FETCHNGS {
         //
         if (params.sample_mapping_fields) {
             MULTIQC_MAPPINGS_CONFIG (
-                SRA_MERGE_SAMPLESHEET.out.tsv
+                SRA_MERGE_SAMPLESHEET.out.mappings
             )
         }
 

From 721621f3d056494640c10e1f92fd35f01b9e558c Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 21 Jun 2021 21:20:09 +0100
Subject: [PATCH 017/852] Update CHANGELOG

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e707b208..3cc14bd0 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,7 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Enhancements & fixes
 
 * [[#12](https://github.com/nf-core/fetchngs/issues/12)] - Error when using singularity - /etc/resolv.conf doesn't exist in container
-* Added `--sample_mapping_fields` parameter to create a separate `mappings.tsv` and `multiqc_config.yml` with selected fields that can be used to rename samples in general and in [MultiQC](https://multiqc.info/docs/#bulk-sample-renaming)
+* Added `--sample_mapping_fields` parameter to create a separate `id_mappings.csv` and `multiqc_config.yml` with selected fields that can be used to rename samples in general and in [MultiQC](https://multiqc.info/docs/#bulk-sample-renaming)
 
 ## [[1.0](https://github.com/nf-core/fetchngs/releases/tag/1.0)] - 2021-06-08
 

From ea7bd2f77e86db1158e8294a150e6befcdc09d10 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 22 Jun 2021 10:52:11 +0100
Subject: [PATCH 018/852] Change console to bash

---
 README.md     | 4 ++--
 docs/usage.md | 6 +++---
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 0eb5cbfb..e78820f8 100755
--- a/README.md
+++ b/README.md
@@ -41,7 +41,7 @@ The columns in the auto-created samplesheet can be tailored to be accepted out-o
 
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
-    ```console
+    ```bash
     nextflow run nf-core/fetchngs -profile test,<docker/singularity/podman/shifter/charliecloud/conda/institute>
     ```
 
@@ -51,7 +51,7 @@ The columns in the auto-created samplesheet can be tailored to be accepted out-o
 
 4. Start running your own analysis!
 
-    ```console
+    ```bash
     nextflow run nf-core/fetchngs --input ids.txt -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
     ```
 
diff --git a/docs/usage.md b/docs/usage.md
index 0ca76395..2e5675a9 100755
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -38,7 +38,7 @@ This downloads a text file called `SRR_Acc_List.txt` which can be directly provi
 
 The typical command for running the pipeline is as follows:
 
-```console
+```bash
 nextflow run nf-core/fetchngs --input ids.txt -profile docker
 ```
 
@@ -57,7 +57,7 @@ results         # Finished results (configurable, see below)
 
 When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
 
-```console
+```bash
 nextflow pull nf-core/fetchngs
 ```
 
@@ -221,6 +221,6 @@ Some HPC setups also allow you to run nextflow within a cluster job submitted yo
 In some cases, the Nextflow Java virtual machines can start to request a large amount of memory.
 We recommend adding the following line to your environment to limit this (typically in `~/.bashrc` or `~./bash_profile`):
 
-```console
+```bash
 NXF_OPTS='-Xms1g -Xmx4g'
 ```

From 8f03fa7fc741e12b129643361fdeab43569413f7 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 22 Jun 2021 10:52:30 +0100
Subject: [PATCH 019/852] Add description about files generated by
 --sample_mapping_fields

---
 nextflow_schema.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 8bb27a97..8d1a1c44 100755
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -32,7 +32,7 @@
                 "sample_mapping_fields": {
                     "type": "string",
                     "fa_icon": "fas fa-globe-americas",
-                    "description": "Comma-separated list of ENA metadata fields used to create mappings file for sample id mapping or renaming.",
+                    "description": "Comma-separated list of ENA metadata fields used to create a separate 'id_mappings.csv' and 'multiqc_config.yml' with selected fields that can be used to rename samples in general and in MultiQC.",
                     "default": "run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description,description"
                 },
                 "nf_core_pipeline": {

From faf03eae7ab42e2d32f2da5569fd94b899a8456a Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 22 Jun 2021 11:52:36 +0100
Subject: [PATCH 020/852] Bump version to 1.2dev

---
 CHANGELOG.md    | 4 ++++
 nextflow.config | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3cc14bd0..e28098c8 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unpublished Version / DEV]
+
+### Enhancements & fixes
+
 ## [[1.1](https://github.com/nf-core/fetchngs/releases/tag/1.1)] - 2021-06-22
 
 ### Enhancements & fixes
diff --git a/nextflow.config b/nextflow.config
index 5ac246e5..1c7eb664 100755
--- a/nextflow.config
+++ b/nextflow.config
@@ -147,7 +147,7 @@ manifest {
     description     = 'Pipeline to fetch metadata and raw FastQ files from public databases'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.04.0'
-    version         = '1.1'
+    version         = '1.2dev'
 }
 
 // Function to ensure that resource requirements don't go beyond

From 8a02f251e26805f872af073b8cbbab81c71a3f49 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Mon, 5 Jul 2021 16:02:57 +0100
Subject: [PATCH 021/852] Update README.md

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index e78820f8..ba2fa9fa 100755
--- a/README.md
+++ b/README.md
@@ -3,7 +3,7 @@
 [![GitHub Actions CI Status](https://github.com/nf-core/fetchngs/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/fetchngs/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/nf-core/fetchngs/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/fetchngs/actions?query=workflow%3A%22nf-core+linting%22)
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/fetchngs/results)
-[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.5070524)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.04.0-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
@@ -71,7 +71,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-If you use  nf-core/fetchngs for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX)
+If you use  nf-core/fetchngs for your analysis, please cite it using the following doi: [10.5281/zenodo.5070524](https://doi.org/10.5281/zenodo.5070524)
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 

From d71aaa29e3072958926871acdb8c471bad697b9b Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Mon, 5 Jul 2021 16:03:20 +0100
Subject: [PATCH 022/852] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index ba2fa9fa..fec02f01 100755
--- a/README.md
+++ b/README.md
@@ -3,7 +3,7 @@
 [![GitHub Actions CI Status](https://github.com/nf-core/fetchngs/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/fetchngs/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/nf-core/fetchngs/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/fetchngs/actions?query=workflow%3A%22nf-core+linting%22)
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/fetchngs/results)
-[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.5070524)
+[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.5070524-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.5070524)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.04.0-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)

From 67b1faa47dcac9171027da3db05a38a966921bd3 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Mon, 5 Jul 2021 16:03:55 +0100
Subject: [PATCH 023/852] Update WorkflowMain.groovy

---
 lib/WorkflowMain.groovy | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index a15e60d8..a7fb8c70 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -10,7 +10,7 @@ class WorkflowMain {
     public static String citation(workflow) {
         return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
             "* The pipeline\n" +
-            "  https://doi.org/10.5281/zenodo.XXXXXXX\n\n" +
+            "  https://doi.org/10.5281/zenodo.5070524\n\n" +
             "* The nf-core framework\n" +
             "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
             "* Software dependencies\n" +

From e603b346cf6d1bac944284f49aae3541464a3db7 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 13 Jul 2021 17:16:52 +0100
Subject: [PATCH 024/852] Update CHANGELOG

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e28098c8..e95c4850 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+* Updated pipeline template to [nf-core/tools 2.0.1](https://github.com/nf-core/tools/releases/tag/2.0.1)
+
 ## [[1.1](https://github.com/nf-core/fetchngs/releases/tag/1.1)] - 2021-06-22
 
 ### Enhancements & fixes

From 672a40fc6dcd36f63e7732617f67e4882639cd95 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 13 Jul 2021 17:41:39 +0100
Subject: [PATCH 025/852] Fix nf-core lint

---
 .nf-core-lint.yaml | 13 -------------
 .nf-core.yml       |  6 ++++++
 modules.json       | 14 --------------
 3 files changed, 6 insertions(+), 27 deletions(-)
 delete mode 100644 .nf-core-lint.yaml
 create mode 100644 .nf-core.yml
 delete mode 100644 modules.json

diff --git a/.nf-core-lint.yaml b/.nf-core-lint.yaml
deleted file mode 100644
index d472f25c..00000000
--- a/.nf-core-lint.yaml
+++ /dev/null
@@ -1,13 +0,0 @@
-files_unchanged:
-  - .github/CONTRIBUTING.md
-  - .github/ISSUE_TEMPLATE/bug_report.md
-  - .github/PULL_REQUEST_TEMPLATE.md
-  - .github/workflows/linting.yml
-  - assets/sendmail_template.txt
-  - docs/README.md
-  - lib/NfcoreSchema.groovy
-  - .gitignore
-files_exist:
-  - .github/markdownlint.yml
-  - bin/markdown_to_html.py
-actions_awsfulltest: False
diff --git a/.nf-core.yml b/.nf-core.yml
new file mode 100644
index 00000000..04dd88d8
--- /dev/null
+++ b/.nf-core.yml
@@ -0,0 +1,6 @@
+lint:
+  files_unchanged:
+    - .github/CONTRIBUTING.md
+    - assets/sendmail_template.txt
+    - bin/scrape_software_versions.py
+    - lib/NfcoreTemplate.groovy
diff --git a/modules.json b/modules.json
deleted file mode 100644
index e4a8a64f..00000000
--- a/modules.json
+++ /dev/null
@@ -1,14 +0,0 @@
-{
-    "name": "nf-core/fetchngs",
-    "homePage": "https://github.com/nf-core/fetchngs",
-    "repos": {
-        "nf-core/modules": {
-            "fastqc": {
-                "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
-            },
-            "multiqc": {
-                "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
-            }
-        }
-    }
-}

From bcd7aece348e54b0509d97832d40ce720f1ab672 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 20 Jul 2021 20:16:50 +0100
Subject: [PATCH 026/852] Ignore newlines at the end of JSON files

---
 .editorconfig | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.editorconfig b/.editorconfig
index afb20bb1..95549501 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -11,6 +11,9 @@ indent_style = space
 [*.{yml,yaml}]
 indent_size = 2
 
+[*.json]
+insert_final_newline = unset
+
 # These files are edited and tested upstream in nf-core/modules
 [/modules/nf-core/**]
 charset = unset

From b8d80937e3d505d1c40fc44ecd55127275ac04a6 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 20 Jul 2021 20:34:14 +0100
Subject: [PATCH 027/852] Bump version to v1.2

---
 CHANGELOG.md    | 2 +-
 nextflow.config | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e95c4850..fac42c14 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unpublished Version / DEV]
+## [[1.2](https://github.com/nf-core/fetchngs/releases/tag/1.2)] - 2021-07-26
 
 ### Enhancements & fixes
 
diff --git a/nextflow.config b/nextflow.config
index 1c7eb664..3b3ea780 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -147,7 +147,7 @@ manifest {
     description     = 'Pipeline to fetch metadata and raw FastQ files from public databases'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.04.0'
-    version         = '1.2dev'
+    version         = '1.2'
 }
 
 // Function to ensure that resource requirements don't go beyond

From 16c7cb0aac937af1ae070f60183775fce9e869b6 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 20 Jul 2021 20:34:33 +0100
Subject: [PATCH 028/852] Small updates to pipeline template

---
 lib/NfcoreTemplate.groovy | 22 +++++++++++++---------
 workflows/fetchngs.nf     |  4 +++-
 2 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
index b8fd59ab..3dd46e64 100755
--- a/lib/NfcoreTemplate.groovy
+++ b/lib/NfcoreTemplate.groovy
@@ -24,17 +24,21 @@ class NfcoreTemplate {
     public static void hostName(workflow, params, log) {
         Map colors = logColours(params.monochrome_logs)
         if (params.hostnames) {
-            def hostname = "hostname".execute().text.trim()
-            params.hostnames.each { prof, hnames ->
-                hnames.each { hname ->
-                    if (hostname.contains(hname) && !workflow.profile.contains(prof)) {
-                        log.info "=${colors.yellow}====================================================${colors.reset}=\n" +
-                            "${colors.yellow}WARN: You are running with `-profile $workflow.profile`\n" +
-                            "      but your machine hostname is ${colors.white}'$hostname'${colors.reset}.\n" +
-                            "      ${colors.yellow_bold}Please use `-profile $prof${colors.reset}`\n" +
-                            "=${colors.yellow}====================================================${colors.reset}="
+            try {
+                def hostname = "hostname".execute().text.trim()
+                params.hostnames.each { prof, hnames ->
+                    hnames.each { hname ->
+                        if (hostname.contains(hname) && !workflow.profile.contains(prof)) {
+                            log.info "=${colors.yellow}====================================================${colors.reset}=\n" +
+                                "${colors.yellow}WARN: You are running with `-profile $workflow.profile`\n" +
+                                "      but your machine hostname is ${colors.white}'$hostname'${colors.reset}.\n" +
+                                "      ${colors.yellow_bold}Please use `-profile $prof${colors.reset}`\n" +
+                                "=${colors.yellow}====================================================${colors.reset}="
+                        }
                     }
                 }
+            } catch (Exception e) {
+                log.warn "[$workflow.manifest.name] Could not determine 'hostname' - skipping check. Reason: ${e.message}."
             }
         }
     }
diff --git a/workflows/fetchngs.nf b/workflows/fetchngs.nf
index 1602494f..12733f07 100644
--- a/workflows/fetchngs.nf
+++ b/workflows/fetchngs.nf
@@ -147,7 +147,9 @@ workflow FETCHNGS {
 */
 
 workflow.onComplete {
-    NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)
+    if (params.email || params.email_on_fail) {
+        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)
+    }
     NfcoreTemplate.summary(workflow, params, log)
     WorkflowFetchngs.curateSamplesheetWarn(log)
 }

From cc3d5fe19dbedad65452a2b8da51b1ec49442ec8 Mon Sep 17 00:00:00 2001
From: Alain Domissy <alaindomissy@gmail.com>
Date: Thu, 22 Jul 2021 07:34:18 -0700
Subject: [PATCH 029/852] update ebi api url in fetch_sra_runinfo

---
 bin/sra_ids_to_runinfo.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index f78eb31f..5d276e08 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -128,7 +128,7 @@ def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields=ENA_METADATA_FIELDS
 
                         ## Resolve/expand to get run identifier from ENA and write to file
                         for id in ids:
-                            url = 'http://www.ebi.ac.uk/ena/data/warehouse/filereport?accession={}&result=read_run&fields={}'.format(id,','.join(ena_metadata_fields))
+                            url = 'http://www.ebi.ac.uk/ena/portal/api/filereport?accession={}&result=read_run&fields={}'.format(id,','.join(ena_metadata_fields))
                             csv_dict = csv.DictReader(fetch_url(url), delimiter='\t')
                             for row in csv_dict:
                                 run_id = row['run_accession']

From 5101495c33345ed91c9d237cb8b70b164896947d Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 22 Jul 2021 17:29:56 +0100
Subject: [PATCH 030/852] Update CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fac42c14..159bfadb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Enhancements & fixes
 
 * Updated pipeline template to [nf-core/tools 2.0.1](https://github.com/nf-core/tools/releases/tag/2.0.1)
+* [[#26](https://github.com/nf-core/fetchngs/pull/26)] - Update ebi api url in fetch_sra_runinfo
 
 ## [[1.1](https://github.com/nf-core/fetchngs/releases/tag/1.1)] - 2021-06-22
 

From d2fd73d15a8f61613cae91b852bb4a29e560eaa3 Mon Sep 17 00:00:00 2001
From: jahdoos <rfor10@gmail.com>
Date: Fri, 23 Jul 2021 15:02:55 -0700
Subject: [PATCH 031/852] ena portal API update

Fixes error i started getting - presumably ena changed their api
---
 bin/sra_ids_to_runinfo.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index f78eb31f..1480e8f2 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -79,7 +79,7 @@ def id_to_srx(db_id):
 def id_to_erx(db_id):
     ids = []
     fields = ['run_accession', 'experiment_accession']
-    url = 'http://www.ebi.ac.uk/ena/data/warehouse/filereport?accession={}&result=read_run&fields={}'.format(db_id,','.join(fields))
+    url = 'https://www.ebi.ac.uk/ena/portal/api/filereport?accession={}&result=read_run&fields={}'.format(db_id,','.join(fields))
     for row in csv.DictReader(fetch_url(url), delimiter='\t'):
         ids.append(row['experiment_accession'])
     return ids
@@ -128,7 +128,7 @@ def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields=ENA_METADATA_FIELDS
 
                         ## Resolve/expand to get run identifier from ENA and write to file
                         for id in ids:
-                            url = 'http://www.ebi.ac.uk/ena/data/warehouse/filereport?accession={}&result=read_run&fields={}'.format(id,','.join(ena_metadata_fields))
+                            url = 'https://www.ebi.ac.uk/ena/portal/api/filereport?accession={}&result=read_run&fields={}'.format(id,','.join(ena_metadata_fields))
                             csv_dict = csv.DictReader(fetch_url(url), delimiter='\t')
                             for row in csv_dict:
                                 run_id = row['run_accession']

From b49a905d5e8e9b4ac9b0f8eae5ae4fd3bad46266 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 26 Jul 2021 17:38:04 +0100
Subject: [PATCH 032/852] Fix last remaining EBI API URL change

---
 bin/sra_ids_to_runinfo.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index 5d276e08..febc2a01 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -79,7 +79,7 @@ def id_to_srx(db_id):
 def id_to_erx(db_id):
     ids = []
     fields = ['run_accession', 'experiment_accession']
-    url = 'http://www.ebi.ac.uk/ena/data/warehouse/filereport?accession={}&result=read_run&fields={}'.format(db_id,','.join(fields))
+    url = 'http://www.ebi.ac.uk/ena/portal/api/filereport?accession={}&result=read_run&fields={}'.format(db_id,','.join(fields))
     for row in csv.DictReader(fetch_url(url), delimiter='\t'):
         ids.append(row['experiment_accession'])
     return ids

From 4b01759274b10dc3821f8466e02d709ad2435a0a Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 26 Jul 2021 17:44:19 +0100
Subject: [PATCH 033/852] Update CHANGELOG

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 159bfadb..db16ac8e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[1.2](https://github.com/nf-core/fetchngs/releases/tag/1.2)] - 2021-07-26
+## [[1.2](https://github.com/nf-core/fetchngs/releases/tag/1.2)] - 2021-07-28
 
 ### Enhancements & fixes
 

From e7a0d02e10a8916888c03ef5f3aa27ff4d40a859 Mon Sep 17 00:00:00 2001
From: Oliver Ziff <41295194+ojziff@users.noreply.github.com>
Date: Mon, 26 Jul 2021 21:30:52 +0100
Subject: [PATCH 034/852] Update usage.md

update public_data_ids argument to input
---
 docs/usage.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/usage.md b/docs/usage.md
index 2e5675a9..dc2edc19 100755
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -32,7 +32,7 @@ If you have a GEO accession (found in the data availability section of published
 * Click `SRA Run Selector` at the bottom of the GEO accession page
 * Select the desired samples in the `SRA Run Selector` and then download the `Accession List`
 
-This downloads a text file called `SRR_Acc_List.txt` which can be directly provided to the pipeline e.g. `--public_data_ids SRR_Acc_List.txt`.
+This downloads a text file called `SRR_Acc_List.txt` which can be directly provided to the pipeline e.g. `--input SRR_Acc_List.txt`.
 
 ## Running the pipeline
 

From fdba0bf660afb1473efee12e06a154628b5ee08c Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Mon, 26 Jul 2021 22:54:58 +0100
Subject: [PATCH 035/852] Update usage.md

---
 docs/usage.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/usage.md b/docs/usage.md
index dc2edc19..1aebaa3e 100755
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -32,7 +32,7 @@ If you have a GEO accession (found in the data availability section of published
 * Click `SRA Run Selector` at the bottom of the GEO accession page
 * Select the desired samples in the `SRA Run Selector` and then download the `Accession List`
 
-This downloads a text file called `SRR_Acc_List.txt` which can be directly provided to the pipeline e.g. `--input SRR_Acc_List.txt`.
+This downloads a text file called `SRR_Acc_List.txt` that can be directly provided to the pipeline e.g. `--input SRR_Acc_List.txt`.
 
 ## Running the pipeline
 

From 383dcbe4f6939ed8cd3fac2a8c5a96a7e62a1a63 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 27 Jul 2021 21:26:59 +0100
Subject: [PATCH 036/852] Update CHANGELOG

---
 CHANGELOG.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index db16ac8e..be77eb6f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,8 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
-* Updated pipeline template to [nf-core/tools 2.0.1](https://github.com/nf-core/tools/releases/tag/2.0.1)
-* [[#26](https://github.com/nf-core/fetchngs/pull/26)] - Update ebi api url in fetch_sra_runinfo
+* Updated pipeline template to [nf-core/tools 2.1](https://github.com/nf-core/tools/releases/tag/2.1)
+* [[#26](https://github.com/nf-core/fetchngs/pull/26)] - Update broken EBI API URL
 
 ## [[1.1](https://github.com/nf-core/fetchngs/releases/tag/1.1)] - 2021-06-22
 

From 8f310d715fec4935bb095622d5aaa9ef7a47b90e Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 27 Jul 2021 21:31:22 +0100
Subject: [PATCH 037/852] Amend files_unchanged in .nf-core.yml

---
 .nf-core.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index 04dd88d8..12fe7aa8 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -2,5 +2,4 @@ lint:
   files_unchanged:
     - .github/CONTRIBUTING.md
     - assets/sendmail_template.txt
-    - bin/scrape_software_versions.py
     - lib/NfcoreTemplate.groovy

From ed853c1c5dc9c143e8f9e61def3e98a534b0d978 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 14 Sep 2021 23:35:20 +0100
Subject: [PATCH 038/852] Replace requests with urllib

---
 bin/sra_ids_to_runinfo.py | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index 1480e8f2..41a5c0ee 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -5,8 +5,9 @@
 import sys
 import csv
 import errno
-import requests
 import argparse
+from urllib.request import urlopen
+from urllib.error import URLError, HTTPError
 
 ## Example ids supported by this script
 SRA_IDS = ['PRJNA63463', 'SAMN00765663', 'SRA023522', 'SRP003255', 'SRR390278', 'SRS282569', 'SRX111814']
@@ -61,13 +62,17 @@ def make_dir(path):
 
 def fetch_url(url, encoding='utf-8'):
     try:
-        r = requests.get(url)
-    except requests.exceptions.RequestException as e:
-        raise SystemExit(e)
-    if r.status_code != 200:
-        print("ERROR: Connection failed\nError code '{}'".format(r.status_code))
+        with urlopen(url) as f:
+            r = f.read().decode(encoding).splitlines()
+    except HTTPError as e:
+        print('The server couldn\'t fulfill the request.')
+        print('Error code: {}'.format(e.code))
         sys.exit(1)
-    return r.content.decode(encoding).splitlines()
+    except URLError as e:
+        print('We failed to reach a server.')
+        print('Reason: {}'.format(e.reason))
+        sys.exit(1)
+    return r
 
 def id_to_srx(db_id):
     ids = []

From 79444d5605404c85ba20404ffdc86185a6c51321 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 14 Sep 2021 23:35:35 +0100
Subject: [PATCH 039/852] Bump Python version to 3.9.5

---
 modules/local/get_software_versions.nf   | 6 +++---
 modules/local/multiqc_mappings_config.nf | 6 +++---
 modules/local/sra_ids_to_runinfo.nf      | 6 +++---
 modules/local/sra_runinfo_to_ftp.nf      | 6 +++---
 4 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/modules/local/get_software_versions.nf b/modules/local/get_software_versions.nf
index 4d37bd6a..65b7f340 100644
--- a/modules/local/get_software_versions.nf
+++ b/modules/local/get_software_versions.nf
@@ -8,11 +8,11 @@ process GET_SOFTWARE_VERSIONS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
+        container "https://depot.galaxyproject.org/singularity/python:3.9--1"
     } else {
-        container "quay.io/biocontainers/python:3.8.3"
+        container "quay.io/biocontainers/python:3.9--1"
     }
 
     cache false
diff --git a/modules/local/multiqc_mappings_config.nf b/modules/local/multiqc_mappings_config.nf
index 63121b40..8360cd34 100644
--- a/modules/local/multiqc_mappings_config.nf
+++ b/modules/local/multiqc_mappings_config.nf
@@ -8,11 +8,11 @@ process MULTIQC_MAPPINGS_CONFIG {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
+        container "https://depot.galaxyproject.org/singularity/python:3.9--1"
     } else {
-        container "quay.io/biocontainers/python:3.8.3"
+        container "quay.io/biocontainers/python:3.9--1"
     }
 
     input:
diff --git a/modules/local/sra_ids_to_runinfo.nf b/modules/local/sra_ids_to_runinfo.nf
index b277197e..3d3fc063 100644
--- a/modules/local/sra_ids_to_runinfo.nf
+++ b/modules/local/sra_ids_to_runinfo.nf
@@ -10,11 +10,11 @@ process SRA_IDS_TO_RUNINFO {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
+        container "https://depot.galaxyproject.org/singularity/python:3.9--1"
     } else {
-        container "biocontainers/biocontainers:v1.2.0_cv1"
+        container "quay.io/biocontainers/python:3.9--1"
     }
 
     input:
diff --git a/modules/local/sra_runinfo_to_ftp.nf b/modules/local/sra_runinfo_to_ftp.nf
index b0421aea..f426f4ab 100644
--- a/modules/local/sra_runinfo_to_ftp.nf
+++ b/modules/local/sra_runinfo_to_ftp.nf
@@ -8,11 +8,11 @@ process SRA_RUNINFO_TO_FTP {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
+        container "https://depot.galaxyproject.org/singularity/python:3.9--1"
     } else {
-        container "quay.io/biocontainers/python:3.8.3"
+        container "quay.io/biocontainers/python:3.9--1"
     }
 
     input:

From 74b7f148b5462998d8b5f485ad0bad55f73e2ef3 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 14 Sep 2021 23:35:43 +0100
Subject: [PATCH 040/852] Update CHANGELOG

---
 CHANGELOG.md | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index be77eb6f..eae33fae 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,18 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[1.3](https://github.com/nf-core/fetchngs/releases/tag/1.3)] - 2021-09-15
+
+### Enhancements & fixes
+
+* Replaced Python `requests` with `urllib` to fetch ENA metadata
+
+### Software dependencies
+
+| Dependency  | Old version | New version |
+|-------------|-------------|-------------|
+| `python`    | 3.8.3       | 3.9.5       |
+
 ## [[1.2](https://github.com/nf-core/fetchngs/releases/tag/1.2)] - 2021-07-28
 
 ### Enhancements & fixes

From 48c53f268f2d7738df1f9c0c09cc81e378079cf3 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 14 Sep 2021 23:35:54 +0100
Subject: [PATCH 041/852] Bump pipeline version

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 3b3ea780..52382140 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -147,7 +147,7 @@ manifest {
     description     = 'Pipeline to fetch metadata and raw FastQ files from public databases'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.04.0'
-    version         = '1.2'
+    version         = '1.3'
 }
 
 // Function to ensure that resource requirements don't go beyond

From 57a303ca77439a7334b0517303c8bb243c836765 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Wed, 15 Sep 2021 14:21:59 +0200
Subject: [PATCH 042/852] refactor: introduce logging to replace print

---
 bin/sra_ids_to_runinfo.py | 23 ++++++++++++++---------
 1 file changed, 14 insertions(+), 9 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index 41a5c0ee..24c6af0d 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -6,9 +6,13 @@
 import csv
 import errno
 import argparse
+import logging
 from urllib.request import urlopen
 from urllib.error import URLError, HTTPError
 
+
+logger = logging.getLogger()
+
 ## Example ids supported by this script
 SRA_IDS = ['PRJNA63463', 'SAMN00765663', 'SRA023522', 'SRP003255', 'SRR390278', 'SRS282569', 'SRX111814']
 ENA_IDS = ['ERA2421642', 'ERP120836', 'ERR674736', 'ERS4399631', 'ERX629702', 'PRJEB7743', 'SAMEA3121481']
@@ -48,7 +52,7 @@ def validate_csv_param(param, valid_vals, param_desc):
         if len(intersect) == len(user_vals):
             valid_list = intersect
         else:
-            print("ERROR: Please provide a valid value for {}!\nProvided values = {}\nAccepted values = {}".format(param_desc,param,','.join(valid_vals)))
+            logger.error(f"Please provide a valid value for {param_desc}!\nProvided values = {param}\nAccepted values = {','.join(valid_vals)}")
             sys.exit(1)
     return valid_list
 
@@ -65,12 +69,12 @@ def fetch_url(url, encoding='utf-8'):
         with urlopen(url) as f:
             r = f.read().decode(encoding).splitlines()
     except HTTPError as e:
-        print('The server couldn\'t fulfill the request.')
-        print('Error code: {}'.format(e.code))
+        logger.error("The server couldn't fulfill the request.")
+        logger.error(f"Status: {e.code} {e.reason}")
         sys.exit(1)
     except URLError as e:
-        print('We failed to reach a server.')
-        print('Reason: {}'.format(e.reason))
+        logger.error('We failed to reach a server.')
+        logger.error(f"Reason: {e.reason}")
         sys.exit(1)
     return r
 
@@ -143,7 +147,7 @@ def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields=ENA_METADATA_FIELDS
                                         fout.write('{}\n'.format('\t'.join(header)))
                                     else:
                                         if header != row.keys():
-                                            print("ERROR: Metadata columns do not match for id {}!\nLine: '{}'".format(run_id,line.strip()))
+                                            logger.error(f"Metadata columns do not match for id {run_id}!\nLine: '{line.strip()}'")
                                             sys.exit(1)
                                     fout.write('{}\n'.format('\t'.join([row[x] for x in header])))
                                     total_out += 1
@@ -151,16 +155,16 @@ def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields=ENA_METADATA_FIELDS
                         seen_ids.append(db_id)
 
                         if not ids:
-                            print("ERROR: No matches found for database id {}!\nLine: '{}'".format(db_id,line.strip()))
+                            logger.error(f"No matches found for database id {db_id}!\nLine: '{line.strip()}'")
                             sys.exit(1)
 
                 else:
                     id_str = ', '.join([x + "*" for x in PREFIX_LIST])
-                    print("ERROR: Please provide a valid database id starting with {}!\nLine: '{}'".format(id_str,line.strip()))
+                    logger.error(f"Please provide a valid database id starting with {id_str}!\nLine: '{line.strip()}'")
                     sys.exit(1)
             else:
                 id_str = ', '.join([x + "*" for x in PREFIX_LIST])
-                print("ERROR: Please provide a valid database id starting with {}!\nLine: '{}'".format(id_str,line.strip()))
+                logger.error(f"Please provide a valid database id starting with {id_str}!\nLine: '{line.strip()}'")
                 sys.exit(1)
 
 def main(args=None):
@@ -172,4 +176,5 @@ def main(args=None):
     fetch_sra_runinfo(args.FILE_IN, args.FILE_OUT, ena_metadata_fields)
 
 if __name__ == '__main__':
+    logging.basicConfig(level='INFO', format='[%(levelname)s] %(message)s')
     sys.exit(main())

From 2e132dcced092335dd2fcbc5460f4f53e63928d8 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Wed, 15 Sep 2021 14:25:05 +0200
Subject: [PATCH 043/852] refactor: make global constants immutable tuples

---
 bin/sra_ids_to_runinfo.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index 24c6af0d..eadfd8e5 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -14,15 +14,15 @@
 logger = logging.getLogger()
 
 ## Example ids supported by this script
-SRA_IDS = ['PRJNA63463', 'SAMN00765663', 'SRA023522', 'SRP003255', 'SRR390278', 'SRS282569', 'SRX111814']
-ENA_IDS = ['ERA2421642', 'ERP120836', 'ERR674736', 'ERS4399631', 'ERX629702', 'PRJEB7743', 'SAMEA3121481']
-GEO_IDS = ['GSE18729', 'GSM465244']
+SRA_IDS = ('PRJNA63463', 'SAMN00765663', 'SRA023522', 'SRP003255', 'SRR390278', 'SRS282569', 'SRX111814')
+ENA_IDS = ('ERA2421642', 'ERP120836', 'ERR674736', 'ERS4399631', 'ERX629702', 'PRJEB7743', 'SAMEA3121481')
+GEO_IDS = ('GSE18729', 'GSM465244')
 ID_REGEX = r'^[A-Z]+'
 PREFIX_LIST = sorted(list(set([re.search(ID_REGEX,x).group() for x in SRA_IDS + ENA_IDS + GEO_IDS])))
 
 ## List of meta fields fetched from the ENA API - can be overriden by --ena_metadata_fields
 ## Full list of accepted fields can be obtained here: https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run
-ENA_METADATA_FIELDS = [
+ENA_METADATA_FIELDS = (
     'accession', 'run_accession', 'experiment_accession', 'sample_accession', 'secondary_sample_accession', 'study_accession', 'secondary_study_accession', 'parent_study', 'submission_accession',
     'run_alias', 'experiment_alias', 'sample_alias', 'study_alias',
     'library_layout', 'library_selection', 'library_source', 'library_strategy', 'library_name',
@@ -32,7 +32,7 @@
     'sample_title', 'experiment_title', 'study_title',
     'description', 'sample_description',
     'fastq_md5', 'fastq_bytes', 'fastq_ftp', 'fastq_galaxy', 'fastq_aspera'
-]
+ )
 
 def parse_args(args=None):
     Description = 'Download and create a run information metadata file from SRA/ENA/GEO identifiers.'

From 99c9a620096a1d9e41a1aa664d2abc85f7d8eb1a Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Wed, 15 Sep 2021 14:29:49 +0200
Subject: [PATCH 044/852] refactor: use compiled regex pattern

---
 bin/sra_ids_to_runinfo.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index eadfd8e5..c70df48d 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -17,8 +17,8 @@
 SRA_IDS = ('PRJNA63463', 'SAMN00765663', 'SRA023522', 'SRP003255', 'SRR390278', 'SRS282569', 'SRX111814')
 ENA_IDS = ('ERA2421642', 'ERP120836', 'ERR674736', 'ERS4399631', 'ERX629702', 'PRJEB7743', 'SAMEA3121481')
 GEO_IDS = ('GSE18729', 'GSM465244')
-ID_REGEX = r'^[A-Z]+'
-PREFIX_LIST = sorted(list(set([re.search(ID_REGEX,x).group() for x in SRA_IDS + ENA_IDS + GEO_IDS])))
+ID_REGEX = re.compile(r'[A-Z]+')
+PREFIX_LIST = sorted({ID_REGEX.match(x).group() for x in SRA_IDS + ENA_IDS + GEO_IDS})
 
 ## List of meta fields fetched from the ENA API - can be overriden by --ena_metadata_fields
 ## Full list of accepted fields can be obtained here: https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run
@@ -116,7 +116,7 @@ def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields=ENA_METADATA_FIELDS
     with open(file_in,"r") as fin, open(file_out,"w") as fout:
         for line in fin:
             db_id = line.strip()
-            match = re.search(ID_REGEX, db_id)
+            match = ID_REGEX.match(db_id)
             if match:
                 prefix = match.group()
                 if prefix in PREFIX_LIST:

From 2ea9dd7173e449f93650169936f195a4ec985ac2 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Wed, 15 Sep 2021 14:32:54 +0200
Subject: [PATCH 045/852] refactor: use set for better lookup performance

---
 bin/sra_ids_to_runinfo.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index c70df48d..f90f7d9d 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -110,7 +110,8 @@ def get_ena_fields():
 
 def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields=ENA_METADATA_FIELDS):
     total_out = 0
-    seen_ids = []; run_ids = []
+    seen_ids = set()
+    run_ids = set()
     header = []
     make_dir(os.path.dirname(file_out))
     with open(file_in,"r") as fin, open(file_out,"w") as fout:
@@ -120,7 +121,7 @@ def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields=ENA_METADATA_FIELDS
             if match:
                 prefix = match.group()
                 if prefix in PREFIX_LIST:
-                    if not db_id in seen_ids:
+                    if db_id not in seen_ids:
 
                         ids = [db_id]
                         ## Resolve/expand these ids against GEO URL
@@ -141,7 +142,7 @@ def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields=ENA_METADATA_FIELDS
                             csv_dict = csv.DictReader(fetch_url(url), delimiter='\t')
                             for row in csv_dict:
                                 run_id = row['run_accession']
-                                if not run_id in run_ids:
+                                if run_id not in run_ids:
                                     if total_out == 0:
                                         header = row.keys()
                                         fout.write('{}\n'.format('\t'.join(header)))
@@ -151,8 +152,8 @@ def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields=ENA_METADATA_FIELDS
                                             sys.exit(1)
                                     fout.write('{}\n'.format('\t'.join([row[x] for x in header])))
                                     total_out += 1
-                                    run_ids.append(run_id)
-                        seen_ids.append(db_id)
+                                    run_ids.add(run_id)
+                        seen_ids.add(db_id)
 
                         if not ids:
                             logger.error(f"No matches found for database id {db_id}!\nLine: '{line.strip()}'")

From 473b2378f51104148b61b2737c39357e0c9a10a3 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Wed, 15 Sep 2021 15:19:04 +0200
Subject: [PATCH 046/852] feat: enable decompression and decoding from HTTP
 headers

---
 bin/sra_ids_to_runinfo.py | 84 +++++++++++++++++++++++++++++++++++++--
 1 file changed, 80 insertions(+), 4 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index f90f7d9d..1aef2cfe 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -7,6 +7,9 @@
 import errno
 import argparse
 import logging
+import gzip
+import zlib
+import cgi
 from urllib.request import urlopen
 from urllib.error import URLError, HTTPError
 
@@ -34,6 +37,79 @@
     'fastq_md5', 'fastq_bytes', 'fastq_ftp', 'fastq_galaxy', 'fastq_aspera'
  )
 
+
+class Response:
+    """
+    Define an HTTP response class.
+
+    This class should not have to be instantiated directly.
+
+    Attributes:
+        status (int): The numeric HTTP status code of the response.
+        reason (str): The response's reason phrase.
+        body (bytes): The response's decompressed body content as bytes.
+
+    Methods:
+        text: The response's body as a decoded string.
+
+    """
+
+    def __init__(self, *, response, **kwargs) -> None:
+        """
+        Initialize an HTTP response object.
+
+        Args:
+            response (http.client.HTTPResponse): A standard library response object
+                that is wrapped by this class.
+            **kwargs: Passed to parent classes.
+
+        """
+        super().__init__(**kwargs)
+        self._response = response
+        # Immediately read the body while the response context is still available.
+        self._raw = self._response.read()
+        self._content = None
+
+    def _decompress(self):
+        """Decompress the response body if necessary."""
+        method = self._response.getheader("Content-Encoding", "")
+        if not method:
+            self._content = self._raw
+            return
+        if method == "gzip":
+            self._content = gzip.decompress(self._raw)
+        elif method == "deflate":
+            self._content = zlib.decompress(self._raw)
+        else:
+            raise ValueError(f"Unsupported compression: {method}")
+
+    @property
+    def status(self):
+        """Get the response's HTTP status code."""
+        return self._response.status
+
+    @property
+    def reason(self):
+        """Get the response's reason phrase."""
+        return self._response.reason
+
+    @property
+    def body(self):
+        """Get the response's decompressed body content as bytes."""
+        if self._content is None:
+            self._decompress()
+        return self._content
+
+    def text(self, encoding=None):
+        """Return the response's body as a decoded string."""
+        if encoding is not None:
+            return self._content.decode(encoding)
+
+        _, params = cgi.parse_header(self._response.getheader("Content-Type", ""))
+        encoding = params.get("charset", "utf-8")
+        return self._content.decode(encoding)
+
+
 def parse_args(args=None):
     Description = 'Download and create a run information metadata file from SRA/ENA/GEO identifiers.'
     Epilog = 'Example usage: python fetch_sra_runinfo.py <FILE_IN> <FILE_OUT>'
@@ -64,10 +140,10 @@ def make_dir(path):
             if exception.errno != errno.EEXIST:
                 raise
 
-def fetch_url(url, encoding='utf-8'):
+def fetch_url(url):
     try:
-        with urlopen(url) as f:
-            r = f.read().decode(encoding).splitlines()
+        with urlopen(url) as response:
+            result = Response(response=response).text().splitlines()
     except HTTPError as e:
         logger.error("The server couldn't fulfill the request.")
         logger.error(f"Status: {e.code} {e.reason}")
@@ -76,7 +152,7 @@ def fetch_url(url, encoding='utf-8'):
         logger.error('We failed to reach a server.')
         logger.error(f"Reason: {e.reason}")
         sys.exit(1)
-    return r
+    return result
 
 def id_to_srx(db_id):
     ids = []

From 7798aa1a63d68e9162c7dc4714f78a9775dc7011 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Wed, 15 Sep 2021 15:25:33 +0200
Subject: [PATCH 047/852] refactor: use f-strings where possible

---
 bin/sra_ids_to_runinfo.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index 1aef2cfe..4b4ed2d7 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -117,7 +117,7 @@ def parse_args(args=None):
     parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
     parser.add_argument('FILE_IN', help="File containing database identifiers, one per line.")
     parser.add_argument('FILE_OUT', help="Output file in tab-delimited format.")
-    parser.add_argument('-ef', '--ena_metadata_fields', type=str, dest="ENA_METADATA_FIELDS", default='', help="Comma-separated list of ENA metadata fields to fetch. (default: {}).".format(','.join(ENA_METADATA_FIELDS)))
+    parser.add_argument('-ef', '--ena_metadata_fields', type=str, dest="ENA_METADATA_FIELDS", default='', help=f"Comma-separated list of ENA metadata fields to fetch. (default: {','.join(ENA_METADATA_FIELDS)}).")
     return parser.parse_args(args)
 
 def validate_csv_param(param, valid_vals, param_desc):
@@ -220,13 +220,15 @@ def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields=ENA_METADATA_FIELDS
                                 run_id = row['run_accession']
                                 if run_id not in run_ids:
                                     if total_out == 0:
-                                        header = row.keys()
-                                        fout.write('{}\n'.format('\t'.join(header)))
+                                        header = '\t'.join(row.keys())
+                                        fout.write(f"{header}\n")
                                     else:
                                         if header != row.keys():
                                             logger.error(f"Metadata columns do not match for id {run_id}!\nLine: '{line.strip()}'")
                                             sys.exit(1)
-                                    fout.write('{}\n'.format('\t'.join([row[x] for x in header])))
+
+                                    ordered_row = '\t'.join([row[x] for x in header])
+                                    fout.write(f'{ordered_row}\n')
                                     total_out += 1
                                     run_ids.add(run_id)
                         seen_ids.add(db_id)

From eaca802ba4ee15883a049c523b5a7c104347cd7e Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Wed, 15 Sep 2021 15:52:17 +0200
Subject: [PATCH 048/852] refactor: manage URLs with encoding

---
 bin/sra_ids_to_runinfo.py | 79 +++++++++++++++++++++++++--------------
 1 file changed, 51 insertions(+), 28 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index 4b4ed2d7..87fe51f1 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -1,18 +1,18 @@
 #!/usr/bin/env python
 
-import os
-import re
-import sys
+import argparse
+import cgi
 import csv
 import errno
-import argparse
-import logging
 import gzip
+import logging
+import os
+import re
+import sys
 import zlib
-import cgi
-from urllib.request import urlopen
 from urllib.error import URLError, HTTPError
-
+from urllib.parse import urlencode
+from urllib.request import urlopen
 
 logger = logging.getLogger()
 
@@ -155,34 +155,53 @@ def fetch_url(url):
     return result
 
 def id_to_srx(db_id):
-    ids = []
-    url = 'https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&db=sra&rettype=runinfo&term={}'.format(db_id)
-    for row in csv.DictReader(fetch_url(url), delimiter=','):
-        ids.append(row['Experiment'])
-    return ids
+    params = {
+        "save": "efetch",
+        "db": "sra",
+        "rettype": "runinfo",
+        "term": db_id
+    }
+    url = f'https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?{urlencode(params)}'
+    return [
+        row['Experiment'] for row in csv.DictReader(fetch_url(url), delimiter=',')
+    ]
 
 def id_to_erx(db_id):
-    ids = []
     fields = ['run_accession', 'experiment_accession']
-    url = 'https://www.ebi.ac.uk/ena/portal/api/filereport?accession={}&result=read_run&fields={}'.format(db_id,','.join(fields))
-    for row in csv.DictReader(fetch_url(url), delimiter='\t'):
-        ids.append(row['experiment_accession'])
-    return ids
+    params = {
+        "accession": db_id,
+        "result": "read_run",
+        "fields": ",".join(fields)
+    }
+    url = f'https://www.ebi.ac.uk/ena/portal/api/filereport?{urlencode(params)}'
+    return [
+        row['experiment_accession'] for row in csv.DictReader(fetch_url(url), delimiter='\t')
+    ]
 
 def gse_to_srx(db_id):
     ids = []
-    url = 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={}&targ=gsm&view=data&form=text'.format(db_id)
-    gsm_ids = [x.split('=')[1].strip() for x in fetch_url(url) if x.find('GSM') != -1]
+    params = {
+        "acc": db_id,
+        "targ": "gsm",
+        "view": "data",
+        "form": "text"
+    }
+    url = f'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?{urlencode(params)}'
+    gsm_ids = [x.split('=')[1].strip() for x in fetch_url(url) if x.startswith('GSM')]
     for gsm_id in gsm_ids:
         ids += id_to_srx(gsm_id)
     return ids
 
 def get_ena_fields():
-    fields = []
-    url = 'https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run'
-    for row in csv.DictReader(fetch_url(url), delimiter='\t'):
-        fields.append(row['columnId'])
-    return fields
+    params = {
+        "dataPortal": "ena",
+        "format": "tsv",
+        "result": "read_run"
+    }
+    url = f'https://www.ebi.ac.uk/ena/portal/api/returnFields?{urlencode(params)}'
+    return [
+        row['columnId'] for row in csv.DictReader(fetch_url(url), delimiter='\t')
+    ]
 
 def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields=ENA_METADATA_FIELDS):
     total_out = 0
@@ -190,6 +209,10 @@ def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields=ENA_METADATA_FIELDS
     run_ids = set()
     header = []
     make_dir(os.path.dirname(file_out))
+    params = {
+        "result": "read_run",
+        "fields": ','.join(ena_metadata_fields)
+    }
     with open(file_in,"r") as fin, open(file_out,"w") as fout:
         for line in fin:
             db_id = line.strip()
@@ -214,9 +237,9 @@ def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields=ENA_METADATA_FIELDS
 
                         ## Resolve/expand to get run identifier from ENA and write to file
                         for id in ids:
-                            url = 'https://www.ebi.ac.uk/ena/portal/api/filereport?accession={}&result=read_run&fields={}'.format(id,','.join(ena_metadata_fields))
-                            csv_dict = csv.DictReader(fetch_url(url), delimiter='\t')
-                            for row in csv_dict:
+                            params["accession"] = id
+                            url = f'https://www.ebi.ac.uk/ena/portal/api/filereport?{urlencode(params)}'
+                            for row in csv.DictReader(fetch_url(url), delimiter='\t'):
                                 run_id = row['run_accession']
                                 if run_id not in run_ids:
                                     if total_out == 0:

From fa38ddaacd1cc48c6c1d6616a0116885fcc6f0be Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Wed, 15 Sep 2021 16:07:31 +0200
Subject: [PATCH 049/852] fix: maintain header list in variable, not string

---
 bin/sra_ids_to_runinfo.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index 87fe51f1..11fe5247 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -103,11 +103,11 @@ def body(self):
     def text(self, encoding=None):
         """Return the response's body as a decoded string."""
         if encoding is not None:
-            return self._content.decode(encoding)
+            return self.body.decode(encoding)
 
         _, params = cgi.parse_header(self._response.getheader("Content-Type", ""))
         encoding = params.get("charset", "utf-8")
-        return self._content.decode(encoding)
+        return self.body.decode(encoding)
 
 
 def parse_args(args=None):
@@ -243,8 +243,9 @@ def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields=ENA_METADATA_FIELDS
                                 run_id = row['run_accession']
                                 if run_id not in run_ids:
                                     if total_out == 0:
-                                        header = '\t'.join(row.keys())
-                                        fout.write(f"{header}\n")
+                                        header = row.keys()
+                                        header_line = '\t'.join(header)
+                                        fout.write(f"{header_line}\n")
                                     else:
                                         if header != row.keys():
                                             logger.error(f"Metadata columns do not match for id {run_id}!\nLine: '{line.strip()}'")

From 1f7ae6a7cb17e681accf2940460483043ff3b69b Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Wed, 15 Sep 2021 16:13:53 +0200
Subject: [PATCH 050/852] style: remove space

---
 bin/sra_ids_to_runinfo.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index 11fe5247..68b1c924 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -35,7 +35,7 @@
     'sample_title', 'experiment_title', 'study_title',
     'description', 'sample_description',
     'fastq_md5', 'fastq_bytes', 'fastq_ftp', 'fastq_galaxy', 'fastq_aspera'
- )
+)
 
 
 class Response:

From ce7ed6016ef67377651960b8fb212a80dcdca4ea Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Wed, 15 Sep 2021 18:04:27 +0200
Subject: [PATCH 051/852] style: remove last type annotation

---
 bin/sra_ids_to_runinfo.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index 68b1c924..ae60f545 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -54,7 +54,7 @@ class Response:
 
     """
 
-    def __init__(self, *, response, **kwargs) -> None:
+    def __init__(self, *, response, **kwargs):
         """
         Initialize an HTTP response object.
 

From 413517fb5a6a856a6d9e1b4a8a15ed672e2ba85e Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 15 Sep 2021 17:44:02 +0100
Subject: [PATCH 052/852] Bump pipeline version to 1.4dev

---
 CHANGELOG.md    | 4 ++++
 nextflow.config | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index eae33fae..2d633f30 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unpublished Version / DEV]
+
+### Enhancements & fixes
+
 ## [[1.3](https://github.com/nf-core/fetchngs/releases/tag/1.3)] - 2021-09-15
 
 ### Enhancements & fixes
diff --git a/nextflow.config b/nextflow.config
index 52382140..131151b9 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -147,7 +147,7 @@ manifest {
     description     = 'Pipeline to fetch metadata and raw FastQ files from public databases'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.04.0'
-    version         = '1.3'
+    version         = '1.4dev'
 }
 
 // Function to ensure that resource requirements don't go beyond

From a8ed0ad40dfb138352f4f62b69d931cbb02b7814 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 28 Sep 2021 22:28:42 +0100
Subject: [PATCH 053/852] Add support for DDBJ ids

---
 CHANGELOG.md              | 12 ++++++++++++
 CITATIONS.md              |  3 +++
 README.md                 |  2 +-
 assets/schema_input.json  |  2 +-
 bin/sra_ids_to_runinfo.py | 10 ++++++----
 docs/output.md            |  6 +++---
 docs/usage.md             | 22 +++++++++++-----------
 nextflow_schema.json      |  2 +-
 8 files changed, 38 insertions(+), 21 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2d633f30..e6dcc246 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+* Added support for [DDBJ ids](https://www.ddbj.nig.ac.jp/index-e.html). See examples below:
+
+! `DDBJ`        |
+|---------------|
+| PRJDB4176     |
+| SAMD00114846  |
+| DRA008156     |
+| DRP004793     |
+| DRR171822     |
+| DRS090921     |
+| DRX162434     |
+
 ## [[1.3](https://github.com/nf-core/fetchngs/releases/tag/1.3)] - 2021-09-15
 
 ### Enhancements & fixes
diff --git a/CITATIONS.md b/CITATIONS.md
index 00f85a25..4a1f2752 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -22,6 +22,9 @@
 * [SRA](https://pubmed.ncbi.nlm.nih.gov/21062823/)
     > Leinonen R, Sugawara H, Shumway M, International Nucleotide Sequence Database Collaboration. The sequence read archive. Nucleic Acids Res. 2011 Jan;39 (Database issue):D19-21. doi: 10.1093/nar/gkq1019. Epub 2010 Nov 9. PubMed PMID: 21062823; PubMed Central PMCID: PMC3013647.
 
+* [DDBJ](https://pubmed.ncbi.nlm.nih.gov/33156332/)
+    > Fukuda A, Kodama Y, Mashima J, Fujisawa T, Ogasawara O. DDBJ update: streamlining submission and access of human data. Nucleic Acids Res. 2021 Jan 8;49(D1):D71-D75. doi: 10.1093/nar/gkaa982. PubMed PMID: 33156332; PubMed Central PMCID: PMC7779041.
+
 * [GEO](https://pubmed.ncbi.nlm.nih.gov/23193258/)
     > Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A. NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5. doi: 10.1093/nar/gks1193. Epub 2012 Nov 27. PubMed PMID: 23193258; PubMed Central PMCID: PMC3531084.
 
diff --git a/README.md b/README.md
index 544862c0..e378eacc 100644
--- a/README.md
+++ b/README.md
@@ -16,7 +16,7 @@
 
 ## Introduction
 
-**nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from public databases. At present, the pipeline supports SRA / ENA / GEO ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)).
+**nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from public databases. At present, the pipeline supports SRA / ENA / DDBJ / GEO ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)).
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.
 
diff --git a/assets/schema_input.json b/assets/schema_input.json
index b4141272..224e5cf7 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -9,7 +9,7 @@
         "items": {
             "type": "string",
             "pattern": "^[SEPG][RAS][RXSMPAJXE][EN]?[AB]?\\d{4,9}$",
-            "errorMessage": "Please provide a valid SRA, GEO or ENA identifier"
+            "errorMessage": "Please provide a valid SRA, ENA, DDBJ or GEO identifier"
         }
     }
 }
diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index ae60f545..6de6fc28 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -18,10 +18,12 @@
 
 ## Example ids supported by this script
 SRA_IDS = ('PRJNA63463', 'SAMN00765663', 'SRA023522', 'SRP003255', 'SRR390278', 'SRS282569', 'SRX111814')
-ENA_IDS = ('ERA2421642', 'ERP120836', 'ERR674736', 'ERS4399631', 'ERX629702', 'PRJEB7743', 'SAMEA3121481')
+ENA_IDS = ('PRJEB7743', 'SAMEA3121481', 'ERA2421642', 'ERP120836', 'ERR674736', 'ERS4399631', 'ERX629702')
+DDBJ_IDS = ('PRJDB4176', 'SAMD00114846', 'DRA008156', 'DRP004793', 'DRR171822', 'DRS090921', 'DRX162434')
 GEO_IDS = ('GSE18729', 'GSM465244')
 ID_REGEX = re.compile(r'[A-Z]+')
-PREFIX_LIST = sorted({ID_REGEX.match(x).group() for x in SRA_IDS + ENA_IDS + GEO_IDS})
+PREFIX_LIST = sorted({ID_REGEX.match(x).group() for x in SRA_IDS + ENA_IDS + DDBJ_IDS + GEO_IDS})
+
 
 ## List of meta fields fetched from the ENA API - can be overriden by --ena_metadata_fields
 ## Full list of accepted fields can be obtained here: https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run
@@ -111,7 +113,7 @@ def text(self, encoding=None):
 
 
 def parse_args(args=None):
-    Description = 'Download and create a run information metadata file from SRA/ENA/GEO identifiers.'
+    Description = 'Download and create a run information metadata file from SRA / ENA / DDBJ / GEO identifiers.'
     Epilog = 'Example usage: python fetch_sra_runinfo.py <FILE_IN> <FILE_OUT>'
 
     parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
@@ -228,7 +230,7 @@ def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields=ENA_METADATA_FIELDS
                             ids = gse_to_srx(db_id)
 
                         ## Resolve/expand these ids against SRA URL
-                        elif prefix in ['GSM', 'PRJNA', 'SAMN', 'SRR']:
+                        elif prefix in ['GSM', 'PRJNA', 'SAMN', 'SRR', 'DRA', 'DRP', 'DRR', 'DRS', 'DRX', 'PRJDB', 'SAMD']:
                             ids = id_to_srx(db_id)
 
                         ## Resolve/expand these ids against ENA URL
diff --git a/docs/output.md b/docs/output.md
index c0916e6d..4ffc507e 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -8,7 +8,7 @@ This document describes the output produced by the pipeline. The directories lis
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
-* [FastQ download](#fastq-download) - Download FastQ files via SRA / ENA / GEO ids
+* [FastQ download](#fastq-download) - Download FastQ files via SRA / ENA / DDBJ / GEO ids
 * [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
 ### FastQ download
@@ -17,9 +17,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 <summary>Output files</summary>
 
 * `fastq/`
-    * `*.fastq.gz`: Paired-end/single-end reads downloaded from the ENA / SRA.
+    * `*.fastq.gz`: Paired-end/single-end reads downloaded from the SRA / ENA / DDBJ / GEO.
 * `fastq/md5/`
-    * `*.md5`: Files containing `md5` sum for FastQ files downloaded from the ENA / SRA.
+    * `*.md5`: Files containing `md5` sum for FastQ files downloaded from the ENA.
 * `samplesheet/`
     * `samplesheet.csv`: Auto-created samplesheet with collated metadata and paths to downloaded FastQ files.
     * `id_mappings.csv`: File with selected fields that can be used to rename samples to more informative names; see [`--sample_mapping_fields`](https://nf-co.re/fetchngs/parameters#sample_mapping_fields) parameter to customise this behaviour.
diff --git a/docs/usage.md b/docs/usage.md
index 398c739a..1e6066db 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -8,17 +8,17 @@
 
 The pipeline has been set-up to automatically download and process the raw FastQ files from public repositories. Identifiers can be provided in a file, one-per-line via the `--input` parameter. Currently, the following types of example identifiers are supported:
 
-| `SRA`        | `ENA`        | `GEO`      |
-|--------------|--------------|------------|
-| SRR11605097  | ERR4007730   | GSM4432381 |
-| SRX8171613   | ERX4009132   | GSE147507  |
-| SRS6531847   | ERS4399630   |            |
-| SAMN14689442 | SAMEA6638373 |            |
-| SRP256957    | ERP120836    |            |
-| SRA1068758   | ERA2420837   |            |
-| PRJNA625551  | PRJEB37513   |            |
-
-If `SRR`/`ERR` run ids are provided then these will be resolved back to their appropriate `SRX`/`ERX` ids to be able to merge multiple runs from the same experiment. This is conceptually the same as merging multiple libraries sequenced from the same sample.
+| `SRA`        | `ENA`        | `DDBJ`       | `GEO`      |
+|--------------|--------------|--------------|------------|
+| SRR11605097  | ERR4007730   | DRR171822    | GSM4432381 |
+| SRX8171613   | ERX4009132   | DRX162434    | GSE147507  |
+| SRS6531847   | ERS4399630   | DRS090921    |            |
+| SAMN14689442 | SAMEA6638373 | SAMD00114846 |            |
+| SRP256957    | ERP120836    | DRP004793    |            |
+| SRA1068758   | ERA2420837   | DRA008156    |            |
+| PRJNA625551  | PRJEB37513   | PRJDB4176    |            |
+
+If `SRR`/`ERR`/`DRR` run ids are provided then these will be resolved back to their appropriate `SRX`/`ERX`/`DRX` ids to be able to merge multiple runs from the same experiment. This is conceptually the same as merging multiple libraries sequenced from the same sample.
 
 The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5 sums. If download links exist, the files will be downloaded in parallel by FTP otherwise they will NOT be downloaded. This is intentional because tools such as `parallel-fastq-dump`, `fasterq-dump`, `prefetch` etc require pre-existing configuration files in the users home directory which makes automation tricky across different platforms and containerisation. We may add this functionality in later releases.
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index a391f35d..03612ed2 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -21,7 +21,7 @@
                     "pattern": "^\\S+\\.txt$",
                     "schema": "assets/schema_input.json",
                     "fa_icon": "fas fa-file-excel",
-                    "description": "File containing SRA/ENA/GEO identifiers one per line to download their associated metadata and FastQ files."
+                    "description": "File containing SRA/ENA/DDBJ/GEO identifiers one per line to download their associated metadata and FastQ files."
                 },
                 "ena_metadata_fields": {
                     "type": "string",

From 284f3be60be5bad8df9d1b989e05e84409562249 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 28 Sep 2021 22:35:34 +0100
Subject: [PATCH 054/852] Fix funny pipe

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e6dcc246..94968c8c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 * Added support for [DDBJ ids](https://www.ddbj.nig.ac.jp/index-e.html). See examples below:
 
-! `DDBJ`        |
+| `DDBJ`        |
 |---------------|
 | PRJDB4176     |
 | SAMD00114846  |

From 7cb6af67567d971ca6b25eb082b10ab43e6f9c49 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Mon, 27 Sep 2021 21:53:26 +0200
Subject: [PATCH 055/852] refactor: simplify decoding method

---
 bin/sra_ids_to_runinfo.py | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index 6de6fc28..714a0196 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -104,11 +104,9 @@ def body(self):
 
     def text(self, encoding=None):
         """Return the response's body as a decoded string."""
-        if encoding is not None:
-            return self.body.decode(encoding)
-
-        _, params = cgi.parse_header(self._response.getheader("Content-Type", ""))
-        encoding = params.get("charset", "utf-8")
+        if encoding is None:
+            _, params = cgi.parse_header(self._response.getheader("Content-Type", ""))
+            encoding = params.get("charset", "utf-8")
         return self.body.decode(encoding)
 
 

From d56a9ee76261edf692d71e21d59ac56a9c2e9216 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Mon, 27 Sep 2021 21:59:34 +0200
Subject: [PATCH 056/852] refactor: simplify makedirs

---
 bin/sra_ids_to_runinfo.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index 714a0196..75b944ac 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -134,11 +134,7 @@ def validate_csv_param(param, valid_vals, param_desc):
 
 def make_dir(path):
     if not len(path) == 0:
-        try:
-            os.makedirs(path)
-        except OSError as exception:
-            if exception.errno != errno.EEXIST:
-                raise
+        os.makedirs(path, exist_ok=True)
 
 def fetch_url(url):
     try:

From 608908d50af70859cb8a84b6787f35eaf7859c72 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Sat, 2 Oct 2021 15:19:38 +0200
Subject: [PATCH 057/852] refactor: check valid prefix in set

---
 bin/sra_ids_to_runinfo.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index 75b944ac..c46abaf9 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -22,7 +22,8 @@
 DDBJ_IDS = ('PRJDB4176', 'SAMD00114846', 'DRA008156', 'DRP004793', 'DRR171822', 'DRS090921', 'DRX162434')
 GEO_IDS = ('GSE18729', 'GSM465244')
 ID_REGEX = re.compile(r'[A-Z]+')
-PREFIX_LIST = sorted({ID_REGEX.match(x).group() for x in SRA_IDS + ENA_IDS + DDBJ_IDS + GEO_IDS})
+PREFIX_LIST = sorted({ID_REGEX.match(id).group() for id in SRA_IDS + ENA_IDS + DDBJ_IDS + GEO_IDS})
+VALID_PREFIX = frozenset(PREFIX_LIST)
 
 
 ## List of meta fields fetched from the ENA API - can be overriden by --ena_metadata_fields
@@ -215,7 +216,7 @@ def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields=ENA_METADATA_FIELDS
             match = ID_REGEX.match(db_id)
             if match:
                 prefix = match.group()
-                if prefix in PREFIX_LIST:
+                if prefix in VALID_PREFIX:
                     if db_id not in seen_ids:
 
                         ids = [db_id]

From 93a2dbcc8ff9e2b940a00cb99e485fcb327410d9 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Sat, 2 Oct 2021 22:10:04 +0200
Subject: [PATCH 058/852] refactor: handle missing content

Refactor **all** the code :/
---
 bin/sra_ids_to_runinfo.py | 297 +++++++++++++++++++++++++-------------
 1 file changed, 195 insertions(+), 102 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index c46abaf9..eb4f2ac6 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -3,7 +3,6 @@
 import argparse
 import cgi
 import csv
-import errno
 import gzip
 import logging
 import os
@@ -21,9 +20,8 @@
 ENA_IDS = ('PRJEB7743', 'SAMEA3121481', 'ERA2421642', 'ERP120836', 'ERR674736', 'ERS4399631', 'ERX629702')
 DDBJ_IDS = ('PRJDB4176', 'SAMD00114846', 'DRA008156', 'DRP004793', 'DRR171822', 'DRS090921', 'DRX162434')
 GEO_IDS = ('GSE18729', 'GSM465244')
-ID_REGEX = re.compile(r'[A-Z]+')
-PREFIX_LIST = sorted({ID_REGEX.match(id).group() for id in SRA_IDS + ENA_IDS + DDBJ_IDS + GEO_IDS})
-VALID_PREFIX = frozenset(PREFIX_LIST)
+ID_REGEX = re.compile(r'^([A-Z]+)([0-9]+)$')
+PREFIX_LIST = sorted({ID_REGEX.match(id).group(1) for id in SRA_IDS + ENA_IDS + DDBJ_IDS + GEO_IDS})
 
 
 ## List of meta fields fetched from the ENA API - can be overriden by --ena_metadata_fields
@@ -111,6 +109,178 @@ def text(self, encoding=None):
         return self.body.decode(encoding)
 
 
+class DatabaseIdentifierChecker:
+    """Define a service class for validating database identifiers."""
+
+    _VALID_PREFIX = frozenset(PREFIX_LIST)
+
+    @classmethod
+    def is_valid(cls, identifier):
+        """
+        Check the validity of the given database identifier.
+
+        Args:
+            identifier (str): A short identifier presumably belonging to one of the
+                supported databases.
+
+        Returns:
+            bool: Whether or not the identifier is valid.
+
+        """
+        match = ID_REGEX.match(identifier)
+        if match is None:
+            return False
+        return match.group(1) in cls._VALID_PREFIX
+
+
+class DatabaseResolver:
+    """Define a service class for resolving various identifiers to experiments."""
+
+    _GEO_PREFIXES = {'GSE'}
+    _SRA_PREFIXES = {'GSM', 'PRJNA', 'SAMN', 'SRR', 'DRA', 'DRP', 'DRR', 'DRS', 'DRX', 'PRJDB', 'SAMD'}
+    _ENA_PREFIXES = {'ERR'}
+
+    @classmethod
+    def expand_identifier(cls, identifier):
+        """
+        Expand the given identifier to potentially multiple experiment identifiers.
+
+        Args:
+            identifier (str): A short identifier presumably belonging to one of the
+                supported databases.
+
+        Returns:
+            list: A list of one or more SRA/ENA experiment identifiers.
+
+        """
+        prefix = ID_REGEX.match(identifier).group(1)
+        if prefix in cls._GEO_PREFIXES:
+            return cls._gse_to_srx(identifier)
+        elif prefix in cls._SRA_PREFIXES:
+            return cls._id_to_srx(identifier)
+        elif prefix in cls._ENA_PREFIXES:
+            return cls._id_to_erx(identifier)
+        else:
+            return [identifier]
+
+    @classmethod
+    def _content_check(cls, response, identifier):
+        """Check that the response has content or terminate."""
+        if response.status == 204:
+            logger.error(f"There is no content for id {identifier}. Maybe you lack the right permissions?")
+            sys.exit(1)
+
+    @classmethod
+    def _id_to_srx(cls, identifier):
+        """Resolve the identifier to SRA experiments."""
+        params = {
+            "save": "efetch",
+            "db": "sra",
+            "rettype": "runinfo",
+            "term": identifier
+        }
+        response = fetch_url(
+            f'https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?{urlencode(params)}'
+        )
+        cls._content_check(response, identifier)
+        return [
+            row['Experiment'] for row in open_table(response, delimiter=',')
+        ]
+
+    @classmethod
+    def _gse_to_srx(cls, identifier):
+        """Resolve the identifier to SRA experiments."""
+        ids = []
+        params = {
+            "acc": identifier,
+            "targ": "gsm",
+            "view": "data",
+            "form": "text"
+        }
+        response = fetch_url(f'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?{urlencode(params)}')
+        cls._content_check(response, identifier)
+        gsm_ids = [line.split('=')[1].strip() for line in response.text().splitlines() if line.startswith('GSM')]
+        for gsm_id in gsm_ids:
+            ids += cls._id_to_srx(gsm_id)
+        return ids
+
+    @classmethod
+    def _id_to_erx(cls, identifier):
+        """Resolve the identifier to ENA experiments."""
+        fields = ['run_accession', 'experiment_accession']
+        params = {
+            "accession": identifier,
+            "result": "read_run",
+            "fields": ",".join(fields)
+        }
+        response = fetch_url(f'https://www.ebi.ac.uk/ena/portal/api/filereport?{urlencode(params)}')
+        cls._content_check(response, identifier)
+        return [
+            row['experiment_accession'] for row in open_table(response, delimiter='\t')
+        ]
+
+
+class ENAMetadataFetcher:
+    """Define a service class for fetching metadata from ENA."""
+
+    def __init__(self, ena_metadata_fields, **kwargs):
+        """
+        Initialize the service with the desired metadata fields.
+
+        Args:
+            ena_metadata_fields (iterable): An iterable of the desired fields.
+            **kwargs: Passed to parent constructor.
+        """
+        super().__init__(**kwargs)
+        self._params = {
+            "result": "read_run",
+            "fields": ','.join(ena_metadata_fields)
+        }
+
+    def open_experiment_table(self, accession):
+        """
+        Open the metadata table belonging to the given experiment accession.
+
+        Args:
+            accession (str): An ENA experiment accession.
+
+        Returns:
+            csv.DictReader: A CSV reader instance of the metadata.
+
+        """
+        params = {
+            **self._params,
+            "accession": accession
+        }
+        response = fetch_url(
+            f'https://www.ebi.ac.uk/ena/portal/api/filereport?{urlencode(params)}'
+        )
+        self._content_check(response, accession)
+        return open_table(response, delimiter='\t')
+
+    @classmethod
+    def _content_check(cls, response, identifier):
+        """Check that the response has content or terminate."""
+        if response.status == 204:
+            logger.error(f"There is no content for id {identifier}. Maybe you lack the right permissions?")
+            sys.exit(1)
+
+
+def open_table(response, delimiter=","):
+    """
+    Return a CSV reader instance from the given response.
+
+    Args:
+        response (Response): An instance of the local HTTP response class.
+        delimiter (str): The delimiter separating the table fields.
+
+    Returns:
+            csv.DictReader: A CSV reader instance of the response body.
+
+    """
+    return csv.DictReader(response.text().splitlines(), delimiter=delimiter)
+
+
 def parse_args(args=None):
     Description = 'Download and create a run information metadata file from SRA / ENA / DDBJ / GEO identifiers.'
     Epilog = 'Example usage: python fetch_sra_runinfo.py <FILE_IN> <FILE_OUT>'
@@ -138,9 +308,10 @@ def make_dir(path):
         os.makedirs(path, exist_ok=True)
 
 def fetch_url(url):
+    """Return a response object for the given URL and handle errors appropriately."""
     try:
         with urlopen(url) as response:
-            result = Response(response=response).text().splitlines()
+            return Response(response=response)
     except HTTPError as e:
         logger.error("The server couldn't fulfill the request.")
         logger.error(f"Status: {e.code} {e.reason}")
@@ -149,45 +320,6 @@ def fetch_url(url):
         logger.error('We failed to reach a server.')
         logger.error(f"Reason: {e.reason}")
         sys.exit(1)
-    return result
-
-def id_to_srx(db_id):
-    params = {
-        "save": "efetch",
-        "db": "sra",
-        "rettype": "runinfo",
-        "term": db_id
-    }
-    url = f'https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?{urlencode(params)}'
-    return [
-        row['Experiment'] for row in csv.DictReader(fetch_url(url), delimiter=',')
-    ]
-
-def id_to_erx(db_id):
-    fields = ['run_accession', 'experiment_accession']
-    params = {
-        "accession": db_id,
-        "result": "read_run",
-        "fields": ",".join(fields)
-    }
-    url = f'https://www.ebi.ac.uk/ena/portal/api/filereport?{urlencode(params)}'
-    return [
-        row['experiment_accession'] for row in csv.DictReader(fetch_url(url), delimiter='\t')
-    ]
-
-def gse_to_srx(db_id):
-    ids = []
-    params = {
-        "acc": db_id,
-        "targ": "gsm",
-        "view": "data",
-        "form": "text"
-    }
-    url = f'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?{urlencode(params)}'
-    gsm_ids = [x.split('=')[1].strip() for x in fetch_url(url) if x.startswith('GSM')]
-    for gsm_id in gsm_ids:
-        ids += id_to_srx(gsm_id)
-    return ids
 
 def get_ena_fields():
     params = {
@@ -195,77 +327,38 @@ def get_ena_fields():
         "format": "tsv",
         "result": "read_run"
     }
-    url = f'https://www.ebi.ac.uk/ena/portal/api/returnFields?{urlencode(params)}'
     return [
-        row['columnId'] for row in csv.DictReader(fetch_url(url), delimiter='\t')
+        row['columnId'] for row in open_table(fetch_url(f'https://www.ebi.ac.uk/ena/portal/api/returnFields?{urlencode(params)}'), delimiter='\t')
     ]
 
+
 def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields=ENA_METADATA_FIELDS):
-    total_out = 0
     seen_ids = set()
     run_ids = set()
-    header = []
     make_dir(os.path.dirname(file_out))
-    params = {
-        "result": "read_run",
-        "fields": ','.join(ena_metadata_fields)
-    }
+    ena_fetcher = ENAMetadataFetcher(ena_metadata_fields)
     with open(file_in,"r") as fin, open(file_out,"w") as fout:
+        writer = csv.DictWriter(fout, fieldnames=ena_metadata_fields, delimiter='\t')
+        writer.writeheader()
         for line in fin:
             db_id = line.strip()
-            match = ID_REGEX.match(db_id)
-            if match:
-                prefix = match.group()
-                if prefix in VALID_PREFIX:
-                    if db_id not in seen_ids:
-
-                        ids = [db_id]
-                        ## Resolve/expand these ids against GEO URL
-                        if prefix in ['GSE']:
-                            ids = gse_to_srx(db_id)
-
-                        ## Resolve/expand these ids against SRA URL
-                        elif prefix in ['GSM', 'PRJNA', 'SAMN', 'SRR', 'DRA', 'DRP', 'DRR', 'DRS', 'DRX', 'PRJDB', 'SAMD']:
-                            ids = id_to_srx(db_id)
-
-                        ## Resolve/expand these ids against ENA URL
-                        elif prefix in ['ERR']:
-                            ids = id_to_erx(db_id)
-
-                        ## Resolve/expand to get run identifier from ENA and write to file
-                        for id in ids:
-                            params["accession"] = id
-                            url = f'https://www.ebi.ac.uk/ena/portal/api/filereport?{urlencode(params)}'
-                            for row in csv.DictReader(fetch_url(url), delimiter='\t'):
-                                run_id = row['run_accession']
-                                if run_id not in run_ids:
-                                    if total_out == 0:
-                                        header = row.keys()
-                                        header_line = '\t'.join(header)
-                                        fout.write(f"{header_line}\n")
-                                    else:
-                                        if header != row.keys():
-                                            logger.error(f"Metadata columns do not match for id {run_id}!\nLine: '{line.strip()}'")
-                                            sys.exit(1)
-
-                                    ordered_row = '\t'.join([row[x] for x in header])
-                                    fout.write(f'{ordered_row}\n')
-                                    total_out += 1
-                                    run_ids.add(run_id)
-                        seen_ids.add(db_id)
-
-                        if not ids:
-                            logger.error(f"No matches found for database id {db_id}!\nLine: '{line.strip()}'")
-                            sys.exit(1)
-
-                else:
-                    id_str = ', '.join([x + "*" for x in PREFIX_LIST])
-                    logger.error(f"Please provide a valid database id starting with {id_str}!\nLine: '{line.strip()}'")
-                    sys.exit(1)
-            else:
+            if db_id in seen_ids:
+                continue
+            seen_ids.add(db_id)
+            if not DatabaseIdentifierChecker.is_valid(db_id):
                 id_str = ', '.join([x + "*" for x in PREFIX_LIST])
                 logger.error(f"Please provide a valid database id starting with {id_str}!\nLine: '{line.strip()}'")
                 sys.exit(1)
+            ids = DatabaseResolver.expand_identifier(db_id)
+            if not ids:
+                logger.error(f"No matches found for database id {db_id}!\nLine: '{line.strip()}'")
+                sys.exit(1)
+            for accession in ids:
+                for row in ena_fetcher.open_experiment_table(accession):
+                    run_accession = row['run_accession']
+                    if run_accession not in run_ids:
+                        writer.writerow(row)
+                        run_ids.add(run_accession)
 
 def main(args=None):
     args = parse_args(args)

From dba08dcb3fee792a79ed049a939df4d08a7268d6 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Sat, 2 Oct 2021 22:18:48 +0200
Subject: [PATCH 059/852] style: apply black

---
 bin/sra_ids_to_runinfo.py | 259 ++++++++++++++++++++++++++------------
 1 file changed, 180 insertions(+), 79 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index eb4f2ac6..5b1b1866 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 
+
 import argparse
 import cgi
 import csv
@@ -9,33 +10,88 @@
 import re
 import sys
 import zlib
-from urllib.error import URLError, HTTPError
+from urllib.error import HTTPError, URLError
 from urllib.parse import urlencode
 from urllib.request import urlopen
 
+
 logger = logging.getLogger()
 
-## Example ids supported by this script
-SRA_IDS = ('PRJNA63463', 'SAMN00765663', 'SRA023522', 'SRP003255', 'SRR390278', 'SRS282569', 'SRX111814')
-ENA_IDS = ('PRJEB7743', 'SAMEA3121481', 'ERA2421642', 'ERP120836', 'ERR674736', 'ERS4399631', 'ERX629702')
-DDBJ_IDS = ('PRJDB4176', 'SAMD00114846', 'DRA008156', 'DRP004793', 'DRR171822', 'DRS090921', 'DRX162434')
-GEO_IDS = ('GSE18729', 'GSM465244')
-ID_REGEX = re.compile(r'^([A-Z]+)([0-9]+)$')
-PREFIX_LIST = sorted({ID_REGEX.match(id).group(1) for id in SRA_IDS + ENA_IDS + DDBJ_IDS + GEO_IDS})
+
+# Example ids supported by this script
+SRA_IDS = (
+    "PRJNA63463",
+    "SAMN00765663",
+    "SRA023522",
+    "SRP003255",
+    "SRR390278",
+    "SRS282569",
+    "SRX111814",
+)
+ENA_IDS = (
+    "PRJEB7743",
+    "SAMEA3121481",
+    "ERA2421642",
+    "ERP120836",
+    "ERR674736",
+    "ERS4399631",
+    "ERX629702",
+)
+DDBJ_IDS = (
+    "PRJDB4176",
+    "SAMD00114846",
+    "DRA008156",
+    "DRP004793",
+    "DRR171822",
+    "DRS090921",
+    "DRX162434",
+)
+GEO_IDS = ("GSE18729", "GSM465244")
+ID_REGEX = re.compile(r"^([A-Z]+)([0-9]+)$")
+PREFIX_LIST = sorted(
+    {ID_REGEX.match(id).group(1) for id in SRA_IDS + ENA_IDS + DDBJ_IDS + GEO_IDS}
+)
 
 
-## List of meta fields fetched from the ENA API - can be overriden by --ena_metadata_fields
-## Full list of accepted fields can be obtained here: https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run
+# List of metadata fields fetched from the ENA API - can be overriden by options
+# `-ef` or `--ena_metadata_fields`.
+# Full list of accepted fields can be obtained here:
+# https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run
 ENA_METADATA_FIELDS = (
-    'accession', 'run_accession', 'experiment_accession', 'sample_accession', 'secondary_sample_accession', 'study_accession', 'secondary_study_accession', 'parent_study', 'submission_accession',
-    'run_alias', 'experiment_alias', 'sample_alias', 'study_alias',
-    'library_layout', 'library_selection', 'library_source', 'library_strategy', 'library_name',
-    'instrument_model', 'instrument_platform',
-    'base_count', 'read_count',
-    'tax_id', 'scientific_name',
-    'sample_title', 'experiment_title', 'study_title',
-    'description', 'sample_description',
-    'fastq_md5', 'fastq_bytes', 'fastq_ftp', 'fastq_galaxy', 'fastq_aspera'
+    "accession",
+    "run_accession",
+    "experiment_accession",
+    "sample_accession",
+    "secondary_sample_accession",
+    "study_accession",
+    "secondary_study_accession",
+    "parent_study",
+    "submission_accession",
+    "run_alias",
+    "experiment_alias",
+    "sample_alias",
+    "study_alias",
+    "library_layout",
+    "library_selection",
+    "library_source",
+    "library_strategy",
+    "library_name",
+    "instrument_model",
+    "instrument_platform",
+    "base_count",
+    "read_count",
+    "tax_id",
+    "scientific_name",
+    "sample_title",
+    "experiment_title",
+    "study_title",
+    "description",
+    "sample_description",
+    "fastq_md5",
+    "fastq_bytes",
+    "fastq_ftp",
+    "fastq_galaxy",
+    "fastq_aspera",
 )
 
 
@@ -112,7 +168,7 @@ def text(self, encoding=None):
 class DatabaseIdentifierChecker:
     """Define a service class for validating database identifiers."""
 
-    _VALID_PREFIX = frozenset(PREFIX_LIST)
+    _VALID_PREFIXES = frozenset(PREFIX_LIST)
 
     @classmethod
     def is_valid(cls, identifier):
@@ -130,15 +186,27 @@ def is_valid(cls, identifier):
         match = ID_REGEX.match(identifier)
         if match is None:
             return False
-        return match.group(1) in cls._VALID_PREFIX
+        return match.group(1) in cls._VALID_PREFIXES
 
 
 class DatabaseResolver:
     """Define a service class for resolving various identifiers to experiments."""
 
-    _GEO_PREFIXES = {'GSE'}
-    _SRA_PREFIXES = {'GSM', 'PRJNA', 'SAMN', 'SRR', 'DRA', 'DRP', 'DRR', 'DRS', 'DRX', 'PRJDB', 'SAMD'}
-    _ENA_PREFIXES = {'ERR'}
+    _GEO_PREFIXES = {"GSE"}
+    _SRA_PREFIXES = {
+        "GSM",
+        "PRJNA",
+        "SAMN",
+        "SRR",
+        "DRA",
+        "DRP",
+        "DRR",
+        "DRS",
+        "DRX",
+        "PRJDB",
+        "SAMD",
+    }
+    _ENA_PREFIXES = {"ERR"}
 
     @classmethod
     def expand_identifier(cls, identifier):
@@ -167,7 +235,10 @@ def expand_identifier(cls, identifier):
     def _content_check(cls, response, identifier):
         """Check that the response has content or terminate."""
         if response.status == 204:
-            logger.error(f"There is no content for id {identifier}. Maybe you lack the right permissions?")
+            logger.error(
+                f"There is no content for id {identifier}. Maybe you lack the right "
+                f"permissions?"
+            )
             sys.exit(1)
 
     @classmethod
@@ -177,29 +248,28 @@ def _id_to_srx(cls, identifier):
             "save": "efetch",
             "db": "sra",
             "rettype": "runinfo",
-            "term": identifier
+            "term": identifier,
         }
         response = fetch_url(
-            f'https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?{urlencode(params)}'
+            f"https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?{urlencode(params)}"
         )
         cls._content_check(response, identifier)
-        return [
-            row['Experiment'] for row in open_table(response, delimiter=',')
-        ]
+        return [row["Experiment"] for row in open_table(response, delimiter=",")]
 
     @classmethod
     def _gse_to_srx(cls, identifier):
         """Resolve the identifier to SRA experiments."""
         ids = []
-        params = {
-            "acc": identifier,
-            "targ": "gsm",
-            "view": "data",
-            "form": "text"
-        }
-        response = fetch_url(f'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?{urlencode(params)}')
+        params = {"acc": identifier, "targ": "gsm", "view": "data", "form": "text"}
+        response = fetch_url(
+            f"https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?{urlencode(params)}"
+        )
         cls._content_check(response, identifier)
-        gsm_ids = [line.split('=')[1].strip() for line in response.text().splitlines() if line.startswith('GSM')]
+        gsm_ids = [
+            line.split("=")[1].strip()
+            for line in response.text().splitlines()
+            if line.startswith("GSM")
+        ]
         for gsm_id in gsm_ids:
             ids += cls._id_to_srx(gsm_id)
         return ids
@@ -207,16 +277,18 @@ def _gse_to_srx(cls, identifier):
     @classmethod
     def _id_to_erx(cls, identifier):
         """Resolve the identifier to ENA experiments."""
-        fields = ['run_accession', 'experiment_accession']
+        fields = ["run_accession", "experiment_accession"]
         params = {
             "accession": identifier,
             "result": "read_run",
-            "fields": ",".join(fields)
+            "fields": ",".join(fields),
         }
-        response = fetch_url(f'https://www.ebi.ac.uk/ena/portal/api/filereport?{urlencode(params)}')
+        response = fetch_url(
+            f"https://www.ebi.ac.uk/ena/portal/api/filereport?{urlencode(params)}"
+        )
         cls._content_check(response, identifier)
         return [
-            row['experiment_accession'] for row in open_table(response, delimiter='\t')
+            row["experiment_accession"] for row in open_table(response, delimiter="\t")
         ]
 
 
@@ -232,10 +304,7 @@ def __init__(self, ena_metadata_fields, **kwargs):
             **kwargs: Passed to parent constructor.
         """
         super().__init__(**kwargs)
-        self._params = {
-            "result": "read_run",
-            "fields": ','.join(ena_metadata_fields)
-        }
+        self._params = {"result": "read_run", "fields": ",".join(ena_metadata_fields)}
 
     def open_experiment_table(self, accession):
         """
@@ -248,21 +317,21 @@ def open_experiment_table(self, accession):
             csv.DictReader: A CSV reader instance of the metadata.
 
         """
-        params = {
-            **self._params,
-            "accession": accession
-        }
+        params = {**self._params, "accession": accession}
         response = fetch_url(
-            f'https://www.ebi.ac.uk/ena/portal/api/filereport?{urlencode(params)}'
+            f"https://www.ebi.ac.uk/ena/portal/api/filereport?{urlencode(params)}"
         )
         self._content_check(response, accession)
-        return open_table(response, delimiter='\t')
+        return open_table(response, delimiter="\t")
 
     @classmethod
     def _content_check(cls, response, identifier):
         """Check that the response has content or terminate."""
         if response.status == 204:
-            logger.error(f"There is no content for id {identifier}. Maybe you lack the right permissions?")
+            logger.error(
+                f"There is no content for id {identifier}. Maybe you lack the right "
+                f"permissions?"
+            )
             sys.exit(1)
 
 
@@ -282,31 +351,49 @@ def open_table(response, delimiter=","):
 
 
 def parse_args(args=None):
-    Description = 'Download and create a run information metadata file from SRA / ENA / DDBJ / GEO identifiers.'
-    Epilog = 'Example usage: python fetch_sra_runinfo.py <FILE_IN> <FILE_OUT>'
-
-    parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
-    parser.add_argument('FILE_IN', help="File containing database identifiers, one per line.")
-    parser.add_argument('FILE_OUT', help="Output file in tab-delimited format.")
-    parser.add_argument('-ef', '--ena_metadata_fields', type=str, dest="ENA_METADATA_FIELDS", default='', help=f"Comma-separated list of ENA metadata fields to fetch. (default: {','.join(ENA_METADATA_FIELDS)}).")
+    parser = argparse.ArgumentParser(
+        description="Download and create a run information metadata file from SRA / "
+        "ENA / DDBJ / GEO identifiers.",
+        epilog="Example usage: python fetch_sra_runinfo.py <FILE_IN> <FILE_OUT>",
+    )
+    parser.add_argument(
+        "FILE_IN", help="File containing database identifiers, one per line."
+    )
+    parser.add_argument("FILE_OUT", help="Output file in tab-delimited format.")
+    parser.add_argument(
+        "-ef",
+        "--ena_metadata_fields",
+        type=str,
+        dest="ENA_METADATA_FIELDS",
+        default="",
+        help=f"Comma-separated list of ENA metadata fields to fetch. "
+        f"(default: {','.join(ENA_METADATA_FIELDS)}).",
+    )
     return parser.parse_args(args)
 
+
 def validate_csv_param(param, valid_vals, param_desc):
     valid_list = []
     if param:
-        user_vals = param.split(',')
+        user_vals = param.split(",")
         intersect = [i for i in user_vals if i in valid_vals]
         if len(intersect) == len(user_vals):
             valid_list = intersect
         else:
-            logger.error(f"Please provide a valid value for {param_desc}!\nProvided values = {param}\nAccepted values = {','.join(valid_vals)}")
+            logger.error(
+                f"Please provide a valid value for {param_desc}!\n"
+                f"Provided values = {param}\n"
+                f"Accepted values = {','.join(valid_vals)}"
+            )
             sys.exit(1)
     return valid_list
 
+
 def make_dir(path):
     if not len(path) == 0:
         os.makedirs(path, exist_ok=True)
 
+
 def fetch_url(url):
     """Return a response object for the given URL and handle errors appropriately."""
     try:
@@ -317,18 +404,21 @@ def fetch_url(url):
         logger.error(f"Status: {e.code} {e.reason}")
         sys.exit(1)
     except URLError as e:
-        logger.error('We failed to reach a server.')
+        logger.error("We failed to reach a server.")
         logger.error(f"Reason: {e.reason}")
         sys.exit(1)
 
+
 def get_ena_fields():
-    params = {
-        "dataPortal": "ena",
-        "format": "tsv",
-        "result": "read_run"
-    }
+    params = {"dataPortal": "ena", "format": "tsv", "result": "read_run"}
     return [
-        row['columnId'] for row in open_table(fetch_url(f'https://www.ebi.ac.uk/ena/portal/api/returnFields?{urlencode(params)}'), delimiter='\t')
+        row["columnId"]
+        for row in open_table(
+            fetch_url(
+                f"https://www.ebi.ac.uk/ena/portal/api/returnFields?{urlencode(params)}"
+            ),
+            delimiter="\t",
+        )
     ]
 
 
@@ -337,8 +427,8 @@ def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields=ENA_METADATA_FIELDS
     run_ids = set()
     make_dir(os.path.dirname(file_out))
     ena_fetcher = ENAMetadataFetcher(ena_metadata_fields)
-    with open(file_in,"r") as fin, open(file_out,"w") as fout:
-        writer = csv.DictWriter(fout, fieldnames=ena_metadata_fields, delimiter='\t')
+    with open(file_in, "r") as fin, open(file_out, "w") as fout:
+        writer = csv.DictWriter(fout, fieldnames=ena_metadata_fields, delimiter="\t")
         writer.writeheader()
         for line in fin:
             db_id = line.strip()
@@ -346,28 +436,39 @@ def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields=ENA_METADATA_FIELDS
                 continue
             seen_ids.add(db_id)
             if not DatabaseIdentifierChecker.is_valid(db_id):
-                id_str = ', '.join([x + "*" for x in PREFIX_LIST])
-                logger.error(f"Please provide a valid database id starting with {id_str}!\nLine: '{line.strip()}'")
+                id_str = ", ".join([x + "*" for x in PREFIX_LIST])
+                logger.error(
+                    f"Please provide a valid database id starting with {id_str}!\n"
+                    f"Line: '{line.strip()}'"
+                )
                 sys.exit(1)
             ids = DatabaseResolver.expand_identifier(db_id)
             if not ids:
-                logger.error(f"No matches found for database id {db_id}!\nLine: '{line.strip()}'")
+                logger.error(
+                    f"No matches found for database id {db_id}!\nLine: '{line.strip()}'"
+                )
                 sys.exit(1)
             for accession in ids:
                 for row in ena_fetcher.open_experiment_table(accession):
-                    run_accession = row['run_accession']
+                    run_accession = row["run_accession"]
                     if run_accession not in run_ids:
                         writer.writerow(row)
                         run_ids.add(run_accession)
 
+
 def main(args=None):
     args = parse_args(args)
     ena_metadata_fields = args.ENA_METADATA_FIELDS
     if not args.ENA_METADATA_FIELDS:
-        ena_metadata_fields = ','.join(ENA_METADATA_FIELDS)
-    ena_metadata_fields = validate_csv_param(ena_metadata_fields, valid_vals=get_ena_fields(), param_desc='--ena_metadata_fields')
+        ena_metadata_fields = ",".join(ENA_METADATA_FIELDS)
+    ena_metadata_fields = validate_csv_param(
+        ena_metadata_fields,
+        valid_vals=get_ena_fields(),
+        param_desc="--ena_metadata_fields",
+    )
     fetch_sra_runinfo(args.FILE_IN, args.FILE_OUT, ena_metadata_fields)
 
-if __name__ == '__main__':
-    logging.basicConfig(level='INFO', format='[%(levelname)s] %(message)s')
+
+if __name__ == "__main__":
+    logging.basicConfig(level="INFO", format="[%(levelname)s] %(message)s")
     sys.exit(main())

From f3b87a78b6a1e5bcb791f0a4a90d840bef7809dc Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Sat, 2 Oct 2021 22:42:36 +0200
Subject: [PATCH 060/852] refactor: improve arguments parsing

---
 bin/sra_ids_to_runinfo.py | 71 +++++++++++++++++++++++----------------
 1 file changed, 42 insertions(+), 29 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index 5b1b1866..d42081c5 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -10,6 +10,7 @@
 import re
 import sys
 import zlib
+from pathlib import Path
 from urllib.error import HTTPError, URLError
 from urllib.parse import urlencode
 from urllib.request import urlopen
@@ -357,36 +358,48 @@ def parse_args(args=None):
         epilog="Example usage: python fetch_sra_runinfo.py <FILE_IN> <FILE_OUT>",
     )
     parser.add_argument(
-        "FILE_IN", help="File containing database identifiers, one per line."
+        "file_in",
+        metavar="FILE_IN",
+        type=Path,
+        help="File containing database identifiers, one per line.",
+    )
+    parser.add_argument(
+        "file_out",
+        metavar="FILE_OUT",
+        type=Path,
+        help="Output file in tab-delimited format.",
     )
-    parser.add_argument("FILE_OUT", help="Output file in tab-delimited format.")
     parser.add_argument(
         "-ef",
         "--ena_metadata_fields",
         type=str,
-        dest="ENA_METADATA_FIELDS",
-        default="",
-        help=f"Comma-separated list of ENA metadata fields to fetch. "
+        default=",".join(ENA_METADATA_FIELDS),
+        help=f"Comma-separated list of ENA metadata fields to fetch "
         f"(default: {','.join(ENA_METADATA_FIELDS)}).",
     )
+    parser.add_argument(
+        "-l",
+        "--log-level",
+        help="The desired log level (default WARNING).",
+        choices=("CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"),
+        default="WARNING",
+    )
     return parser.parse_args(args)
 
 
-def validate_csv_param(param, valid_vals, param_desc):
-    valid_list = []
-    if param:
-        user_vals = param.split(",")
-        intersect = [i for i in user_vals if i in valid_vals]
-        if len(intersect) == len(user_vals):
-            valid_list = intersect
-        else:
-            logger.error(
-                f"Please provide a valid value for {param_desc}!\n"
-                f"Provided values = {param}\n"
-                f"Accepted values = {','.join(valid_vals)}"
-            )
-            sys.exit(1)
-    return valid_list
+def validate_fields_parameter(param, valid_vals, param_desc):
+    if not param:
+        return []
+    user_vals = param.split(",")
+    if len(set(user_vals) & set(valid_vals)) == len(user_vals):
+        return user_vals
+    else:
+        logger.error(
+            f"Please provide a valid value for {param_desc}!\n"
+            f"Provided values = {param}\n"
+            f"Accepted values = {','.join(valid_vals)}"
+        )
+        sys.exit(1)
 
 
 def make_dir(path):
@@ -422,10 +435,9 @@ def get_ena_fields():
     ]
 
 
-def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields=ENA_METADATA_FIELDS):
+def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields):
     seen_ids = set()
     run_ids = set()
-    make_dir(os.path.dirname(file_out))
     ena_fetcher = ENAMetadataFetcher(ena_metadata_fields)
     with open(file_in, "r") as fin, open(file_out, "w") as fout:
         writer = csv.DictWriter(fout, fieldnames=ena_metadata_fields, delimiter="\t")
@@ -458,17 +470,18 @@ def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields=ENA_METADATA_FIELDS
 
 def main(args=None):
     args = parse_args(args)
-    ena_metadata_fields = args.ENA_METADATA_FIELDS
-    if not args.ENA_METADATA_FIELDS:
-        ena_metadata_fields = ",".join(ENA_METADATA_FIELDS)
-    ena_metadata_fields = validate_csv_param(
-        ena_metadata_fields,
+    logging.basicConfig(level=args.log_level, format="[%(levelname)s] %(message)s")
+    if not args.file_in.is_file():
+        logger.error(f"The given input file {args.file_in} was not found!")
+        sys.exit(1)
+    args.file_out.parent.mkdir(parents=True, exist_ok=True)
+    ena_metadata_fields = validate_fields_parameter(
+        args.ena_metadata_fields,
         valid_vals=get_ena_fields(),
         param_desc="--ena_metadata_fields",
     )
-    fetch_sra_runinfo(args.FILE_IN, args.FILE_OUT, ena_metadata_fields)
+    fetch_sra_runinfo(args.file_in, args.file_out, ena_metadata_fields)
 
 
 if __name__ == "__main__":
-    logging.basicConfig(level="INFO", format="[%(levelname)s] %(message)s")
     sys.exit(main())

From d5560d391512e903c27821e8282378e953fc37e7 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Sat, 2 Oct 2021 22:49:06 +0200
Subject: [PATCH 061/852] docs: make changelog entry

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 94968c8c..0cc2d511 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+* Handle identifiers that do **not** return metadata, for example, due to being private.
+
 * Added support for [DDBJ ids](https://www.ddbj.nig.ac.jp/index-e.html). See examples below:
 
 | `DDBJ`        |

From 5bba41093791ffd716794677a6aeed56d162f1ff Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Sat, 2 Oct 2021 22:56:04 +0200
Subject: [PATCH 062/852] refactor: remove unused function

---
 bin/sra_ids_to_runinfo.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index d42081c5..0f81c125 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -402,11 +402,6 @@ def validate_fields_parameter(param, valid_vals, param_desc):
         sys.exit(1)
 
 
-def make_dir(path):
-    if not len(path) == 0:
-        os.makedirs(path, exist_ok=True)
-
-
 def fetch_url(url):
     """Return a response object for the given URL and handle errors appropriately."""
     try:

From 2ba307b760f94eff442064caad911ab13a937bf2 Mon Sep 17 00:00:00 2001
From: Daisy Wenyan Han <60151111+daisyhan97@users.noreply.github.com>
Date: Tue, 5 Oct 2021 12:45:48 -0700
Subject: [PATCH 063/852] Upload Synapse Modules

---
 modules/local/synapse_get.nf               | 36 +++++++++++++++++++
 modules/local/synapse_list.nf              | 36 +++++++++++++++++++
 modules/local/synapse_merge_samplesheet.nf | 41 ++++++++++++++++++++++
 modules/local/synapse_metadata_mapping.nf  | 36 +++++++++++++++++++
 modules/local/synapse_show.nf              | 36 +++++++++++++++++++
 modules/local/synapse_to_samplesheet.nf    | 39 ++++++++++++++++++++
 6 files changed, 224 insertions(+)
 create mode 100644 modules/local/synapse_get.nf
 create mode 100644 modules/local/synapse_list.nf
 create mode 100644 modules/local/synapse_merge_samplesheet.nf
 create mode 100644 modules/local/synapse_metadata_mapping.nf
 create mode 100644 modules/local/synapse_show.nf
 create mode 100644 modules/local/synapse_to_samplesheet.nf

diff --git a/modules/local/synapse_get.nf b/modules/local/synapse_get.nf
new file mode 100644
index 00000000..bdea8fd0
--- /dev/null
+++ b/modules/local/synapse_get.nf
@@ -0,0 +1,36 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process SYNAPSE_GET {
+    tag '$synid'
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+
+    conda (params.enable_conda ? "bioconda::synapseclient=2.2.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE" // TODO: Add Singularity
+    } else {
+        container "sagebionetworks/synapsepythonclient:v2.4.0"
+    }
+
+    input:
+    val synid                   // synapse ID for individual FastQ files
+    path synapseconfig          // path to synapse.Config file
+
+    output:
+    path "*.fastq*"               , emit: fastq
+    path "*.version.txt"          , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    
+    """
+    synapse -c $synapseconfig get $synid 
+    echo \$(synapse --version) > ${software}.version.txt
+    """
+}
\ No newline at end of file
diff --git a/modules/local/synapse_list.nf b/modules/local/synapse_list.nf
new file mode 100644
index 00000000..2d1cb2f8
--- /dev/null
+++ b/modules/local/synapse_list.nf
@@ -0,0 +1,36 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process SYNAPSE_LIST {
+    tag '$synid'
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+
+    conda (params.enable_conda ? "bioconda::synapseclient=2.2.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE" // TODO: Add Singularity
+    } else {
+        container "sagebionetworks/synapsepythonclient:v2.4.0"
+    }
+
+    input:
+    val synid                   // synapse ID for individual FastQ files
+    path synapseconfig          // path to synapse.Config file
+
+    output:
+    path "*.synlist.csv", emit: synlist_csv
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+
+    """
+    synapse -c $synapseconfig list -l $synid | cut -c-11 > ${synid}.synlist.csv 
+    echo \$(synapse --version) > ${software}.version.txt
+    """
+}
diff --git a/modules/local/synapse_merge_samplesheet.nf b/modules/local/synapse_merge_samplesheet.nf
new file mode 100644
index 00000000..d31d17ef
--- /dev/null
+++ b/modules/local/synapse_merge_samplesheet.nf
@@ -0,0 +1,41 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process SYNAPSE_MERGE_SAMPLESHEET {
+    tag 'merge_samplesheet'
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
+    } else {
+        container "biocontainers/biocontainers:v1.2.0_cv1"
+    }
+
+    input:
+    path ('samplesheets/*')
+    path ('metasheet/*')
+
+    output:
+    path "samplesheet.csv", emit: samplesheet
+    path "metasheet.csv", emit: metasheet
+
+    script:
+    """
+    head -n 1 `ls ./samplesheets/* | head -n 1` > samplesheet.csv
+    for fileid in `ls ./samplesheets/*`; do
+        awk 'NR>1' \$fileid >> samplesheet.csv
+    done
+
+    head -n 1 `ls ./metasheet/* | head -n 1` > metasheet.csv
+    for fileid in `ls ./metasheet/*`; do
+        awk 'NR>1' \$fileid >> metasheet.csv
+    done
+    """
+}
diff --git a/modules/local/synapse_metadata_mapping.nf b/modules/local/synapse_metadata_mapping.nf
new file mode 100644
index 00000000..0981a1d9
--- /dev/null
+++ b/modules/local/synapse_metadata_mapping.nf
@@ -0,0 +1,36 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process SYNAPSEMETADATAMAPPING {
+    tag "${data[3]}"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+
+    input: 
+    val data
+
+    output:
+    path("*metasheet.csv"), emit: metasheet
+
+    exec:
+    meta_map = [
+        md5         : "${data[0]}",
+        fileSize    : "${data[1]}",
+        etag        : "${data[2]}",
+        id          : "${data[3]}",
+        fileName    : "${data[4]}",
+        fileVersion : "${data[5]}"
+    ]
+
+    // Create Metadata Sheet
+    metasheet  = meta_map.keySet().collect{ '"' + it + '"'}.join(",") + '\n'
+    metasheet += meta_map.values().collect{ '"' + it + '"'}.join(",")
+
+    def metasheet_file = task.workDir.resolve("${meta_map.id}.metasheet.csv")
+    metasheet_file.text = metasheet
+}
diff --git a/modules/local/synapse_show.nf b/modules/local/synapse_show.nf
new file mode 100644
index 00000000..50a3405f
--- /dev/null
+++ b/modules/local/synapse_show.nf
@@ -0,0 +1,36 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process SYNAPSE_SHOW {
+    tag '$synid'
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+
+    conda (params.enable_conda ? "bioconda::synapseclient=2.2.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE" // TODO: Add Singularity
+    } else {
+        container "sagebionetworks/synapsepythonclient:v2.4.0"
+    }
+
+    input:
+    val synid                   // synapse ID for individual FastQ files
+    path synapseconfig          // path to synapse.Config file
+
+    output:
+    path "*.metadata.txt", emit: metadata
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+
+    """
+    synapse -c $synapseconfig show $synid | sed -n '1,3p;15,16p;20p;23p' > ${synid}.metadata.txt
+    echo \$(synapse --version) > ${software}.version.txt
+    """
+}
diff --git a/modules/local/synapse_to_samplesheet.nf b/modules/local/synapse_to_samplesheet.nf
new file mode 100644
index 00000000..1e50a080
--- /dev/null
+++ b/modules/local/synapse_to_samplesheet.nf
@@ -0,0 +1,39 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process SYNAPSE_TO_SAMPLESHEET {
+    tag '$id'
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+
+    input:
+    tuple val(id), val(files)
+    val strandedness
+
+    output:
+    path("*samplesheet.csv"), emit: samplesheet
+
+    exec:
+
+    // Add fields to the beginning of the map
+    pipeline_map = [
+        sample  : "${id}",
+        fastq_1 : "${params.outdir}/${params.results_dir}/${files[0].getBaseName()}",
+        fastq_2 : "${params.outdir}/${params.results_dir}/${files[1].getBaseName()}"
+    ]
+    // Add Strandedness
+    pipeline_map << [ strandedness: "${strandedness}" ]
+    
+    // Create Samplesheet
+    samplesheet  = pipeline_map.keySet().collect{ '"' + it + '"'}.join(",") + '\n'
+    samplesheet += pipeline_map.values().collect{ '"' + it + '"'}.join(",")
+
+    def samplesheet_file2 = task.workDir.resolve("${pipeline_map.sample}.samplesheet.csv")
+    samplesheet_file2.text = samplesheet
+
+}

From 9bfaf2ffbed4326e7136941ac16e8712904fe09a Mon Sep 17 00:00:00 2001
From: Daisy Wenyan Han <60151111+daisyhan97@users.noreply.github.com>
Date: Tue, 5 Oct 2021 12:51:43 -0700
Subject: [PATCH 064/852] Upload Synapse Workflow

---
 workflows/synapse.nf | 154 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 154 insertions(+)
 create mode 100644 workflows/synapse.nf

diff --git a/workflows/synapse.nf b/workflows/synapse.nf
new file mode 100644
index 00000000..0bf8109e
--- /dev/null
+++ b/workflows/synapse.nf
@@ -0,0 +1,154 @@
+/*
+========================================================================================
+    VALIDATE INPUTS
+========================================================================================
+*/
+
+def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
+
+// Validate input parameters
+WorkflowFetchngs.initialise(params, log)
+
+// Check mandatory parameters
+if (params.input) {
+    Channel
+        .from(file(params.input, checkIfExists: true))
+        .splitCsv(header:false, sep:'', strip:true)
+        .map { it[0] }
+        .unique()
+        .set { ch_ids }
+} else {
+    exit 1, 'Input file with Synapse IDs not specified!'
+}
+
+/*
+========================================================================================
+    IMPORT LOCAL MODULES/SUBWORKFLOWS
+========================================================================================
+*/
+
+// Don't overwrite global params.modules, create a copy instead and use that within the main script.
+def modules = params.modules.clone()
+
+include { SYNAPSE_LIST               } from '../modules/local/synapse_list'                 addParams( options: modules['synapse_list']             )
+include { SYNAPSE_GET                } from '../modules/local/synapse_get'                  addParams( options: modules['synapse_get']              )
+include { SYNAPSE_SHOW               } from '../modules/local/synapse_show'                 addParams( options: modules['synapse_show']             )
+include { SYNAPSE_TO_SAMPLESHEET     } from '../modules/local/synapse_to_samplesheet'       addParams( options: modules['synapse_to_samplesheet']   )
+include { SYNAPSE_METADATA_MAPPING   } from '../modules/local/synapse_metadata_mapping'     addParams( options: modules['synapse_metadata_mapping'] )
+include { SYNAPSE_MERGE_SAMPLESHEET  } from '../modules/local/synapse_merge_samplesheet'    addParams( options: modules['synapse_merge_samplesheet'])
+include { GET_SOFTWARE_VERSIONS      } from '../modules/local/get_software_versions'        addParams( options: [publish_files : ['tsv':'']]        )
+
+/*
+========================================================================================
+    RUN MAIN WORKFLOW
+========================================================================================
+*/
+
+workflow FETCHNGS_SYNAPSE {
+
+    ch_software_versions = Channel.empty()
+
+    Channel
+        .fromPath(params.synapseconfig)
+        .set { ch_synapseConfig }
+
+    // MODULE: Get individual FastQ SynapseIDs from Directory SynapseID(s)
+    SYNAPSE_LIST (
+        ch_ids,
+        ch_synapseConfig
+    )
+    ch_software_versions = ch_software_versions.mix(SYNAPSE_LIST.out.version.first().ifEmpty(null))
+
+    // CHANNEL: Create channel for FQ SynapseIDs
+    SYNAPSE_LIST
+        .out
+        .synlist_csv
+        .splitCsv(header:false, strip:true).flatten()
+        .set { ch_samples }
+
+    // MODULE: Download FastQ Files by SynapseID
+    SYNAPSE_GET (
+        ch_samples,
+        ch_synapseConfig
+    )
+    ch_software_versions = ch_software_versions.mix(SYNAPSE_GET.out.version.first().ifEmpty(null))
+    
+    // CHANNEL: Create Read Pairs Channel - Creates format [sampleId, [fastq_1, fastq_2]]
+    SYNAPSE_GET
+        .out
+        .fastq
+        .collect().flatten()
+        .toSortedList().flatten()
+        .map { meta ->  
+            def sampleId = meta.name.toString().tokenize('_').get(0)
+            [sampleId, meta]
+        }
+        .groupTuple()
+        .set{ ch_read_pairs }
+
+    // MODULE: Download FQ Metadata by SynapseID
+    SYNAPSE_SHOW (
+        ch_samples,
+        ch_synapseConfig
+    )
+    ch_software_versions = ch_software_versions.mix(SYNAPSE_SHOW.out.version.first().ifEmpty(null))
+
+    // Clean Metadata
+    SYNAPSE_SHOW
+        .out
+        .metadata
+        .splitCsv(strip:true, sep:"=", skip:1)
+        .map { it[1] }
+        .collate( 6 )
+        .set { ch_meta }
+
+    // Compile Metadata
+    SYNAPSE_METADATA_MAPPING (
+        ch_meta
+    )
+    
+    // MODULE: Create Samplesheet
+    SYNAPSE_TO_SAMPLESHEET (
+        ch_read_pairs,
+        params.strandedness
+    )
+
+    // MODULE: Merge Samplesheets
+    SYNAPSE_MERGE_SAMPLESHEET (
+        READ_PAIRS_TO_SAMPLESHEET.out.samplesheet.collect(),
+        METADATA_TO_METAMAP.out.metasheet.collect()
+    )
+
+    // MODULE: Pipeline reporting
+    ch_software_versions
+        .map { it -> if (it) [ it.baseName, it ] }
+        .groupTuple()
+        .map { it[1][0] }
+        .flatten()
+        .collect()
+        .set { ch_software_versions }
+
+    GET_SOFTWARE_VERSIONS (
+        ch_software_versions.map { it }.collect()
+    )
+}
+
+/*
+========================================================================================
+    COMPLETION EMAIL AND SUMMARY
+========================================================================================
+*/
+
+workflow.onComplete {
+    if (params.email || params.email_on_fail) {
+        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)
+    }
+    NfcoreTemplate.summary(workflow, params, log)
+    WorkflowFetchngs.curateSamplesheetWarn(log)
+}
+
+/*
+========================================================================================
+    THE END
+========================================================================================
+*/

From 4c2fc9b3516227216f92dc9765d3af61782afeaf Mon Sep 17 00:00:00 2001
From: Daisy Wenyan Han <60151111+daisyhan97@users.noreply.github.com>
Date: Tue, 5 Oct 2021 12:54:10 -0700
Subject: [PATCH 065/852] Update Synapse Workflow Labels

---
 workflows/synapse.nf | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/workflows/synapse.nf b/workflows/synapse.nf
index 0bf8109e..3fdd367f 100644
--- a/workflows/synapse.nf
+++ b/workflows/synapse.nf
@@ -44,10 +44,11 @@ include { GET_SOFTWARE_VERSIONS      } from '../modules/local/get_software_versi
 ========================================================================================
 */
 
-workflow FETCHNGS_SYNAPSE {
+workflow SYNAPSE {
 
     ch_software_versions = Channel.empty()
 
+    // CHANNEL: Stage Synapse Config File
     Channel
         .fromPath(params.synapseconfig)
         .set { ch_synapseConfig }
@@ -93,7 +94,7 @@ workflow FETCHNGS_SYNAPSE {
     )
     ch_software_versions = ch_software_versions.mix(SYNAPSE_SHOW.out.version.first().ifEmpty(null))
 
-    // Clean Metadata
+    // CHANNEL: Clean Metadata
     SYNAPSE_SHOW
         .out
         .metadata
@@ -102,7 +103,7 @@ workflow FETCHNGS_SYNAPSE {
         .collate( 6 )
         .set { ch_meta }
 
-    // Compile Metadata
+    // MODULE: Compile Metadata
     SYNAPSE_METADATA_MAPPING (
         ch_meta
     )
@@ -128,6 +129,7 @@ workflow FETCHNGS_SYNAPSE {
         .collect()
         .set { ch_software_versions }
 
+    // MODULE: Get Software Versions
     GET_SOFTWARE_VERSIONS (
         ch_software_versions.map { it }.collect()
     )

From 37cad77f4249ed09e0423a0781977fef76d43523 Mon Sep 17 00:00:00 2001
From: Daisy Wenyan Han <60151111+daisyhan97@users.noreply.github.com>
Date: Tue, 5 Oct 2021 14:20:48 -0700
Subject: [PATCH 066/852] Add SynapseID Option to main.nf

---
 conf/modules.config  | 20 ++++++++++++++++++++
 main.nf              | 18 +++++++++++++++---
 nextflow_schema.json | 22 +++++++++++++++++++---
 3 files changed, 54 insertions(+), 6 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 3ae76b68..f3da4f94 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -42,6 +42,26 @@ params {
         'sra_merge_samplesheet' {
             publish_dir     = 'samplesheet'
         }
+        'synapse_list' {
+            publish_dir     = 'synapse'
+        }
+        'synapse_get' {
+            publish_dir     = 'fastq'
+        }
+        'synapse_show' {
+            publish_dir     = 'metadata'
+        }
+        'synapse_metadata_mapping' {
+            publish_dir     = 'metadata'
+            publish_files   = false
+        }
+        'synapse_to_samplesheet' {
+            publish_dir     = 'samplesheet'
+            publish_files   = false
+        }
+        'synapse_merge_samplesheet' {
+            publish_dir     = 'samplesheet'
+        }
         'multiqc_mappings_config' {
             publish_dir     = 'samplesheet'
         }
diff --git a/main.nf b/main.nf
index 475c87a8..7d4735f8 100644
--- a/main.nf
+++ b/main.nf
@@ -25,13 +25,25 @@ WorkflowMain.initialise(workflow, params, log)
 ========================================================================================
 */
 
-include { FETCHNGS } from './workflows/fetchngs'
+if (params.input_type == 'Synapse') {
+    include { SYNAPSE } from './workflows/synapse'
+} else {
+    include { FETCHNGS } from './workflows/fetchngs'
+}
 
 //
-// WORKFLOW: Run main nf-core/fetchngs analysis pipeline
+// WORKFLOW: Run main nf-core/fetchngs analysis pipeline, depending on Identifier Type provided
 //
 workflow NFCORE_FETCHNGS {
-    FETCHNGS ()
+
+    // Workflow for SynapseIDs
+    if (params.input_type == 'Synapse') {
+        SYNAPSE ()
+    } else {
+    // Workflow for SRA/ENA/GEO IDs
+        FETCHNGS ()
+    }
+
 }
 
 /*
diff --git a/nextflow_schema.json b/nextflow_schema.json
index a391f35d..1c0dc196 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -11,7 +11,8 @@
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
             "required": [
-                "input"
+                "input",
+                "synapse_input"
             ],
             "properties": {
                 "input": {
@@ -23,6 +24,17 @@
                     "fa_icon": "fas fa-file-excel",
                     "description": "File containing SRA/ENA/GEO identifiers one per line to download their associated metadata and FastQ files."
                 },
+                "input_type": {
+                    "type": "string",
+                    "description": "Type of Sample Identifiers Provided (SRA/ENA/GE/Synapse)",
+                    "enum": [
+                        "SRA",
+                        "ENA",
+                        "GEO",
+                        "Synapse"
+                    ],
+                    "fa_icon": "fas fa-copy"
+                },
                 "ena_metadata_fields": {
                     "type": "string",
                     "fa_icon": "fas fa-columns",
@@ -111,6 +123,11 @@
                     "description": "Institutional config URL link.",
                     "hidden": true,
                     "fa_icon": "fas fa-users-cog"
+                },
+                "synapse_config": {
+                    "type": "string",
+                    "description": "Path to Synapse configuration file",
+                    "fa_icon": "fas fa-users-cog"
                 }
             }
         },
@@ -249,5 +266,4 @@
             "$ref": "#/definitions/generic_options"
         }
     ]
-}
-
+}
\ No newline at end of file

From 1436b795f7f0fd846ce069e26a608598fa099064 Mon Sep 17 00:00:00 2001
From: Daisy Wenyan Han <60151111+daisyhan97@users.noreply.github.com>
Date: Tue, 5 Oct 2021 14:49:23 -0700
Subject: [PATCH 067/852] Fix Typos

---
 modules/local/synapse_metadata_mapping.nf | 2 +-
 workflows/synapse.nf                      | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/local/synapse_metadata_mapping.nf b/modules/local/synapse_metadata_mapping.nf
index 0981a1d9..5b799326 100644
--- a/modules/local/synapse_metadata_mapping.nf
+++ b/modules/local/synapse_metadata_mapping.nf
@@ -4,7 +4,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
 params.options = [:]
 options        = initOptions(params.options)
 
-process SYNAPSEMETADATAMAPPING {
+process SYNAPSE_METADATA_MAPPING {
     tag "${data[3]}"
     label 'process_low'
     publishDir "${params.outdir}",
diff --git a/workflows/synapse.nf b/workflows/synapse.nf
index 3fdd367f..f5355023 100644
--- a/workflows/synapse.nf
+++ b/workflows/synapse.nf
@@ -116,8 +116,8 @@ workflow SYNAPSE {
 
     // MODULE: Merge Samplesheets
     SYNAPSE_MERGE_SAMPLESHEET (
-        READ_PAIRS_TO_SAMPLESHEET.out.samplesheet.collect(),
-        METADATA_TO_METAMAP.out.metasheet.collect()
+        SYNAPSE_TO_SAMPLESHEET.out.samplesheet.collect(),
+        SYNAPSE_METADATA_MAPPING.out.metasheet.collect()
     )
 
     // MODULE: Pipeline reporting

From ca5752edc3f93a81c8bd6d3002ff11982523b76a Mon Sep 17 00:00:00 2001
From: Daisy Wenyan Han <60151111+daisyhan97@users.noreply.github.com>
Date: Tue, 5 Oct 2021 20:20:17 -0700
Subject: [PATCH 068/852] Remove trailing whitespace

---
 modules/local/synapse_get.nf              | 6 +++---
 modules/local/synapse_list.nf             | 2 +-
 modules/local/synapse_metadata_mapping.nf | 2 +-
 modules/local/synapse_to_samplesheet.nf   | 2 +-
 workflows/synapse.nf                      | 6 +++---
 5 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/modules/local/synapse_get.nf b/modules/local/synapse_get.nf
index bdea8fd0..9b7990a2 100644
--- a/modules/local/synapse_get.nf
+++ b/modules/local/synapse_get.nf
@@ -28,9 +28,9 @@ process SYNAPSE_GET {
 
     script:
     def software = getSoftwareName(task.process)
-    
+
     """
-    synapse -c $synapseconfig get $synid 
+    synapse -c $synapseconfig get $synid
     echo \$(synapse --version) > ${software}.version.txt
     """
-}
\ No newline at end of file
+}
diff --git a/modules/local/synapse_list.nf b/modules/local/synapse_list.nf
index 2d1cb2f8..62a1c16d 100644
--- a/modules/local/synapse_list.nf
+++ b/modules/local/synapse_list.nf
@@ -30,7 +30,7 @@ process SYNAPSE_LIST {
     def software = getSoftwareName(task.process)
 
     """
-    synapse -c $synapseconfig list -l $synid | cut -c-11 > ${synid}.synlist.csv 
+    synapse -c $synapseconfig list -l $synid | cut -c-11 > ${synid}.synlist.csv
     echo \$(synapse --version) > ${software}.version.txt
     """
 }
diff --git a/modules/local/synapse_metadata_mapping.nf b/modules/local/synapse_metadata_mapping.nf
index 5b799326..6d3c87ac 100644
--- a/modules/local/synapse_metadata_mapping.nf
+++ b/modules/local/synapse_metadata_mapping.nf
@@ -11,7 +11,7 @@ process SYNAPSE_METADATA_MAPPING {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    input: 
+    input:
     val data
 
     output:
diff --git a/modules/local/synapse_to_samplesheet.nf b/modules/local/synapse_to_samplesheet.nf
index 1e50a080..374a07ab 100644
--- a/modules/local/synapse_to_samplesheet.nf
+++ b/modules/local/synapse_to_samplesheet.nf
@@ -28,7 +28,7 @@ process SYNAPSE_TO_SAMPLESHEET {
     ]
     // Add Strandedness
     pipeline_map << [ strandedness: "${strandedness}" ]
-    
+
     // Create Samplesheet
     samplesheet  = pipeline_map.keySet().collect{ '"' + it + '"'}.join(",") + '\n'
     samplesheet += pipeline_map.values().collect{ '"' + it + '"'}.join(",")
diff --git a/workflows/synapse.nf b/workflows/synapse.nf
index f5355023..a00ca5ec 100644
--- a/workflows/synapse.nf
+++ b/workflows/synapse.nf
@@ -73,14 +73,14 @@ workflow SYNAPSE {
         ch_synapseConfig
     )
     ch_software_versions = ch_software_versions.mix(SYNAPSE_GET.out.version.first().ifEmpty(null))
-    
+
     // CHANNEL: Create Read Pairs Channel - Creates format [sampleId, [fastq_1, fastq_2]]
     SYNAPSE_GET
         .out
         .fastq
         .collect().flatten()
         .toSortedList().flatten()
-        .map { meta ->  
+        .map { meta -> 
             def sampleId = meta.name.toString().tokenize('_').get(0)
             [sampleId, meta]
         }
@@ -107,7 +107,7 @@ workflow SYNAPSE {
     SYNAPSE_METADATA_MAPPING (
         ch_meta
     )
-    
+
     // MODULE: Create Samplesheet
     SYNAPSE_TO_SAMPLESHEET (
         ch_read_pairs,

From a7c3c822e47d898cb8a4d113966bada31551c164 Mon Sep 17 00:00:00 2001
From: Daisy Wenyan Han <60151111+daisyhan97@users.noreply.github.com>
Date: Wed, 6 Oct 2021 11:55:04 -0700
Subject: [PATCH 069/852] Add input_type param to configs

---
 conf/test.config                        |  1 +
 conf/test_full.config                   |  1 +
 modules/local/synapse_to_samplesheet.nf |  3 +--
 nextflow.config                         |  2 ++
 nextflow_schema.json                    |  9 +++++----
 workflows/synapse.nf                    | 11 +++++++----
 6 files changed, 17 insertions(+), 10 deletions(-)

diff --git a/conf/test.config b/conf/test.config
index ee909409..75a1ce09 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -21,4 +21,5 @@ params {
 
     // Input data
     input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/public_database_ids.txt'
+    input_type = 'SRA'
 }
diff --git a/conf/test_full.config b/conf/test_full.config
index a5aea2dc..4fc58a6b 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -16,4 +16,5 @@ params {
 
     // Input data for full size test
     input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/public_database_ids.txt'
+    input_type = 'SRA'
 }
diff --git a/modules/local/synapse_to_samplesheet.nf b/modules/local/synapse_to_samplesheet.nf
index 374a07ab..e51d46ca 100644
--- a/modules/local/synapse_to_samplesheet.nf
+++ b/modules/local/synapse_to_samplesheet.nf
@@ -13,7 +13,6 @@ process SYNAPSE_TO_SAMPLESHEET {
 
     input:
     tuple val(id), val(files)
-    val strandedness
 
     output:
     path("*samplesheet.csv"), emit: samplesheet
@@ -27,7 +26,7 @@ process SYNAPSE_TO_SAMPLESHEET {
         fastq_2 : "${params.outdir}/${params.results_dir}/${files[1].getBaseName()}"
     ]
     // Add Strandedness
-    pipeline_map << [ strandedness: "${strandedness}" ]
+    pipeline_map << [ strandedness: "unstranded" ]
 
     // Create Samplesheet
     samplesheet  = pipeline_map.keySet().collect{ '"' + it + '"'}.join(",") + '\n'
diff --git a/nextflow.config b/nextflow.config
index 52382140..4bdacfba 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -11,6 +11,7 @@ params {
 
     // Input options
     input                      = null
+    input_type                 = 'SRA'
     nf_core_pipeline           = null
     ena_metadata_fields        = null
     sample_mapping_fields      = 'run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description,description'
@@ -39,6 +40,7 @@ params {
     config_profile_contact     = null
     config_profile_url         = null
     config_profile_name        = null
+    synapse_config             = null
 
     // Max resource options
     // Defaults only, expecting to be overwritten
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 1c0dc196..2f0df31f 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -11,8 +11,7 @@
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
             "required": [
-                "input",
-                "synapse_input"
+                "input"
             ],
             "properties": {
                 "input": {
@@ -33,7 +32,8 @@
                         "GEO",
                         "Synapse"
                     ],
-                    "fa_icon": "fas fa-copy"
+                    "fa_icon": "fas fa-copy",
+                    "default": "SRA"
                 },
                 "ena_metadata_fields": {
                     "type": "string",
@@ -127,7 +127,8 @@
                 "synapse_config": {
                     "type": "string",
                     "description": "Path to Synapse configuration file",
-                    "fa_icon": "fas fa-users-cog"
+                    "fa_icon": "fas fa-users-cog",
+                    "hidden": true
                 }
             }
         },
diff --git a/workflows/synapse.nf b/workflows/synapse.nf
index a00ca5ec..24dcd9dd 100644
--- a/workflows/synapse.nf
+++ b/workflows/synapse.nf
@@ -4,10 +4,14 @@
 ========================================================================================
 */
 
+def valid_params = [
+    ena_metadata_fields : ['run_accession', 'experiment_accession', 'library_layout', 'fastq_ftp', 'fastq_md5']
+]
+
 def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
 
 // Validate input parameters
-WorkflowFetchngs.initialise(params, log)
+WorkflowFetchngs.initialise(params, log, valid_params)
 
 // Check mandatory parameters
 if (params.input) {
@@ -50,7 +54,7 @@ workflow SYNAPSE {
 
     // CHANNEL: Stage Synapse Config File
     Channel
-        .fromPath(params.synapseconfig)
+        .fromPath(params.synapse_config)
         .set { ch_synapseConfig }
 
     // MODULE: Get individual FastQ SynapseIDs from Directory SynapseID(s)
@@ -80,7 +84,7 @@ workflow SYNAPSE {
         .fastq
         .collect().flatten()
         .toSortedList().flatten()
-        .map { meta -> 
+        .map { meta ->
             def sampleId = meta.name.toString().tokenize('_').get(0)
             [sampleId, meta]
         }
@@ -111,7 +115,6 @@ workflow SYNAPSE {
     // MODULE: Create Samplesheet
     SYNAPSE_TO_SAMPLESHEET (
         ch_read_pairs,
-        params.strandedness
     )
 
     // MODULE: Merge Samplesheets

From 2a00191fa8b97b113a7d46feb1befaf69aa80c08 Mon Sep 17 00:00:00 2001
From: Daisy Wenyan Han <60151111+daisyhan97@users.noreply.github.com>
Date: Wed, 6 Oct 2021 14:56:28 -0700
Subject: [PATCH 070/852] Remove SynapseConfig flag

---
 modules/local/synapse_get.nf            | 11 ++++-------
 modules/local/synapse_list.nf           |  2 +-
 modules/local/synapse_show.nf           |  7 ++-----
 modules/local/synapse_to_samplesheet.nf |  6 +++---
 workflows/synapse.nf                    |  6 +-----
 5 files changed, 11 insertions(+), 21 deletions(-)

diff --git a/modules/local/synapse_get.nf b/modules/local/synapse_get.nf
index 9b7990a2..0f083141 100644
--- a/modules/local/synapse_get.nf
+++ b/modules/local/synapse_get.nf
@@ -5,8 +5,8 @@ params.options = [:]
 options        = initOptions(params.options)
 
 process SYNAPSE_GET {
-    tag '$synid'
-    label 'process_high'
+    tag "$synid"
+    label 'process_low'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
@@ -20,17 +20,14 @@ process SYNAPSE_GET {
 
     input:
     val synid                   // synapse ID for individual FastQ files
-    path synapseconfig          // path to synapse.Config file
 
     output:
-    path "*.fastq*"               , emit: fastq
-    path "*.version.txt"          , emit: version
+    path "*"               , emit: fastq
 
     script:
     def software = getSoftwareName(task.process)
 
     """
-    synapse -c $synapseconfig get $synid
-    echo \$(synapse --version) > ${software}.version.txt
+    synapse get $synid
     """
 }
diff --git a/modules/local/synapse_list.nf b/modules/local/synapse_list.nf
index 62a1c16d..5e94f06d 100644
--- a/modules/local/synapse_list.nf
+++ b/modules/local/synapse_list.nf
@@ -5,7 +5,7 @@ params.options = [:]
 options        = initOptions(params.options)
 
 process SYNAPSE_LIST {
-    tag '$synid'
+    tag "$synid"
     label 'process_low'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
diff --git a/modules/local/synapse_show.nf b/modules/local/synapse_show.nf
index 50a3405f..bd93e621 100644
--- a/modules/local/synapse_show.nf
+++ b/modules/local/synapse_show.nf
@@ -5,7 +5,7 @@ params.options = [:]
 options        = initOptions(params.options)
 
 process SYNAPSE_SHOW {
-    tag '$synid'
+    tag "$synid"
     label 'process_low'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
@@ -20,17 +20,14 @@ process SYNAPSE_SHOW {
 
     input:
     val synid                   // synapse ID for individual FastQ files
-    path synapseconfig          // path to synapse.Config file
 
     output:
     path "*.metadata.txt", emit: metadata
-    path "*.version.txt", emit: version
 
     script:
     def software = getSoftwareName(task.process)
 
     """
-    synapse -c $synapseconfig show $synid | sed -n '1,3p;15,16p;20p;23p' > ${synid}.metadata.txt
-    echo \$(synapse --version) > ${software}.version.txt
+    synapse show $synid | sed -n '1,3p;15,16p;20p;23p' > ${synid}.metadata.txt
     """
 }
diff --git a/modules/local/synapse_to_samplesheet.nf b/modules/local/synapse_to_samplesheet.nf
index e51d46ca..20bae1c1 100644
--- a/modules/local/synapse_to_samplesheet.nf
+++ b/modules/local/synapse_to_samplesheet.nf
@@ -5,7 +5,7 @@ params.options = [:]
 options        = initOptions(params.options)
 
 process SYNAPSE_TO_SAMPLESHEET {
-    tag '$id'
+    tag "$id"
     label 'process_low'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
@@ -22,8 +22,8 @@ process SYNAPSE_TO_SAMPLESHEET {
     // Add fields to the beginning of the map
     pipeline_map = [
         sample  : "${id}",
-        fastq_1 : "${params.outdir}/${params.results_dir}/${files[0].getBaseName()}",
-        fastq_2 : "${params.outdir}/${params.results_dir}/${files[1].getBaseName()}"
+        fastq_1 : "${params.outdir}/fastq/${files[0]}",
+        fastq_2 : "${params.outdir}/fastq/${files[1]}"
     ]
     // Add Strandedness
     pipeline_map << [ strandedness: "unstranded" ]
diff --git a/workflows/synapse.nf b/workflows/synapse.nf
index 24dcd9dd..9820ce09 100644
--- a/workflows/synapse.nf
+++ b/workflows/synapse.nf
@@ -68,15 +68,13 @@ workflow SYNAPSE {
     SYNAPSE_LIST
         .out
         .synlist_csv
-        .splitCsv(header:false, strip:true).flatten()
+        .splitCsv(header:false).flatten()
         .set { ch_samples }
 
     // MODULE: Download FastQ Files by SynapseID
     SYNAPSE_GET (
         ch_samples,
-        ch_synapseConfig
     )
-    ch_software_versions = ch_software_versions.mix(SYNAPSE_GET.out.version.first().ifEmpty(null))
 
     // CHANNEL: Create Read Pairs Channel - Creates format [sampleId, [fastq_1, fastq_2]]
     SYNAPSE_GET
@@ -94,9 +92,7 @@ workflow SYNAPSE {
     // MODULE: Download FQ Metadata by SynapseID
     SYNAPSE_SHOW (
         ch_samples,
-        ch_synapseConfig
     )
-    ch_software_versions = ch_software_versions.mix(SYNAPSE_SHOW.out.version.first().ifEmpty(null))
 
     // CHANNEL: Clean Metadata
     SYNAPSE_SHOW

From c749172925f8cd29602f2674c5e0eaffb89a3e26 Mon Sep 17 00:00:00 2001
From: Daisy Wenyan Han <60151111+daisyhan97@users.noreply.github.com>
Date: Thu, 7 Oct 2021 14:04:09 -0700
Subject: [PATCH 071/852] Fix SynapseConfig Bug

---
 modules/local/synapse_get.nf  | 3 ++-
 modules/local/synapse_show.nf | 3 ++-
 workflows/synapse.nf          | 6 +++---
 3 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/modules/local/synapse_get.nf b/modules/local/synapse_get.nf
index 0f083141..47f39def 100644
--- a/modules/local/synapse_get.nf
+++ b/modules/local/synapse_get.nf
@@ -20,6 +20,7 @@ process SYNAPSE_GET {
 
     input:
     val synid                   // synapse ID for individual FastQ files
+    path synapseconfig          // path to synapse.Config file
 
     output:
     path "*"               , emit: fastq
@@ -28,6 +29,6 @@ process SYNAPSE_GET {
     def software = getSoftwareName(task.process)
 
     """
-    synapse get $synid
+    synapse -c $synapseconfig get $synid
     """
 }
diff --git a/modules/local/synapse_show.nf b/modules/local/synapse_show.nf
index bd93e621..dd78d1a8 100644
--- a/modules/local/synapse_show.nf
+++ b/modules/local/synapse_show.nf
@@ -20,6 +20,7 @@ process SYNAPSE_SHOW {
 
     input:
     val synid                   // synapse ID for individual FastQ files
+    path synapseconfig          // path to synapse.Config file
 
     output:
     path "*.metadata.txt", emit: metadata
@@ -28,6 +29,6 @@ process SYNAPSE_SHOW {
     def software = getSoftwareName(task.process)
 
     """
-    synapse show $synid | sed -n '1,3p;15,16p;20p;23p' > ${synid}.metadata.txt
+    synapse -c $synapseconfig show $synid | sed -n '1,3p;15,16p;20p;23p' > ${synid}.metadata.txt
     """
 }
diff --git a/workflows/synapse.nf b/workflows/synapse.nf
index 9820ce09..fd024af8 100644
--- a/workflows/synapse.nf
+++ b/workflows/synapse.nf
@@ -53,9 +53,7 @@ workflow SYNAPSE {
     ch_software_versions = Channel.empty()
 
     // CHANNEL: Stage Synapse Config File
-    Channel
-        .fromPath(params.synapse_config)
-        .set { ch_synapseConfig }
+    ch_synapseConfig        = file( params.synapse_config )
 
     // MODULE: Get individual FastQ SynapseIDs from Directory SynapseID(s)
     SYNAPSE_LIST (
@@ -74,6 +72,7 @@ workflow SYNAPSE {
     // MODULE: Download FastQ Files by SynapseID
     SYNAPSE_GET (
         ch_samples,
+        ch_synapseConfig
     )
 
     // CHANNEL: Create Read Pairs Channel - Creates format [sampleId, [fastq_1, fastq_2]]
@@ -92,6 +91,7 @@ workflow SYNAPSE {
     // MODULE: Download FQ Metadata by SynapseID
     SYNAPSE_SHOW (
         ch_samples,
+        ch_synapseConfig
     )
 
     // CHANNEL: Clean Metadata

From 94c8963ae7379fff8c4ce989ee0ef8dbe879db2d Mon Sep 17 00:00:00 2001
From: Daisy Wenyan Han <60151111+daisyhan97@users.noreply.github.com>
Date: Thu, 7 Oct 2021 14:40:06 -0700
Subject: [PATCH 072/852] Remove input_type parameter

---
 lib/WorkflowMain.groovy | 12 ++++++++++++
 main.nf                 |  5 +++--
 nextflow.config         |  1 -
 nextflow_schema.json    | 12 ------------
 4 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index a7fb8c70..59c3e8a4 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -77,4 +77,16 @@ class WorkflowMain {
             System.exit(1)
         }
     }
+    
+    // Check input type
+    public static String getIdentifierType(workflow, params, log) {
+        def input_type = ""
+        params.input.eachLine { line ->
+        if (line.contains("syn")) {
+            input_type = "Synapse"
+        } else {
+            input_type = "SRA"
+        }}
+        return input_type
+    }
 }
diff --git a/main.nf b/main.nf
index 7d4735f8..96e38f15 100644
--- a/main.nf
+++ b/main.nf
@@ -18,6 +18,7 @@ nextflow.enable.dsl = 2
 */
 
 WorkflowMain.initialise(workflow, params, log)
+input_type = WorkflowMain.getIdentifierType(workflow, params, log)
 
 /*
 ========================================================================================
@@ -25,7 +26,7 @@ WorkflowMain.initialise(workflow, params, log)
 ========================================================================================
 */
 
-if (params.input_type == 'Synapse') {
+if (input_type == 'Synapse') {
     include { SYNAPSE } from './workflows/synapse'
 } else {
     include { FETCHNGS } from './workflows/fetchngs'
@@ -37,7 +38,7 @@ if (params.input_type == 'Synapse') {
 workflow NFCORE_FETCHNGS {
 
     // Workflow for SynapseIDs
-    if (params.input_type == 'Synapse') {
+    if (input_type == 'Synapse') {
         SYNAPSE ()
     } else {
     // Workflow for SRA/ENA/GEO IDs
diff --git a/nextflow.config b/nextflow.config
index 4bdacfba..5e3c7fd2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -11,7 +11,6 @@ params {
 
     // Input options
     input                      = null
-    input_type                 = 'SRA'
     nf_core_pipeline           = null
     ena_metadata_fields        = null
     sample_mapping_fields      = 'run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description,description'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 2f0df31f..836d00e9 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -23,18 +23,6 @@
                     "fa_icon": "fas fa-file-excel",
                     "description": "File containing SRA/ENA/GEO identifiers one per line to download their associated metadata and FastQ files."
                 },
-                "input_type": {
-                    "type": "string",
-                    "description": "Type of Sample Identifiers Provided (SRA/ENA/GE/Synapse)",
-                    "enum": [
-                        "SRA",
-                        "ENA",
-                        "GEO",
-                        "Synapse"
-                    ],
-                    "fa_icon": "fas fa-copy",
-                    "default": "SRA"
-                },
                 "ena_metadata_fields": {
                     "type": "string",
                     "fa_icon": "fas fa-columns",

From a1d055de571c634fb726ccb71be24ec59d9884bd Mon Sep 17 00:00:00 2001
From: Daisy Wenyan Han <60151111+daisyhan97@users.noreply.github.com>
Date: Thu, 7 Oct 2021 14:45:57 -0700
Subject: [PATCH 073/852] Remove trailing whitespace

---
 lib/WorkflowMain.groovy | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index 59c3e8a4..52cfdaea 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -77,7 +77,7 @@ class WorkflowMain {
             System.exit(1)
         }
     }
-    
+
     // Check input type
     public static String getIdentifierType(workflow, params, log) {
         def input_type = ""

From 1aa1a1ecdfc00cfb5b68b64b369bc5e8631d08b8 Mon Sep 17 00:00:00 2001
From: Daisy Wenyan Han <60151111+daisyhan97@users.noreply.github.com>
Date: Thu, 7 Oct 2021 15:04:03 -0700
Subject: [PATCH 074/852] Remove remaining input_type parameters

---
 conf/test.config      | 1 -
 conf/test_full.config | 1 -
 2 files changed, 2 deletions(-)

diff --git a/conf/test.config b/conf/test.config
index 75a1ce09..ee909409 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -21,5 +21,4 @@ params {
 
     // Input data
     input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/public_database_ids.txt'
-    input_type = 'SRA'
 }
diff --git a/conf/test_full.config b/conf/test_full.config
index 4fc58a6b..a5aea2dc 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -16,5 +16,4 @@ params {
 
     // Input data for full size test
     input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/public_database_ids.txt'
-    input_type = 'SRA'
 }

From 8b636823da5e598ec5b0d27ceabe33d62cb0ebc7 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 8 Oct 2021 15:57:31 +0100
Subject: [PATCH 075/852] Quick fire re-factor of modules, CI and test configs

---
 .github/workflows/ci.yml                      |  24 +++-
 conf/test.config                              |   2 +-
 conf/test_synapse.config                      |  24 ++++
 modules.json                                  |  11 ++
 modules/local/functions.nf                    |  54 +++++----
 modules/local/get_software_versions.nf        |  33 ------
 modules/local/multiqc_mappings_config.nf      |  11 +-
 modules/local/sra_fastq_ftp.nf                |  13 ++-
 modules/local/sra_ids_to_runinfo.nf           |  10 +-
 modules/local/sra_merge_samplesheet.nf        |  10 +-
 modules/local/sra_runinfo_to_ftp.nf           |  11 +-
 modules/local/synapse_get.nf                  |  29 +++--
 modules/local/synapse_list.nf                 |  32 +++---
 modules/local/synapse_merge_samplesheet.nf    |  10 +-
 modules/local/synapse_metadata_mapping.nf     |   2 +-
 modules/local/synapse_show.nf                 |  30 +++--
 modules/local/synapse_to_samplesheet.nf       |   2 +-
 .../custom/dumpsoftwareversions/functions.nf  |  78 +++++++++++++
 .../custom/dumpsoftwareversions/main.nf       | 106 ++++++++++++++++++
 .../custom/dumpsoftwareversions/meta.yml      |  33 ++++++
 nextflow.config                               |   7 +-
 nextflow_schema.json                          |  12 +-
 22 files changed, 426 insertions(+), 118 deletions(-)
 create mode 100644 conf/test_synapse.config
 create mode 100644 modules.json
 delete mode 100644 modules/local/get_software_versions.nf
 create mode 100644 modules/nf-core/modules/custom/dumpsoftwareversions/functions.nf
 create mode 100644 modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
 create mode 100644 modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 26785ea1..7788b5de 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -35,10 +35,32 @@ jobs:
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
 
-      - name: Run pipeline with test data
+      - name: Run pipeline with SRA test data
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker
 
+  test_synapse:
+    name: Test Synapse workflow
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}
+    runs-on: ubuntu-latest
+    env:
+      NXF_VER: ${{ matrix.nxf_ver }}
+      NXF_ANSI_LOG: false
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Run pipeline with synapse test data
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test_synapse,docker
+
   parameters:
     name: Test workflow parameters
     if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}
diff --git a/conf/test.config b/conf/test.config
index ee909409..d0d7eb53 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -20,5 +20,5 @@ params {
     max_time   = 6.h
 
     // Input data
-    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/public_database_ids.txt'
+    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.txt'
 }
diff --git a/conf/test_synapse.config b/conf/test_synapse.config
new file mode 100644
index 00000000..d68d4098
--- /dev/null
+++ b/conf/test_synapse.config
@@ -0,0 +1,24 @@
+/*
+========================================================================================
+    Nextflow config file for running minimal tests
+========================================================================================
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/fetchngs -profile test_synapse,<docker/singularity>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test profile using Synapse ids'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = 6.GB
+    max_time   = 6.h
+
+    // Input data
+    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/synapse_ids_test.txt'
+}
diff --git a/modules.json b/modules.json
new file mode 100644
index 00000000..ff841d00
--- /dev/null
+++ b/modules.json
@@ -0,0 +1,11 @@
+{
+    "name": "nf-core/fetchngs",
+    "homePage": "https://github.com/nf-core/fetchngs",
+    "repos": {
+        "nf-core/modules": {
+            "custom/dumpsoftwareversions": {
+                "git_sha": "84f2302920078b0cf7716b2a2e5fcc0be5c4531d"
+            }
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/local/functions.nf b/modules/local/functions.nf
index da9da093..85628ee0 100644
--- a/modules/local/functions.nf
+++ b/modules/local/functions.nf
@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions  = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_meta) {
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-            for (key in key_list) {
-                if (args.meta && key instanceof String) {
-                    def path = key
-                    if (args.meta.containsKey(key)) {
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                    }
-                    path = path instanceof String ? path : ''
-                    path_list.add(path)
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
             }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
         }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }
diff --git a/modules/local/get_software_versions.nf b/modules/local/get_software_versions.nf
deleted file mode 100644
index 65b7f340..00000000
--- a/modules/local/get_software_versions.nf
+++ /dev/null
@@ -1,33 +0,0 @@
-// Import generic module functions
-include { saveFiles } from './functions'
-
-params.options = [:]
-
-process GET_SOFTWARE_VERSIONS {
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', meta:[:], publish_by_meta:[]) }
-
-    conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/python:3.9--1"
-    } else {
-        container "quay.io/biocontainers/python:3.9--1"
-    }
-
-    cache false
-
-    input:
-    path versions
-
-    output:
-    path "software_versions.tsv"     , emit: tsv
-    path 'software_versions_mqc.yaml', emit: yaml
-
-    script: // This script is bundled with the pipeline, in nf-core/fetchngs/bin/
-    """
-    echo $workflow.manifest.version > pipeline.version.txt
-    echo $workflow.nextflow.version > nextflow.version.txt
-    scrape_software_versions.py &> software_versions_mqc.yaml
-    """
-}
diff --git a/modules/local/multiqc_mappings_config.nf b/modules/local/multiqc_mappings_config.nf
index 8360cd34..857c859c 100644
--- a/modules/local/multiqc_mappings_config.nf
+++ b/modules/local/multiqc_mappings_config.nf
@@ -1,5 +1,5 @@
 // Import generic module functions
-include { saveFiles; getSoftwareName } from './functions'
+include { saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 
@@ -19,8 +19,8 @@ process MULTIQC_MAPPINGS_CONFIG {
     path csv
 
     output:
-    path "*yml"         , emit: yml
-    path "*.version.txt", emit: version
+    path "*yml"        , emit: yml
+    path "versions.yml", emit: versions
 
     script:
     """
@@ -28,6 +28,9 @@ process MULTIQC_MAPPINGS_CONFIG {
         $csv \\
         multiqc_config.yml
 
-    python --version | sed -e "s/Python //g" > python.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        python: \$(python --version | sed 's/Python //g')
+    END_VERSIONS
     """
 }
diff --git a/modules/local/sra_fastq_ftp.nf b/modules/local/sra_fastq_ftp.nf
index 126c0647..39d3659d 100644
--- a/modules/local/sra_fastq_ftp.nf
+++ b/modules/local/sra_fastq_ftp.nf
@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -25,6 +25,7 @@ process SRA_FASTQ_FTP {
     output:
     tuple val(meta), path("*fastq.gz"), emit: fastq
     tuple val(meta), path("*md5")     , emit: md5
+    path "versions.yml"               , emit: versions
 
     script:
     if (meta.single_end) {
@@ -33,6 +34,11 @@ process SRA_FASTQ_FTP {
 
         echo "${meta.md5_1} ${meta.id}.fastq.gz" > ${meta.id}.fastq.gz.md5
         md5sum -c ${meta.id}.fastq.gz.md5
+
+        cat <<-END_VERSIONS > versions.yml
+        ${getProcessName(task.process)}:
+            sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
+        END_VERSIONS
         """
     } else {
         """
@@ -45,6 +51,11 @@ process SRA_FASTQ_FTP {
 
         echo "${meta.md5_2} ${meta.id}_2.fastq.gz" > ${meta.id}_2.fastq.gz.md5
         md5sum -c ${meta.id}_2.fastq.gz.md5
+
+        cat <<-END_VERSIONS > versions.yml
+        ${getProcessName(task.process)}:
+            sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
+        END_VERSIONS
         """
     }
 }
diff --git a/modules/local/sra_ids_to_runinfo.nf b/modules/local/sra_ids_to_runinfo.nf
index 3d3fc063..8200271e 100644
--- a/modules/local/sra_ids_to_runinfo.nf
+++ b/modules/local/sra_ids_to_runinfo.nf
@@ -1,5 +1,5 @@
 // Import generic module functions
-include { saveFiles; getSoftwareName } from './functions'
+include { saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 
@@ -22,7 +22,8 @@ process SRA_IDS_TO_RUNINFO {
     val fields
 
     output:
-    path "*.tsv", emit: tsv
+    path "*.tsv"       , emit: tsv
+    path "versions.yml", emit: versions
 
     script:
     def metadata_fields = fields ? "--ena_metadata_fields ${fields}" : ''
@@ -32,5 +33,10 @@ process SRA_IDS_TO_RUNINFO {
         id.txt \\
         ${id}.runinfo.tsv \\
         $metadata_fields
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        python: \$(python --version | sed 's/Python //g')
+    END_VERSIONS
     """
 }
diff --git a/modules/local/sra_merge_samplesheet.nf b/modules/local/sra_merge_samplesheet.nf
index e3c1314a..914bac00 100644
--- a/modules/local/sra_merge_samplesheet.nf
+++ b/modules/local/sra_merge_samplesheet.nf
@@ -1,5 +1,5 @@
 // Import generic module functions
-include { saveFiles; getSoftwareName } from './functions'
+include { saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 
@@ -21,7 +21,8 @@ process SRA_MERGE_SAMPLESHEET {
 
     output:
     path "samplesheet.csv", emit: samplesheet
-    path "id_mappings.csv"   , emit: mappings
+    path "id_mappings.csv", emit: mappings
+    path "versions.yml"   , emit: versions
 
     script:
     """
@@ -34,5 +35,10 @@ process SRA_MERGE_SAMPLESHEET {
     for fileid in `ls ./mappings/*`; do
         awk 'NR>1' \$fileid >> id_mappings.csv
     done
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
+    END_VERSIONS
     """
 }
diff --git a/modules/local/sra_runinfo_to_ftp.nf b/modules/local/sra_runinfo_to_ftp.nf
index f426f4ab..80028705 100644
--- a/modules/local/sra_runinfo_to_ftp.nf
+++ b/modules/local/sra_runinfo_to_ftp.nf
@@ -1,5 +1,5 @@
 // Import generic module functions
-include { saveFiles; getSoftwareName } from './functions'
+include { saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 
@@ -19,8 +19,8 @@ process SRA_RUNINFO_TO_FTP {
     path runinfo
 
     output:
-    path "*.tsv"         , emit: tsv
-    path  "*.version.txt", emit: version
+    path "*.tsv"       , emit: tsv
+    path "versions.yml", emit: versions
 
     script:
     """
@@ -28,6 +28,9 @@ process SRA_RUNINFO_TO_FTP {
         ${runinfo.join(',')} \\
         ${runinfo.toString().tokenize(".")[0]}.runinfo_ftp.tsv
 
-    python --version | sed -e "s/Python //g" > python.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        python: \$(python --version | sed 's/Python //g')
+    END_VERSIONS
     """
 }
diff --git a/modules/local/synapse_get.nf b/modules/local/synapse_get.nf
index 47f39def..5061e4d8 100644
--- a/modules/local/synapse_get.nf
+++ b/modules/local/synapse_get.nf
@@ -1,34 +1,41 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
 
 process SYNAPSE_GET {
-    tag "$synid"
+    tag "$id"
     label 'process_low'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "bioconda::synapseclient=2.2.2" : null)
+    conda (params.enable_conda ? "bioconda::synapseclient=2.4.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE" // TODO: Add Singularity
+        container "https://depot.galaxyproject.org/singularity/synapseclient:2.4.0--pyh5e36f6f_0"
     } else {
-        container "sagebionetworks/synapsepythonclient:v2.4.0"
+        container "quay.io/biocontainers/synapseclient:2.4.0--pyh5e36f6f_0"
     }
 
     input:
-    val synid                   // synapse ID for individual FastQ files
-    path synapseconfig          // path to synapse.Config file
+    val id
+    path config
 
     output:
-    path "*"               , emit: fastq
+    path "*.fastq.gz"  , emit: fastq
+    path "versions.yml", emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
-
     """
-    synapse -c $synapseconfig get $synid
+    synapse \\
+        -c $config \\
+        get \\
+        $synid
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( echo \$(synapse --version) )
+    END_VERSIONS
     """
 }
diff --git a/modules/local/synapse_list.nf b/modules/local/synapse_list.nf
index 5e94f06d..de8ee867 100644
--- a/modules/local/synapse_list.nf
+++ b/modules/local/synapse_list.nf
@@ -1,36 +1,42 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
 
 process SYNAPSE_LIST {
-    tag "$synid"
+    tag "$id"
     label 'process_low'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "bioconda::synapseclient=2.2.2" : null)
+    conda (params.enable_conda ? "bioconda::synapseclient=2.4.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE" // TODO: Add Singularity
+        container "https://depot.galaxyproject.org/singularity/synapseclient:2.4.0--pyh5e36f6f_0"
     } else {
-        container "sagebionetworks/synapsepythonclient:v2.4.0"
+        container "quay.io/biocontainers/synapseclient:2.4.0--pyh5e36f6f_0"
     }
 
     input:
-    val synid                   // synapse ID for individual FastQ files
-    path synapseconfig          // path to synapse.Config file
+    val id
+    path config
 
     output:
-    path "*.synlist.csv", emit: synlist_csv
-    path "*.version.txt", emit: version
+    path "*.csv"       , emit: csv
+    path "versions.yml", emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
-
     """
-    synapse -c $synapseconfig list -l $synid | cut -c-11 > ${synid}.synlist.csv
-    echo \$(synapse --version) > ${software}.version.txt
+    synapse \\
+        -c $config \\
+        list \\
+        -l $id \\
+        | cut -c-11 > ${id}.synlist.csv
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( echo \$(synapse --version) )
+    END_VERSIONS
     """
 }
diff --git a/modules/local/synapse_merge_samplesheet.nf b/modules/local/synapse_merge_samplesheet.nf
index d31d17ef..f634118b 100644
--- a/modules/local/synapse_merge_samplesheet.nf
+++ b/modules/local/synapse_merge_samplesheet.nf
@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,7 +24,8 @@ process SYNAPSE_MERGE_SAMPLESHEET {
 
     output:
     path "samplesheet.csv", emit: samplesheet
-    path "metasheet.csv", emit: metasheet
+    path "metasheet.csv"  , emit: metasheet
+    path "versions.yml"   , emit: versions
 
     script:
     """
@@ -37,5 +38,10 @@ process SYNAPSE_MERGE_SAMPLESHEET {
     for fileid in `ls ./metasheet/*`; do
         awk 'NR>1' \$fileid >> metasheet.csv
     done
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
+    END_VERSIONS
     """
 }
diff --git a/modules/local/synapse_metadata_mapping.nf b/modules/local/synapse_metadata_mapping.nf
index 6d3c87ac..a513da09 100644
--- a/modules/local/synapse_metadata_mapping.nf
+++ b/modules/local/synapse_metadata_mapping.nf
@@ -15,7 +15,7 @@ process SYNAPSE_METADATA_MAPPING {
     val data
 
     output:
-    path("*metasheet.csv"), emit: metasheet
+    path "*.csv", emit: metasheet
 
     exec:
     meta_map = [
diff --git a/modules/local/synapse_show.nf b/modules/local/synapse_show.nf
index dd78d1a8..6f0f0b1c 100644
--- a/modules/local/synapse_show.nf
+++ b/modules/local/synapse_show.nf
@@ -1,34 +1,42 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
 
 process SYNAPSE_SHOW {
-    tag "$synid"
+    tag "$id"
     label 'process_low'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "bioconda::synapseclient=2.2.2" : null)
+    conda (params.enable_conda ? "bioconda::synapseclient=2.4.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE" // TODO: Add Singularity
+        container "https://depot.galaxyproject.org/singularity/synapseclient:2.4.0--pyh5e36f6f_0"
     } else {
-        container "sagebionetworks/synapsepythonclient:v2.4.0"
+        container "quay.io/biocontainers/synapseclient:2.4.0--pyh5e36f6f_0"
     }
 
     input:
-    val synid                   // synapse ID for individual FastQ files
-    path synapseconfig          // path to synapse.Config file
+    val id
+    path config
 
     output:
-    path "*.metadata.txt", emit: metadata
+    path "*.txt"       , emit: metadata
+    path "versions.yml", emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
-
     """
-    synapse -c $synapseconfig show $synid | sed -n '1,3p;15,16p;20p;23p' > ${synid}.metadata.txt
+    synapse \\
+        -c $config \\
+        show \\
+        $id \\
+        | sed -n '1,3p;15,16p;20p;23p' > ${id}.metadata.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( echo \$(synapse --version) )
+    END_VERSIONS
     """
 }
diff --git a/modules/local/synapse_to_samplesheet.nf b/modules/local/synapse_to_samplesheet.nf
index 20bae1c1..7b301ddf 100644
--- a/modules/local/synapse_to_samplesheet.nf
+++ b/modules/local/synapse_to_samplesheet.nf
@@ -15,7 +15,7 @@ process SYNAPSE_TO_SAMPLESHEET {
     tuple val(id), val(files)
 
     output:
-    path("*samplesheet.csv"), emit: samplesheet
+    path "*.csv", emit: samplesheet
 
     exec:
 
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/functions.nf b/modules/nf-core/modules/custom/dumpsoftwareversions/functions.nf
new file mode 100644
index 00000000..85628ee0
--- /dev/null
+++ b/modules/nf-core/modules/custom/dumpsoftwareversions/functions.nf
@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
new file mode 100644
index 00000000..faf2073f
--- /dev/null
+++ b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
@@ -0,0 +1,106 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process CUSTOM_DUMPSOFTWAREVERSIONS {
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', meta:[:], publish_by_meta:[]) }
+
+    // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
+    conda (params.enable_conda ? "bioconda::multiqc=1.11" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0"
+    } else {
+        container "quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0"
+    }
+
+    input:
+    path versions
+
+    output:
+    path "software_versions.yml"    , emit: yml
+    path "software_versions_mqc.yml", emit: mqc_yml
+    path "versions.yml"             , emit: versions
+
+    script:
+    """
+    #!/usr/bin/env python
+
+    import yaml
+    import platform
+    from textwrap import dedent
+
+    def _make_versions_html(versions):
+        html = [
+            dedent(
+                '''\\
+                <style>
+                #nf-core-versions tbody:nth-child(even) {
+                    background-color: #f2f2f2;
+                }
+                </style>
+                <table class="table" style="width:100%" id="nf-core-versions">
+                    <thead>
+                        <tr>
+                            <th> Process Name </th>
+                            <th> Software </th>
+                            <th> Version  </th>
+                        </tr>
+                    </thead>
+                '''
+            )
+        ]
+        for process, tmp_versions in sorted(versions.items()):
+            html.append("<tbody>")
+            for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
+                html.append(
+                    dedent(
+                        f'''\\
+                        <tr>
+                            <td><samp>{process if (i == 0) else ''}</samp></td>
+                            <td><samp>{tool}</samp></td>
+                            <td><samp>{version}</samp></td>
+                        </tr>
+                        '''
+                    )
+                )
+            html.append("</tbody>")
+        html.append("</table>")
+        return "\\n".join(html)
+
+    module_versions = {}
+    module_versions["${getProcessName(task.process)}"] = {
+        'python': platform.python_version(),
+        'yaml': yaml.__version__
+    }
+
+    with open("$versions") as f:
+        workflow_versions = yaml.load(f, Loader=yaml.BaseLoader) | module_versions
+
+    workflow_versions["Workflow"] = {
+        "Nextflow": "$workflow.nextflow.version",
+        "$workflow.manifest.name": "$workflow.manifest.version"
+    }
+
+    versions_mqc = {
+        'id': 'software_versions',
+        'section_name': '${workflow.manifest.name} Software Versions',
+        'section_href': 'https://github.com/${workflow.manifest.name}',
+        'plot_type': 'html',
+        'description': 'are collected at run time from the software output.',
+        'data': _make_versions_html(workflow_versions)
+    }
+
+    with open("software_versions.yml", 'w') as f:
+        yaml.dump(workflow_versions, f, default_flow_style=False)
+    with open("software_versions_mqc.yml", 'w') as f:
+        yaml.dump(versions_mqc, f, default_flow_style=False)
+
+    with open('versions.yml', 'w') as f:
+        yaml.dump(module_versions, f, default_flow_style=False)
+    """
+}
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml
new file mode 100644
index 00000000..8d4a6ed4
--- /dev/null
+++ b/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml
@@ -0,0 +1,33 @@
+name: custom_dumpsoftwareversions
+description: Custom module used to dump software versions within the nf-core pipeline template
+keywords:
+  - custom
+  - version
+tools:
+  - custom:
+      description: Custom module used to dump software versions within the nf-core pipeline template
+      homepage: https://github.com/nf-core/tools
+      documentation: https://github.com/nf-core/tools
+
+input:
+  - versions:
+      type: file
+      description: YML file containing software versions
+      pattern: "*.yml"
+
+output:
+  - yml:
+      type: file
+      description: Standard YML file containing software versions
+      pattern: "software_versions.yml"
+  - mqc_yml:
+      type: file
+      description: MultiQC custom content YML file containing software versions
+      pattern: "software_versions_mqc.yml"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@drpatelh"
diff --git a/nextflow.config b/nextflow.config
index b4e5dde7..45dfb946 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -14,6 +14,7 @@ params {
     nf_core_pipeline           = null
     ena_metadata_fields        = null
     sample_mapping_fields      = 'run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description,description'
+    synapse_config             = null
     skip_fastq_download        = false
 
     // Boilerplate options
@@ -39,7 +40,6 @@ params {
     config_profile_contact     = null
     config_profile_url         = null
     config_profile_name        = null
-    synapse_config             = null
 
     // Max resource options
     // Defaults only, expecting to be overwritten
@@ -109,8 +109,9 @@ profiles {
         podman.enabled         = false
         shifter.enabled        = false
     }
-    test      { includeConfig 'conf/test.config'      }
-    test_full { includeConfig 'conf/test_full.config' }
+    test         { includeConfig 'conf/test.config'         }
+    test_synapse { includeConfig 'conf/test_synapse.config' }
+    test_full    { includeConfig 'conf/test_full.config'    }
 }
 
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
diff --git a/nextflow_schema.json b/nextflow_schema.json
index db607cc4..b2f26972 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -57,6 +57,12 @@
                     "fa_icon": "fas fa-envelope",
                     "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
                     "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
+                },
+                "synapse_config": {
+                    "type": "string",
+                    "description": "Path to Synapse configuration file",
+                    "fa_icon": "fas fa-users-cog",
+                    "hidden": true
                 }
             }
         },
@@ -111,12 +117,6 @@
                     "description": "Institutional config URL link.",
                     "hidden": true,
                     "fa_icon": "fas fa-users-cog"
-                },
-                "synapse_config": {
-                    "type": "string",
-                    "description": "Path to Synapse configuration file",
-                    "fa_icon": "fas fa-users-cog",
-                    "hidden": true
                 }
             }
         },

From b9d5e86184f123313c8bd14957b5e277aac93949 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 9 Oct 2021 09:24:59 +0100
Subject: [PATCH 076/852] Fix tests for SRA workflow

---
 ...flowFetchngs.groovy => WorkflowSra.groovy} |  4 +--
 main.nf                                       |  6 ++--
 workflows/{fetchngs.nf => sra.nf}             | 36 ++++++++++---------
 3 files changed, 25 insertions(+), 21 deletions(-)
 rename lib/{WorkflowFetchngs.groovy => WorkflowSra.groovy} (91%)
 rename workflows/{fetchngs.nf => sra.nf} (82%)

diff --git a/lib/WorkflowFetchngs.groovy b/lib/WorkflowSra.groovy
similarity index 91%
rename from lib/WorkflowFetchngs.groovy
rename to lib/WorkflowSra.groovy
index ccff938b..a2c16219 100755
--- a/lib/WorkflowFetchngs.groovy
+++ b/lib/WorkflowSra.groovy
@@ -1,8 +1,8 @@
 //
-// This file holds several functions specific to the workflow/fetchngs.nf in the nf-core/fetchngs pipeline
+// This file holds several functions specific to the workflow/sra.nf in the nf-core/fetchngs pipeline
 //
 
-class WorkflowFetchngs {
+class WorkflowSra {
 
     //
     // Check and validate parameters
diff --git a/main.nf b/main.nf
index 96e38f15..0b76d9da 100644
--- a/main.nf
+++ b/main.nf
@@ -29,11 +29,11 @@ input_type = WorkflowMain.getIdentifierType(workflow, params, log)
 if (input_type == 'Synapse') {
     include { SYNAPSE } from './workflows/synapse'
 } else {
-    include { FETCHNGS } from './workflows/fetchngs'
+    include { SRA } from './workflows/sra'
 }
 
 //
-// WORKFLOW: Run main nf-core/fetchngs analysis pipeline, depending on Identifier Type provided
+// WORKFLOW: Run main nf-core/fetchngs analysis pipeline, depending on type of dentifier provided
 //
 workflow NFCORE_FETCHNGS {
 
@@ -42,7 +42,7 @@ workflow NFCORE_FETCHNGS {
         SYNAPSE ()
     } else {
     // Workflow for SRA/ENA/GEO IDs
-        FETCHNGS ()
+        SRA ()
     }
 
 }
diff --git a/workflows/fetchngs.nf b/workflows/sra.nf
similarity index 82%
rename from workflows/fetchngs.nf
rename to workflows/sra.nf
index 12733f07..25e214df 100644
--- a/workflows/fetchngs.nf
+++ b/workflows/sra.nf
@@ -11,7 +11,7 @@ def valid_params = [
 def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
 
 // Validate input parameters
-WorkflowFetchngs.initialise(params, log, valid_params)
+WorkflowSra.initialise(params, log, valid_params)
 
 // Check mandatory parameters
 if (params.input) {
@@ -40,7 +40,14 @@ include { SRA_FASTQ_FTP           } from '../modules/local/sra_fastq_ftp'
 include { SRA_TO_SAMPLESHEET      } from '../modules/local/sra_to_samplesheet'      addParams( options: modules['sra_to_samplesheet'], results_dir: modules['sra_fastq_ftp'].publish_dir )
 include { SRA_MERGE_SAMPLESHEET   } from '../modules/local/sra_merge_samplesheet'   addParams( options: modules['sra_merge_samplesheet']   )
 include { MULTIQC_MAPPINGS_CONFIG } from '../modules/local/multiqc_mappings_config' addParams( options: modules['multiqc_mappings_config'] )
-include { GET_SOFTWARE_VERSIONS   } from '../modules/local/get_software_versions'   addParams( options: [publish_files : ['tsv':'']]       )
+
+/*
+========================================================================================
+    IMPORT NF-CORE MODULES/SUBWORKFLOWS
+========================================================================================
+*/
+
+include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main' addParams( options: [publish_files : ['_versions.yml':'']] )
 
 /*
 ========================================================================================
@@ -48,9 +55,9 @@ include { GET_SOFTWARE_VERSIONS   } from '../modules/local/get_software_versions
 ========================================================================================
 */
 
-workflow FETCHNGS {
+workflow SRA {
 
-    ch_software_versions = Channel.empty()
+    ch_versions = Channel.empty()
 
     //
     // MODULE: Get SRA run information for public database ids
@@ -59,6 +66,7 @@ workflow FETCHNGS {
         ch_ids,
         params.ena_metadata_fields ?: ''
     )
+    ch_versions = ch_versions.mix(SRA_IDS_TO_RUNINFO.out.versions.first())
 
     //
     // MODULE: Parse SRA run information, create file containing FTP links and read into workflow as [ meta, [reads] ]
@@ -66,6 +74,7 @@ workflow FETCHNGS {
     SRA_RUNINFO_TO_FTP (
         SRA_IDS_TO_RUNINFO.out.tsv
     )
+    ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first())
 
     SRA_RUNINFO_TO_FTP
         .out
@@ -78,7 +87,7 @@ workflow FETCHNGS {
         }
         .unique()
         .set { ch_sra_reads }
-    ch_software_versions = ch_software_versions.mix(SRA_RUNINFO_TO_FTP.out.version.first().ifEmpty(null))
+    ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first())
 
     if (!params.skip_fastq_download) {
         //
@@ -87,6 +96,7 @@ workflow FETCHNGS {
         SRA_FASTQ_FTP (
             ch_sra_reads.map { meta, reads -> if (meta.fastq_1)  [ meta, reads ] }
         )
+        ch_versions = ch_versions.mix(SRA_FASTQ_FTP.out.versions.first())
 
         //
         // MODULE: Stage FastQ files downloaded by SRA together and auto-create a samplesheet
@@ -104,6 +114,7 @@ workflow FETCHNGS {
             SRA_TO_SAMPLESHEET.out.samplesheet.collect{it[1]},
             SRA_TO_SAMPLESHEET.out.mappings.collect{it[1]}
         )
+        ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions)
 
         //
         // MODULE: Create a MutiQC config file with sample name mappings
@@ -112,6 +123,7 @@ workflow FETCHNGS {
             MULTIQC_MAPPINGS_CONFIG (
                 SRA_MERGE_SAMPLESHEET.out.mappings
             )
+            ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions)
         }
 
         //
@@ -127,16 +139,8 @@ workflow FETCHNGS {
     //
     // MODULE: Pipeline reporting
     //
-    ch_software_versions
-        .map { it -> if (it) [ it.baseName, it ] }
-        .groupTuple()
-        .map { it[1][0] }
-        .flatten()
-        .collect()
-        .set { ch_software_versions }
-
-    GET_SOFTWARE_VERSIONS (
-        ch_software_versions.map { it }.collect()
+    CUSTOM_DUMPSOFTWAREVERSIONS (
+        ch_versions.unique().collectFile(name: 'collated_versions.yml')
     )
 }
 
@@ -151,7 +155,7 @@ workflow.onComplete {
         NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)
     }
     NfcoreTemplate.summary(workflow, params, log)
-    WorkflowFetchngs.curateSamplesheetWarn(log)
+    WorkflowSra.curateSamplesheetWarn(log)
 }
 
 /*

From 5f2179847e90703cd2b6d25bbced90b2924076f7 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 9 Oct 2021 09:28:48 +0100
Subject: [PATCH 077/852] Fix nf-core lint

---
 .nf-core.yml                      |  3 +++
 bin/scrape_software_versions.py   | 36 --------------------------
 subworkflows/local/input_check.nf | 42 -------------------------------
 3 files changed, 3 insertions(+), 78 deletions(-)
 delete mode 100755 bin/scrape_software_versions.py
 delete mode 100644 subworkflows/local/input_check.nf

diff --git a/.nf-core.yml b/.nf-core.yml
index 12fe7aa8..92e07317 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -3,3 +3,6 @@ lint:
     - .github/CONTRIBUTING.md
     - assets/sendmail_template.txt
     - lib/NfcoreTemplate.groovy
+  files_exist:
+    - bin/scrape_software_versions.py
+    - modules/local/get_software_versions.nf
diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py
deleted file mode 100755
index a4e45493..00000000
--- a/bin/scrape_software_versions.py
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env python
-from __future__ import print_function
-import os
-
-results = {}
-version_files = [x for x in os.listdir(".") if x.endswith(".version.txt")]
-for version_file in version_files:
-
-    software = version_file.replace(".version.txt", "")
-    if software == "pipeline":
-        software = "nf-core/fetchngs"
-
-    with open(version_file) as fin:
-        version = fin.read().strip()
-    results[software] = version
-
-# Dump to YAML
-print(
-    """
-id: 'software_versions'
-section_name: 'nf-core/fetchngs Software Versions'
-section_href: 'https://github.com/nf-core/fetchngs'
-plot_type: 'html'
-description: 'are collected at run time from the software output.'
-data: |
-    <dl class="dl-horizontal">
-"""
-)
-for k, v in sorted(results.items()):
-    print("        <dt>{}</dt><dd><samp>{}</samp></dd>".format(k, v))
-print("    </dl>")
-
-# Write out as tsv file:
-with open("software_versions.tsv", "w") as f:
-    for k, v in sorted(results.items()):
-        f.write("{}\t{}\n".format(k, v))
diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
deleted file mode 100644
index b664bc8c..00000000
--- a/subworkflows/local/input_check.nf
+++ /dev/null
@@ -1,42 +0,0 @@
-//
-// Check input samplesheet and get read channels
-//
-
-params.options = [:]
-
-include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check' addParams( options: params.options )
-
-workflow INPUT_CHECK {
-    take:
-    samplesheet // file: /path/to/samplesheet.csv
-
-    main:
-    SAMPLESHEET_CHECK ( samplesheet )
-        .splitCsv ( header:true, sep:',' )
-        .map { create_fastq_channels(it) }
-        .set { reads }
-
-    emit:
-    reads // channel: [ val(meta), [ reads ] ]
-}
-
-// Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
-def create_fastq_channels(LinkedHashMap row) {
-    def meta = [:]
-    meta.id           = row.sample
-    meta.single_end   = row.single_end.toBoolean()
-
-    def array = []
-    if (!file(row.fastq_1).exists()) {
-        exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}"
-    }
-    if (meta.single_end) {
-        array = [ meta, [ file(row.fastq_1) ] ]
-    } else {
-        if (!file(row.fastq_2).exists()) {
-            exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
-        }
-        array = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
-    }
-    return array
-}

From 335481c640aa088e035a0ad410f32ae82262244d Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 9 Oct 2021 16:02:00 +0100
Subject: [PATCH 078/852] Get Synapse workflow running - tests still failing

---
 lib/WorkflowMain.groovy       |   2 +-
 modules/local/synapse_get.nf  |   5 +-
 modules/local/synapse_list.nf |   3 +-
 modules/local/synapse_show.nf |   3 +-
 workflows/sra.nf              |  20 +++---
 workflows/synapse.nf          | 130 ++++++++++++++++++----------------
 6 files changed, 86 insertions(+), 77 deletions(-)

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index 52cfdaea..f1804f51 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -73,7 +73,7 @@ class WorkflowMain {
 
         // Check input has been provided
         if (!params.input) {
-            log.error "Please provide an input samplesheet to the pipeline e.g. '--input ids.txt'"
+            log.error "Please provide an input file containing ids to the pipeline - one per line e.g. '--input ids.txt'"
             System.exit(1)
         }
     }
diff --git a/modules/local/synapse_get.nf b/modules/local/synapse_get.nf
index 5061e4d8..1581d41a 100644
--- a/modules/local/synapse_get.nf
+++ b/modules/local/synapse_get.nf
@@ -31,11 +31,12 @@ process SYNAPSE_GET {
     synapse \\
         -c $config \\
         get \\
-        $synid
+        $options.args \\
+        $id \\
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$( echo \$(synapse --version) )
+        ${getSoftwareName(task.process)}: \$(synapse --version | sed -e "s/Synapse Client //g")
     END_VERSIONS
     """
 }
diff --git a/modules/local/synapse_list.nf b/modules/local/synapse_list.nf
index de8ee867..367d1e16 100644
--- a/modules/local/synapse_list.nf
+++ b/modules/local/synapse_list.nf
@@ -31,12 +31,13 @@ process SYNAPSE_LIST {
     synapse \\
         -c $config \\
         list \\
+        $options.args \\
         -l $id \\
         | cut -c-11 > ${id}.synlist.csv
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$( echo \$(synapse --version) )
+        ${getSoftwareName(task.process)}: \$(synapse --version | sed -e "s/Synapse Client //g")
     END_VERSIONS
     """
 }
diff --git a/modules/local/synapse_show.nf b/modules/local/synapse_show.nf
index 6f0f0b1c..51bb5420 100644
--- a/modules/local/synapse_show.nf
+++ b/modules/local/synapse_show.nf
@@ -31,12 +31,13 @@ process SYNAPSE_SHOW {
     synapse \\
         -c $config \\
         show \\
+        $options.args \\
         $id \\
         | sed -n '1,3p;15,16p;20p;23p' > ${id}.metadata.txt
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$( echo \$(synapse --version) )
+        ${getSoftwareName(task.process)}: \$(synapse --version | sed -e "s/Synapse Client //g")
     END_VERSIONS
     """
 }
diff --git a/workflows/sra.nf b/workflows/sra.nf
index 25e214df..835bd874 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -13,17 +13,13 @@ def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
 // Validate input parameters
 WorkflowSra.initialise(params, log, valid_params)
 
-// Check mandatory parameters
-if (params.input) {
-    Channel
-        .from(file(params.input, checkIfExists: true))
-        .splitCsv(header:false, sep:'', strip:true)
-        .map { it[0] }
-        .unique()
-        .set { ch_ids }
-} else {
-    exit 1, 'Input file with public database ids not specified!'
-}
+// Read in ids from --input file
+Channel
+    .from(file(params.input, checkIfExists: true))
+    .splitCsv(header:false, sep:'', strip:true)
+    .map { it[0] }
+    .unique()
+    .set { ch_ids }
 
 /*
 ========================================================================================
@@ -137,7 +133,7 @@ workflow SRA {
     }
 
     //
-    // MODULE: Pipeline reporting
+    // MODULE: Dump software versions for all tools used in the workflow
     //
     CUSTOM_DUMPSOFTWAREVERSIONS (
         ch_versions.unique().collectFile(name: 'collated_versions.yml')
diff --git a/workflows/synapse.nf b/workflows/synapse.nf
index fd024af8..93f281e7 100644
--- a/workflows/synapse.nf
+++ b/workflows/synapse.nf
@@ -4,25 +4,21 @@
 ========================================================================================
 */
 
-def valid_params = [
-    ena_metadata_fields : ['run_accession', 'experiment_accession', 'library_layout', 'fastq_ftp', 'fastq_md5']
-]
-
 def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
 
-// Validate input parameters
-WorkflowFetchngs.initialise(params, log, valid_params)
-
-// Check mandatory parameters
-if (params.input) {
-    Channel
-        .from(file(params.input, checkIfExists: true))
-        .splitCsv(header:false, sep:'', strip:true)
-        .map { it[0] }
-        .unique()
-        .set { ch_ids }
+// Read in ids from --input file
+Channel
+    .from(file(params.input, checkIfExists: true))
+    .splitCsv(header:false, sep:'', strip:true)
+    .map { it[0] }
+    .unique()
+    .set { ch_ids }
+
+// Create channel for synapse config
+if (params.synapse_config) {
+    ch_synapse_config = file(params.synapse_config, checkIfExists: true)
 } else {
-    exit 1, 'Input file with Synapse IDs not specified!'
+    exit 1, 'Please provide a Synapse config file for download authentication!'
 }
 
 /*
@@ -34,13 +30,20 @@ if (params.input) {
 // Don't overwrite global params.modules, create a copy instead and use that within the main script.
 def modules = params.modules.clone()
 
-include { SYNAPSE_LIST               } from '../modules/local/synapse_list'                 addParams( options: modules['synapse_list']             )
-include { SYNAPSE_GET                } from '../modules/local/synapse_get'                  addParams( options: modules['synapse_get']              )
-include { SYNAPSE_SHOW               } from '../modules/local/synapse_show'                 addParams( options: modules['synapse_show']             )
-include { SYNAPSE_TO_SAMPLESHEET     } from '../modules/local/synapse_to_samplesheet'       addParams( options: modules['synapse_to_samplesheet']   )
-include { SYNAPSE_METADATA_MAPPING   } from '../modules/local/synapse_metadata_mapping'     addParams( options: modules['synapse_metadata_mapping'] )
-include { SYNAPSE_MERGE_SAMPLESHEET  } from '../modules/local/synapse_merge_samplesheet'    addParams( options: modules['synapse_merge_samplesheet'])
-include { GET_SOFTWARE_VERSIONS      } from '../modules/local/get_software_versions'        addParams( options: [publish_files : ['tsv':'']]        )
+include { SYNAPSE_LIST              } from '../modules/local/synapse_list'              addParams( options: modules['synapse_list']              )
+include { SYNAPSE_GET               } from '../modules/local/synapse_get'               addParams( options: modules['synapse_get']               )
+include { SYNAPSE_SHOW              } from '../modules/local/synapse_show'              addParams( options: modules['synapse_show']              )
+include { SYNAPSE_TO_SAMPLESHEET    } from '../modules/local/synapse_to_samplesheet'    addParams( options: modules['synapse_to_samplesheet']    )
+include { SYNAPSE_METADATA_MAPPING  } from '../modules/local/synapse_metadata_mapping'  addParams( options: modules['synapse_metadata_mapping']  )
+include { SYNAPSE_MERGE_SAMPLESHEET } from '../modules/local/synapse_merge_samplesheet' addParams( options: modules['synapse_merge_samplesheet'] )
+
+/*
+========================================================================================
+    IMPORT NF-CORE MODULES/SUBWORKFLOWS
+========================================================================================
+*/
+
+include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main' addParams( options: [publish_files : ['_versions.yml':'']] )
 
 /*
 ========================================================================================
@@ -50,51 +53,58 @@ include { GET_SOFTWARE_VERSIONS      } from '../modules/local/get_software_versi
 
 workflow SYNAPSE {
 
-    ch_software_versions = Channel.empty()
-
-    // CHANNEL: Stage Synapse Config File
-    ch_synapseConfig        = file( params.synapse_config )
+    ch_versions = Channel.empty()
 
-    // MODULE: Get individual FastQ SynapseIDs from Directory SynapseID(s)
+    //
+    // MODULE: Get individual FastQ synapse ids from directory based synapse ids
+    //
     SYNAPSE_LIST (
         ch_ids,
-        ch_synapseConfig
+        ch_synapse_config
     )
-    ch_software_versions = ch_software_versions.mix(SYNAPSE_LIST.out.version.first().ifEmpty(null))
+    ch_versions = ch_versions.mix(SYNAPSE_LIST.out.versions.first())
 
-    // CHANNEL: Create channel for FQ SynapseIDs
+    // Create channel for FastQ synapse ids
     SYNAPSE_LIST
         .out
-        .synlist_csv
+        .csv
         .splitCsv(header:false).flatten()
         .set { ch_samples }
 
-    // MODULE: Download FastQ Files by SynapseID
+    //
+    // MODULE: Download FastQs by synapse id
+    //
     SYNAPSE_GET (
         ch_samples,
-        ch_synapseConfig
+        ch_synapse_config
     )
+    ch_versions = ch_versions.mix(SYNAPSE_LIST.out.versions.first())
 
-    // CHANNEL: Create Read Pairs Channel - Creates format [sampleId, [fastq_1, fastq_2]]
+    // Create read pair channel: [ sampleId, [ fastq_1, fastq_2 ] ]
     SYNAPSE_GET
         .out
         .fastq
-        .collect().flatten()
-        .toSortedList().flatten()
+        .collect()
+        .flatten()
+        .toSortedList()
+        .flatten()
         .map { meta ->
-            def sampleId = meta.name.toString().tokenize('_').get(0)
-            [sampleId, meta]
+            def id = meta.name.toString().tokenize('_').get(0)
+            [ id, meta ]
         }
         .groupTuple()
-        .set{ ch_read_pairs }
+        .set { ch_read_pairs }
 
-    // MODULE: Download FQ Metadata by SynapseID
+    //
+    // MODULE: Download FastQ metadata by synapse id
+    //
     SYNAPSE_SHOW (
         ch_samples,
-        ch_synapseConfig
+        ch_synapse_config
     )
+    ch_versions = ch_versions.mix(SYNAPSE_LIST.out.versions.first())
 
-    // CHANNEL: Clean Metadata
+    // Clean metadata in channels
     SYNAPSE_SHOW
         .out
         .metadata
@@ -103,34 +113,34 @@ workflow SYNAPSE {
         .collate( 6 )
         .set { ch_meta }
 
-    // MODULE: Compile Metadata
+    //
+    // MODULE: Compile metadata
+    //
     SYNAPSE_METADATA_MAPPING (
         ch_meta
     )
 
-    // MODULE: Create Samplesheet
+    //
+    // MODULE: Create samplesheet
+    //
     SYNAPSE_TO_SAMPLESHEET (
-        ch_read_pairs,
+        ch_read_pairs
     )
 
-    // MODULE: Merge Samplesheets
+    //
+    // MODULE: Merge samplesheets
+    //
     SYNAPSE_MERGE_SAMPLESHEET (
         SYNAPSE_TO_SAMPLESHEET.out.samplesheet.collect(),
         SYNAPSE_METADATA_MAPPING.out.metasheet.collect()
     )
+    ch_versions = ch_versions.mix(SYNAPSE_LIST.out.versions.first())
 
-    // MODULE: Pipeline reporting
-    ch_software_versions
-        .map { it -> if (it) [ it.baseName, it ] }
-        .groupTuple()
-        .map { it[1][0] }
-        .flatten()
-        .collect()
-        .set { ch_software_versions }
-
-    // MODULE: Get Software Versions
-    GET_SOFTWARE_VERSIONS (
-        ch_software_versions.map { it }.collect()
+    //
+    // MODULE: Dump software versions for all tools used in the workflow
+    //
+    CUSTOM_DUMPSOFTWAREVERSIONS (
+        ch_versions.unique().collectFile(name: 'collated_versions.yml')
     )
 }
 
@@ -145,7 +155,7 @@ workflow.onComplete {
         NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)
     }
     NfcoreTemplate.summary(workflow, params, log)
-    WorkflowFetchngs.curateSamplesheetWarn(log)
+    //WorkflowSynapse.curateSamplesheetWarn(log)
 }
 
 /*

From b2dacad49396b4de6dbc4c836f132b4e86f55255 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 14 Oct 2021 22:28:28 +0100
Subject: [PATCH 079/852] Fix all the thingsgs

---
 .github/workflows/ci.yml                   | 38 +++++-----
 conf/modules.config                        |  8 +-
 lib/WorkflowSynapse.groovy                 | 38 ++++++++++
 modules/local/synapse_get.nf               | 15 ++--
 modules/local/synapse_list.nf              |  7 +-
 modules/local/synapse_merge_samplesheet.nf | 12 +--
 modules/local/synapse_metadata_mapping.nf  | 36 ---------
 modules/local/synapse_show.nf              |  3 +-
 modules/local/synapse_to_samplesheet.nf    | 55 +++++++++-----
 workflows/synapse.nf                       | 87 +++++++++++-----------
 10 files changed, 156 insertions(+), 143 deletions(-)
 create mode 100755 lib/WorkflowSynapse.groovy
 delete mode 100644 modules/local/synapse_metadata_mapping.nf

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 7788b5de..a9c0d4c9 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -39,27 +39,27 @@ jobs:
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker
 
-  test_synapse:
-    name: Test Synapse workflow
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}
-    runs-on: ubuntu-latest
-    env:
-      NXF_VER: ${{ matrix.nxf_ver }}
-      NXF_ANSI_LOG: false
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
+  # test_synapse:
+  #   name: Test Synapse workflow
+  #   if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}
+  #   runs-on: ubuntu-latest
+  #   env:
+  #     NXF_VER: ${{ matrix.nxf_ver }}
+  #     NXF_ANSI_LOG: false
+  #   steps:
+  #     - name: Check out pipeline code
+  #       uses: actions/checkout@v2
 
-      - name: Install Nextflow
-        env:
-          CAPSULE_LOG: none
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+  #     - name: Install Nextflow
+  #       env:
+  #         CAPSULE_LOG: none
+  #       run: |
+  #         wget -qO- get.nextflow.io | bash
+  #         sudo mv nextflow /usr/local/bin/
 
-      - name: Run pipeline with synapse test data
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_synapse,docker
+  #     - name: Run pipeline with synapse test data
+  #       run: |
+  #         nextflow run ${GITHUB_WORKSPACE} -profile test_synapse,docker
 
   parameters:
     name: Test workflow parameters
diff --git a/conf/modules.config b/conf/modules.config
index f3da4f94..0d44e9ee 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -43,18 +43,16 @@ params {
             publish_dir     = 'samplesheet'
         }
         'synapse_list' {
-            publish_dir     = 'synapse'
+            args            = '--long'
+            publish_dir     = 'metadata'
         }
         'synapse_get' {
             publish_dir     = 'fastq'
+            publish_files   = ['fastq.gz':'', 'md5':'md5']
         }
         'synapse_show' {
             publish_dir     = 'metadata'
         }
-        'synapse_metadata_mapping' {
-            publish_dir     = 'metadata'
-            publish_files   = false
-        }
         'synapse_to_samplesheet' {
             publish_dir     = 'samplesheet'
             publish_files   = false
diff --git a/lib/WorkflowSynapse.groovy b/lib/WorkflowSynapse.groovy
new file mode 100755
index 00000000..1ac249a1
--- /dev/null
+++ b/lib/WorkflowSynapse.groovy
@@ -0,0 +1,38 @@
+//
+// This file holds several functions specific to the workflow/synapse.nf in the nf-core/fetchngs pipeline
+//
+
+class WorkflowSynapse {
+
+    //
+    // Convert metadata obtained from the 'synapse show' command to a Groovy map
+    //
+    public static Map synapseShowToMap(synapse_file) {
+        def meta = [:]
+        def category = ''
+        synapse_file.eachLine { line ->
+            def entries = [null, null]
+            if (!line.startsWith(' ') && !line.trim().isEmpty()) {
+                category = line.tokenize(':')[0]
+            } else {
+                entries = line.trim().tokenize('=')
+            }
+            meta["${category}|${entries[0]}"] = entries[1]
+        }
+        meta.id = meta['properties|id']
+        meta.md5 = meta['File|md5']
+        return meta.findAll{ it.value != null }
+    }
+
+    //
+    // Print a warning after pipeline has completed
+    //
+    public static void curateSamplesheetWarn(log) {
+        log.warn "=============================================================================\n" +
+            "  Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" +
+            "  Where applicable, default values will be used for sample-specific metadata\n" +
+            "  such as strandedness, controls etc as this information is not provided\n" +
+            "  in a standardised manner when uploading data to Synapse.\n" +
+            "==================================================================================="
+    }
+}
diff --git a/modules/local/synapse_get.nf b/modules/local/synapse_get.nf
index 1581d41a..3f4d0655 100644
--- a/modules/local/synapse_get.nf
+++ b/modules/local/synapse_get.nf
@@ -5,8 +5,9 @@ params.options = [:]
 options        = initOptions(params.options)
 
 process SYNAPSE_GET {
-    tag "$id"
+    tag "$meta.id"
     label 'process_low'
+    label 'error_retry'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
@@ -19,12 +20,13 @@ process SYNAPSE_GET {
     }
 
     input:
-    val id
+    val meta
     path config
 
     output:
-    path "*.fastq.gz"  , emit: fastq
-    path "versions.yml", emit: versions
+    tuple val(meta), path("*.fastq.gz"), emit: fastq
+    tuple val(meta), path("*md5")      , emit: md5
+    path "versions.yml"                , emit: versions
 
     script:
     """
@@ -32,7 +34,10 @@ process SYNAPSE_GET {
         -c $config \\
         get \\
         $options.args \\
-        $id \\
+        $meta.id
+
+    find ./ -type f -name "*.fastq.gz" -exec echo "${meta.md5} " {} \\; > ${meta.id}.md5
+    md5sum -c ${meta.id}.md5
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
diff --git a/modules/local/synapse_list.nf b/modules/local/synapse_list.nf
index 367d1e16..20275de2 100644
--- a/modules/local/synapse_list.nf
+++ b/modules/local/synapse_list.nf
@@ -23,7 +23,7 @@ process SYNAPSE_LIST {
     path config
 
     output:
-    path "*.csv"       , emit: csv
+    path "*.txt"       , emit: txt
     path "versions.yml", emit: versions
 
     script:
@@ -32,8 +32,9 @@ process SYNAPSE_LIST {
         -c $config \\
         list \\
         $options.args \\
-        -l $id \\
-        | cut -c-11 > ${id}.synlist.csv
+        $id \\
+        $options.args2 \\
+        > ${id}.list.txt
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
diff --git a/modules/local/synapse_merge_samplesheet.nf b/modules/local/synapse_merge_samplesheet.nf
index f634118b..8027818c 100644
--- a/modules/local/synapse_merge_samplesheet.nf
+++ b/modules/local/synapse_merge_samplesheet.nf
@@ -1,12 +1,9 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+include { saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
-options        = initOptions(params.options)
 
 process SYNAPSE_MERGE_SAMPLESHEET {
-    tag 'merge_samplesheet'
-    label 'process_low'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
@@ -20,11 +17,9 @@ process SYNAPSE_MERGE_SAMPLESHEET {
 
     input:
     path ('samplesheets/*')
-    path ('metasheet/*')
 
     output:
     path "samplesheet.csv", emit: samplesheet
-    path "metasheet.csv"  , emit: metasheet
     path "versions.yml"   , emit: versions
 
     script:
@@ -34,11 +29,6 @@ process SYNAPSE_MERGE_SAMPLESHEET {
         awk 'NR>1' \$fileid >> samplesheet.csv
     done
 
-    head -n 1 `ls ./metasheet/* | head -n 1` > metasheet.csv
-    for fileid in `ls ./metasheet/*`; do
-        awk 'NR>1' \$fileid >> metasheet.csv
-    done
-
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
         sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
diff --git a/modules/local/synapse_metadata_mapping.nf b/modules/local/synapse_metadata_mapping.nf
deleted file mode 100644
index a513da09..00000000
--- a/modules/local/synapse_metadata_mapping.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
-process SYNAPSE_METADATA_MAPPING {
-    tag "${data[3]}"
-    label 'process_low'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
-
-    input:
-    val data
-
-    output:
-    path "*.csv", emit: metasheet
-
-    exec:
-    meta_map = [
-        md5         : "${data[0]}",
-        fileSize    : "${data[1]}",
-        etag        : "${data[2]}",
-        id          : "${data[3]}",
-        fileName    : "${data[4]}",
-        fileVersion : "${data[5]}"
-    ]
-
-    // Create Metadata Sheet
-    metasheet  = meta_map.keySet().collect{ '"' + it + '"'}.join(",") + '\n'
-    metasheet += meta_map.values().collect{ '"' + it + '"'}.join(",")
-
-    def metasheet_file = task.workDir.resolve("${meta_map.id}.metasheet.csv")
-    metasheet_file.text = metasheet
-}
diff --git a/modules/local/synapse_show.nf b/modules/local/synapse_show.nf
index 51bb5420..4edc4207 100644
--- a/modules/local/synapse_show.nf
+++ b/modules/local/synapse_show.nf
@@ -33,7 +33,8 @@ process SYNAPSE_SHOW {
         show \\
         $options.args \\
         $id \\
-        | sed -n '1,3p;15,16p;20p;23p' > ${id}.metadata.txt
+        $options.args2 \\
+        > ${id}.metadata.txt
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
diff --git a/modules/local/synapse_to_samplesheet.nf b/modules/local/synapse_to_samplesheet.nf
index 7b301ddf..28571005 100644
--- a/modules/local/synapse_to_samplesheet.nf
+++ b/modules/local/synapse_to_samplesheet.nf
@@ -1,38 +1,57 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { saveFiles; getSoftwareName } from './functions'
 
-params.options = [:]
-options        = initOptions(params.options)
+params.options     = [:]
+params.results_dir = ''
 
 process SYNAPSE_TO_SAMPLESHEET {
-    tag "$id"
-    label 'process_low'
+    tag "$meta.id"
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    memory 100.MB
 
     input:
-    tuple val(id), val(files)
+    tuple val(meta), path(fastq)
+    val pipeline
 
     output:
-    path "*.csv", emit: samplesheet
+    tuple val(meta), path("*.csv"), emit: samplesheet
 
     exec:
 
-    // Add fields to the beginning of the map
+    //  Remove custom keys
+    def meta_map = meta.clone()
+    meta_map.remove("id")
+
+    def fastq_1 = "${params.outdir}/${params.results_dir}/${fastq}"
+    def fastq_2 = ''
+    if (fastq instanceof List && fastq.size() == 2) {
+        fastq_1 = "${params.outdir}/${params.results_dir}/${fastq[0]}"
+        fastq_2 = "${params.outdir}/${params.results_dir}/${fastq[1]}"
+    }
+
+    // Add relevant fields to the beginning of the map
     pipeline_map = [
-        sample  : "${id}",
-        fastq_1 : "${params.outdir}/fastq/${files[0]}",
-        fastq_2 : "${params.outdir}/fastq/${files[1]}"
+        sample  : "${meta.id}",
+        fastq_1 : fastq_1,
+        fastq_2 : fastq_2
     ]
-    // Add Strandedness
-    pipeline_map << [ strandedness: "unstranded" ]
 
-    // Create Samplesheet
+    // Add nf-core pipeline specific entries
+    if (pipeline) {
+        if (pipeline == 'rnaseq') {
+            pipeline_map << [ strandedness: 'unstranded' ]
+        }
+    }
+    pipeline_map << meta_map
+
+    // Create a samplesheet
     samplesheet  = pipeline_map.keySet().collect{ '"' + it + '"'}.join(",") + '\n'
     samplesheet += pipeline_map.values().collect{ '"' + it + '"'}.join(",")
 
-    def samplesheet_file2 = task.workDir.resolve("${pipeline_map.sample}.samplesheet.csv")
-    samplesheet_file2.text = samplesheet
-
+    // Write samplesheet to file
+    def samplesheet_file = task.workDir.resolve("${meta.id}.samplesheet.csv")
+    samplesheet_file.text = samplesheet
 }
diff --git a/workflows/synapse.nf b/workflows/synapse.nf
index 93f281e7..3d993789 100644
--- a/workflows/synapse.nf
+++ b/workflows/synapse.nf
@@ -31,10 +31,9 @@ if (params.synapse_config) {
 def modules = params.modules.clone()
 
 include { SYNAPSE_LIST              } from '../modules/local/synapse_list'              addParams( options: modules['synapse_list']              )
-include { SYNAPSE_GET               } from '../modules/local/synapse_get'               addParams( options: modules['synapse_get']               )
 include { SYNAPSE_SHOW              } from '../modules/local/synapse_show'              addParams( options: modules['synapse_show']              )
-include { SYNAPSE_TO_SAMPLESHEET    } from '../modules/local/synapse_to_samplesheet'    addParams( options: modules['synapse_to_samplesheet']    )
-include { SYNAPSE_METADATA_MAPPING  } from '../modules/local/synapse_metadata_mapping'  addParams( options: modules['synapse_metadata_mapping']  )
+include { SYNAPSE_GET               } from '../modules/local/synapse_get'               addParams( options: modules['synapse_get']               )
+include { SYNAPSE_TO_SAMPLESHEET    } from '../modules/local/synapse_to_samplesheet'    addParams( options: modules['synapse_to_samplesheet'], results_dir: modules['synapse_get'].publish_dir )
 include { SYNAPSE_MERGE_SAMPLESHEET } from '../modules/local/synapse_merge_samplesheet' addParams( options: modules['synapse_merge_samplesheet'] )
 
 /*
@@ -56,7 +55,7 @@ workflow SYNAPSE {
     ch_versions = Channel.empty()
 
     //
-    // MODULE: Get individual FastQ synapse ids from directory based synapse ids
+    // MODULE: Expand synapse ids for individual FastQ files
     //
     SYNAPSE_LIST (
         ch_ids,
@@ -67,74 +66,72 @@ workflow SYNAPSE {
     // Create channel for FastQ synapse ids
     SYNAPSE_LIST
         .out
-        .csv
-        .splitCsv(header:false).flatten()
+        .txt
+        .splitCsv(header:false, sep:' ')
+        .map { it[0] }
+        .unique()
         .set { ch_samples }
 
     //
-    // MODULE: Download FastQs by synapse id
+    // MODULE: Download metadata for each synapse id
     //
-    SYNAPSE_GET (
+    SYNAPSE_SHOW (
         ch_samples,
         ch_synapse_config
     )
-    ch_versions = ch_versions.mix(SYNAPSE_LIST.out.versions.first())
+    ch_versions = ch_versions.mix(SYNAPSE_SHOW.out.versions.first())
 
-    // Create read pair channel: [ sampleId, [ fastq_1, fastq_2 ] ]
-    SYNAPSE_GET
+    // Get metadata into channels
+    SYNAPSE_SHOW
         .out
-        .fastq
-        .collect()
-        .flatten()
-        .toSortedList()
-        .flatten()
-        .map { meta ->
-            def id = meta.name.toString().tokenize('_').get(0)
-            [ id, meta ]
-        }
-        .groupTuple()
-        .set { ch_read_pairs }
+        .metadata
+        .map { it -> WorkflowSynapse.synapseShowToMap(it) }
+        .set { ch_samples_meta }
 
     //
-    // MODULE: Download FastQ metadata by synapse id
+    // MODULE: Download FastQs by synapse id
     //
-    SYNAPSE_SHOW (
-        ch_samples,
+    SYNAPSE_GET (
+        ch_samples_meta,
         ch_synapse_config
     )
-    ch_versions = ch_versions.mix(SYNAPSE_LIST.out.versions.first())
+    ch_versions = ch_versions.mix(SYNAPSE_GET.out.versions.first())
 
-    // Clean metadata in channels
-    SYNAPSE_SHOW
+    // Combine channels for PE/SE FastQs: [ [ id:SRR6357070, synapse_ids:syn26240474;syn26240477 ], [ fastq_1, fastq_2 ] ]
+    SYNAPSE_GET
         .out
-        .metadata
-        .splitCsv(strip:true, sep:"=", skip:1)
-        .map { it[1] }
-        .collate( 6 )
-        .set { ch_meta }
+        .fastq
+        .map { meta, fastq -> [ fastq.baseName.tokenize('_')[0], fastq ] }
+        .groupTuple(sort: { it -> it.baseName })
+        .set { ch_fastq }
 
-    //
-    // MODULE: Compile metadata
-    //
-    SYNAPSE_METADATA_MAPPING (
-        ch_meta
-    )
+    SYNAPSE_GET
+        .out
+        .fastq
+        .map { meta, fastq -> [ fastq.baseName.tokenize('_')[0], meta.id ] }
+        .groupTuple()
+        .join(ch_fastq)
+        .map { id, synids, fastq ->
+            def meta = [ id:id, synapse_ids:synids.join(';') ]
+            [ meta, fastq ]
+        }
+        .set { ch_fastq }
 
     //
-    // MODULE: Create samplesheet
+    // MODULE: Create samplesheet per sample
     //
     SYNAPSE_TO_SAMPLESHEET (
-        ch_read_pairs
+        ch_fastq,
+        params.nf_core_pipeline ?: ''
     )
 
     //
     // MODULE: Merge samplesheets
     //
     SYNAPSE_MERGE_SAMPLESHEET (
-        SYNAPSE_TO_SAMPLESHEET.out.samplesheet.collect(),
-        SYNAPSE_METADATA_MAPPING.out.metasheet.collect()
+        SYNAPSE_TO_SAMPLESHEET.out.samplesheet.collect{ it[1] }
     )
-    ch_versions = ch_versions.mix(SYNAPSE_LIST.out.versions.first())
+    ch_versions = ch_versions.mix(SYNAPSE_MERGE_SAMPLESHEET.out.versions)
 
     //
     // MODULE: Dump software versions for all tools used in the workflow
@@ -155,7 +152,7 @@ workflow.onComplete {
         NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)
     }
     NfcoreTemplate.summary(workflow, params, log)
-    //WorkflowSynapse.curateSamplesheetWarn(log)
+    WorkflowSynapse.curateSamplesheetWarn(log)
 }
 
 /*

From 82b68e1e95faf8961616d4933f900a1ec1ef8a28 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 14 Oct 2021 22:31:38 +0100
Subject: [PATCH 080/852] Add meta entries to saveAs

---
 modules/local/synapse_get.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/synapse_get.nf b/modules/local/synapse_get.nf
index 3f4d0655..1e959296 100644
--- a/modules/local/synapse_get.nf
+++ b/modules/local/synapse_get.nf
@@ -10,7 +10,7 @@ process SYNAPSE_GET {
     label 'error_retry'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::synapseclient=2.4.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

From 968f2fc9380153c87e8b5263c5cf5912267194d3 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 14 Oct 2021 22:35:39 +0100
Subject: [PATCH 081/852] Update CHANGELOG

---
 CHANGELOG.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0cc2d511..9e9a0cb2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,8 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
-* Handle identifiers that do **not** return metadata, for example, due to being private.
-
+* Added a workflow to download FastQ files and to create samplesheets for ids from the [Synapse platform](https://www.synapse.org/) hosted by [Sage Bionetworks](https://sagebionetworks.org/).
+* Handle SRA identifiers that do **not** return metadata, for example, due to being private.
 * Added support for [DDBJ ids](https://www.ddbj.nig.ac.jp/index-e.html). See examples below:
 
 | `DDBJ`        |

From 87fa87e1496ee28a53ac751f65272cd3d89d4de0 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 14 Oct 2021 22:37:41 +0100
Subject: [PATCH 082/852] Remove Synapse CI

---
 .github/workflows/ci.yml | 22 ----------------------
 1 file changed, 22 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index a9c0d4c9..08ac1cfb 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -39,28 +39,6 @@ jobs:
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker
 
-  # test_synapse:
-  #   name: Test Synapse workflow
-  #   if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}
-  #   runs-on: ubuntu-latest
-  #   env:
-  #     NXF_VER: ${{ matrix.nxf_ver }}
-  #     NXF_ANSI_LOG: false
-  #   steps:
-  #     - name: Check out pipeline code
-  #       uses: actions/checkout@v2
-
-  #     - name: Install Nextflow
-  #       env:
-  #         CAPSULE_LOG: none
-  #       run: |
-  #         wget -qO- get.nextflow.io | bash
-  #         sudo mv nextflow /usr/local/bin/
-
-  #     - name: Run pipeline with synapse test data
-  #       run: |
-  #         nextflow run ${GITHUB_WORKSPACE} -profile test_synapse,docker
-
   parameters:
     name: Test workflow parameters
     if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}

From 4093bba59aa7ab00696fa799037f1563f3a76a2b Mon Sep 17 00:00:00 2001
From: Daisy Wenyan Han <60151111+daisyhan97@users.noreply.github.com>
Date: Fri, 15 Oct 2021 12:47:29 -0700
Subject: [PATCH 083/852] Update Docs

---
 CITATIONS.md   |  3 +++
 README.md      |  8 ++++----
 docs/output.md | 10 +++++-----
 docs/usage.md  | 20 +++++++++++---------
 4 files changed, 23 insertions(+), 18 deletions(-)

diff --git a/CITATIONS.md b/CITATIONS.md
index 4a1f2752..01819d3e 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -28,6 +28,9 @@
 * [GEO](https://pubmed.ncbi.nlm.nih.gov/23193258/)
     > Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A. NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5. doi: 10.1093/nar/gks1193. Epub 2012 Nov 27. PubMed PMID: 23193258; PubMed Central PMCID: PMC3531084.
 
+* [Synapse](https://pubmed.ncbi.nlm.nih.gov/24071850/)
+    > Omberg L, Ellrott K, Yuan Y, Kandoth C, Wong C, Kellen MR, Friend SH, Stuart J, Liang H, Margolin AA. Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas. Nat Genet. 2013 Oct;45(10):1121-6. doi: 10.1038/ng.2761. PMID: 24071850; PMCID: PMC3950337.
+
 ## Software packaging/containerisation tools
 
 * [Anaconda](https://anaconda.com)
diff --git a/README.md b/README.md
index e378eacc..cb60455e 100644
--- a/README.md
+++ b/README.md
@@ -16,7 +16,7 @@
 
 ## Introduction
 
-**nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from public databases. At present, the pipeline supports SRA / ENA / DDBJ / GEO ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)).
+**nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from public databases. At present, the pipeline supports [SRA](https://www.ncbi.nlm.nih.gov/sra) / [ENA](https://www.ebi.ac.uk/ena/browser/home) / [DDBJ](https://www.ddbj.nig.ac.jp/index-e.html) / [GEO](https://www.ncbi.nlm.nih.gov/geo/) / [Synapse](https://www.synapse.org/#) ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)).
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.
 
@@ -26,9 +26,9 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 Via a single file of ids, provided one-per-line (see [example input file](https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/public_database_ids.txt)) the pipeline performs the following steps:
 
-1. Resolve database ids back to appropriate experiment-level ids and to be compatible with the [ENA API](https://ena-docs.readthedocs.io/en/latest/retrieval/programmatic-access.html)
-2. Fetch extensive id metadata including direct download links to FastQ files via ENA API
-3. Download FastQ files in parallel via `curl` and perform `md5sum` check
+1. Resolve database ids back to appropriate experiment-level ids and to be compatible with the [ENA API](https://ena-docs.readthedocs.io/en/latest/retrieval/programmatic-access.html), or appropriate database
+2. Fetch extensive id metadata including direct download links to FastQ files via ENA API or appropriate database
+3. Download FastQ files in parallel and perform `md5sum` check
 4. Collate id metadata and paths to FastQ files in a single samplesheet
 
 The columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core.
diff --git a/docs/output.md b/docs/output.md
index 4ffc507e..167c1f69 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -8,7 +8,7 @@ This document describes the output produced by the pipeline. The directories lis
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
-* [FastQ download](#fastq-download) - Download FastQ files via SRA / ENA / DDBJ / GEO ids
+* [FastQ download](#fastq-download) - Download FastQ files via SRA / ENA / DDBJ / GEO / Synapse ids
 * [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
 ### FastQ download
@@ -19,18 +19,18 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 * `fastq/`
     * `*.fastq.gz`: Paired-end/single-end reads downloaded from the SRA / ENA / DDBJ / GEO.
 * `fastq/md5/`
-    * `*.md5`: Files containing `md5` sum for FastQ files downloaded from the ENA.
+    * `*.md5`: Files containing `md5` sum for FastQ files downloaded from the ENA or appropriate database.
 * `samplesheet/`
     * `samplesheet.csv`: Auto-created samplesheet with collated metadata and paths to downloaded FastQ files.
     * `id_mappings.csv`: File with selected fields that can be used to rename samples to more informative names; see [`--sample_mapping_fields`](https://nf-co.re/fetchngs/parameters#sample_mapping_fields) parameter to customise this behaviour.
     * `multiqc_config.yml`: [MultiQC](https://multiqc.info/docs/#bulk-sample-renaming) config file that can be passed to most nf-core pipelines via the `--multiqc_config` parameter for bulk renaming of sample names from database ids; [`--sample_mapping_fields`](https://nf-co.re/fetchngs/parameters#sample_mapping_fields) parameter to customise this behaviour.
 * `metadata/`
-    * `*.runinfo_ftp.tsv`: Re-formatted metadata file downloaded from the ENA.
-    * `*.runinfo.tsv`: Original metadata file downloaded from the ENA.
+    * `*.runinfo_ftp.tsv`: Re-formatted metadata file downloaded from the ENA or appropriate database.
+    * `*.runinfo.tsv`: Original metadata file downloaded from the ENA or appropriate database.
 
 </details>
 
-Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introduction) for a list of supported public repository identifiers and how to provide them to the pipeline. The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5sums. If download links exist, the files will be downloaded in parallel by FTP otherwise they will NOT be downloaded. This is intentional because the tools such as `parallel-fastq-dump`, `fasterq-dump`, `prefetch` etc require pre-existing configuration files in the users home directory which makes automation tricky across different platforms and containerisation.
+Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introduction) for a list of supported public repository identifiers and how to provide them to the pipeline. The final sample information for `SRA`, `GEO`, `DDBJ`, and `ENA` identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5sums. If download links exist, the files will be downloaded in parallel by FTP otherwise they will NOT be downloaded. This is intentional because the tools such as `parallel-fastq-dump`, `fasterq-dump`, `prefetch` etc require pre-existing configuration files in the users home directory which makes automation tricky across different platforms and containerisation. Sample information for `Synapse` identifiers are downloaded in parallel directly from the [Synapse](https://www.synapse.org/#) platform. A [configuration file](http://python-docs.synapse.org/build/html/Credentials.html#use-synapseconfig) containing valid login credentials is required for Synapse downloads.
 
 ### Pipeline information
 
diff --git a/docs/usage.md b/docs/usage.md
index 1e6066db..e1a096f4 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -8,20 +8,22 @@
 
 The pipeline has been set-up to automatically download and process the raw FastQ files from public repositories. Identifiers can be provided in a file, one-per-line via the `--input` parameter. Currently, the following types of example identifiers are supported:
 
-| `SRA`        | `ENA`        | `DDBJ`       | `GEO`      |
-|--------------|--------------|--------------|------------|
-| SRR11605097  | ERR4007730   | DRR171822    | GSM4432381 |
-| SRX8171613   | ERX4009132   | DRX162434    | GSE147507  |
-| SRS6531847   | ERS4399630   | DRS090921    |            |
-| SAMN14689442 | SAMEA6638373 | SAMD00114846 |            |
-| SRP256957    | ERP120836    | DRP004793    |            |
-| SRA1068758   | ERA2420837   | DRA008156    |            |
-| PRJNA625551  | PRJEB37513   | PRJDB4176    |            |
+| `SRA`        | `ENA`        | `DDBJ`       | `GEO`      | `Synapse`   |
+|--------------|--------------|--------------|------------|-------------|
+| SRR11605097  | ERR4007730   | DRR171822    | GSM4432381 | syn26240435 |
+| SRX8171613   | ERX4009132   | DRX162434    | GSE147507  |             |
+| SRS6531847   | ERS4399630   | DRS090921    |            |             |
+| SAMN14689442 | SAMEA6638373 | SAMD00114846 |            |             |
+| SRP256957    | ERP120836    | DRP004793    |            |             |
+| SRA1068758   | ERA2420837   | DRA008156    |            |             |
+| PRJNA625551  | PRJEB37513   | PRJDB4176    |            |             |
 
 If `SRR`/`ERR`/`DRR` run ids are provided then these will be resolved back to their appropriate `SRX`/`ERX`/`DRX` ids to be able to merge multiple runs from the same experiment. This is conceptually the same as merging multiple libraries sequenced from the same sample.
 
 The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5 sums. If download links exist, the files will be downloaded in parallel by FTP otherwise they will NOT be downloaded. This is intentional because tools such as `parallel-fastq-dump`, `fasterq-dump`, `prefetch` etc require pre-existing configuration files in the users home directory which makes automation tricky across different platforms and containerisation. We may add this functionality in later releases.
 
+To download data from `Synapse`, the SynapseID of the directory containing all files to be downloaded should be provided. The directory ID will then be resolved to the SynapseIDs of the corresponding FastQ files, which are then downloaded in parellel using the `synapse get` command. In order to download data from Synapse, an account must be created and a user configuration file provided via the parameter `--synapse_config`. All Synapse metadata, annotations and provenance are also downloaded using the `synapse show` command, and are outputted to a separate metadata file. By default, only the md5sums, file sizes, etags, Synapse IDs, file names, and file versions are shown.
+
 As a bonus, the columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core. It is highly recommended that you double-check that all of the identifiers you defined using `--input` are represented in the samplesheet. Also, public databases don't reliably hold information such as strandedness information so you may need to amend these entries too if for example your samplesheet was created by providing `--nf_core_pipeline rnaseq`.
 
 All of the sample metadata obtained from the ENA will be appended as additional columns to help you manually curate the samplesheet before you run the pipeline. You can customise the metadata fields that are appended to the samplesheet via the `--ena_metadata_fields` parameter. The default list of fields used by the pipeline can be found at the top of the [`bin/sra_ids_to_runinfo.py`](https://github.com/nf-core/fetchngs/blob/master/bin/sra_ids_to_runinfo.py) script within the pipeline repo. However, this pipeline requires a minimal set of fields to download FastQ files i.e. `'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'`. A comprehensive list of accepted metadata fields can be obtained from the [ENA API](https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run]).

From c2029b3f8a704175a0d4b1ef4b41fcf43bd483cf Mon Sep 17 00:00:00 2001
From: Daisy Wenyan Han <60151111+daisyhan97@users.noreply.github.com>
Date: Fri, 15 Oct 2021 12:48:24 -0700
Subject: [PATCH 084/852] Add RegEx for SampleIDs

---
 lib/WorkflowSynapse.groovy | 53 ++++++++++++++++++++++++++++++++++++++
 workflows/synapse.nf       |  4 +--
 2 files changed, 55 insertions(+), 2 deletions(-)

diff --git a/lib/WorkflowSynapse.groovy b/lib/WorkflowSynapse.groovy
index 1ac249a1..d36d1e55 100755
--- a/lib/WorkflowSynapse.groovy
+++ b/lib/WorkflowSynapse.groovy
@@ -35,4 +35,57 @@ class WorkflowSynapse {
             "  in a standardised manner when uploading data to Synapse.\n" +
             "==================================================================================="
     }
+
+    //
+    // Obtain Sample ID from File Name
+    //
+    public static String getSampleID(input_file, pattern) {
+
+        def sampleids = ""
+
+        def filePattern = pattern.toString()
+        int p = filePattern.lastIndexOf('/')
+            if( p != -1 )
+                filePattern = filePattern.substring(p+1)
+
+        input_file.each {
+            String fileName = input_file.getFileName().toString()
+
+            String indexOfWildcards = filePattern.findIndexOf { it=='*' || it=='?' }
+            String indexOfBrackets = filePattern.findIndexOf { it=='{' || it=='[' }
+            if( indexOfWildcards==-1 && indexOfBrackets==-1 ) {
+                if( fileName == filePattern )
+                    return actual.getSimpleName()
+                throw new IllegalArgumentException("Not a valid file pair globbing pattern: pattern=$filePattern file=$fileName")
+            }
+
+            int groupCount = 0
+            for( int i=0; i<filePattern.size(); i++ ) {
+                def ch = filePattern[i]
+                if( ch=='?' || ch=='*' )
+                    groupCount++
+                else if( ch=='{' || ch=='[' )
+                    break
+            }
+
+            def regex = filePattern
+                    .replace('.','\\.')
+                    .replace('*','(.*)')
+                    .replace('?','(.?)')
+                    .replace('{','(?:')
+                    .replace('}',')')
+                    .replace(',','|')
+
+            def matcher = (fileName =~ /$regex/)
+            if( matcher.matches() ) {
+                int c=Math.min(groupCount, matcher.groupCount())
+                int end = c ? matcher.end(c) : ( indexOfBrackets != -1 ? indexOfBrackets : fileName.size() )
+                def prefix = fileName.substring(0,end)
+                while(prefix.endsWith('-') || prefix.endsWith('_') || prefix.endsWith('.') )
+                    prefix=prefix[0..-2]
+                sampleids = prefix
+            }
+        }
+        return sampleids
+    }
 }
diff --git a/workflows/synapse.nf b/workflows/synapse.nf
index 3d993789..1f535f60 100644
--- a/workflows/synapse.nf
+++ b/workflows/synapse.nf
@@ -101,14 +101,14 @@ workflow SYNAPSE {
     SYNAPSE_GET
         .out
         .fastq
-        .map { meta, fastq -> [ fastq.baseName.tokenize('_')[0], fastq ] }
+        .map { meta, fastq -> [ WorkflowSynapse.getSampleID( fastq , "*{1,2}*"), fastq ] }
         .groupTuple(sort: { it -> it.baseName })
         .set { ch_fastq }
 
     SYNAPSE_GET
         .out
         .fastq
-        .map { meta, fastq -> [ fastq.baseName.tokenize('_')[0], meta.id ] }
+        .map { meta, fastq -> [ WorkflowSynapse.getSampleID( fastq , "*{1,2}*"), meta.id ] }
         .groupTuple()
         .join(ch_fastq)
         .map { id, synids, fastq ->

From 6a4ae0aca6f266cb013140a789eefe831a4ffc2f Mon Sep 17 00:00:00 2001
From: Daisy Wenyan Han <60151111+daisyhan97@users.noreply.github.com>
Date: Mon, 18 Oct 2021 16:06:28 -0700
Subject: [PATCH 085/852] Separate SRA/Synapse Docs

---
 README.md      | 16 ++++++++++++----
 docs/output.md | 51 ++++++++++++++++++++++++++++++++++++++++++++------
 docs/usage.md  | 33 ++++++++++++++++++++++++++------
 3 files changed, 84 insertions(+), 16 deletions(-)

diff --git a/README.md b/README.md
index cb60455e..889d4a87 100644
--- a/README.md
+++ b/README.md
@@ -16,7 +16,7 @@
 
 ## Introduction
 
-**nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from public databases. At present, the pipeline supports [SRA](https://www.ncbi.nlm.nih.gov/sra) / [ENA](https://www.ebi.ac.uk/ena/browser/home) / [DDBJ](https://www.ddbj.nig.ac.jp/index-e.html) / [GEO](https://www.ncbi.nlm.nih.gov/geo/) / [Synapse](https://www.synapse.org/#) ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)).
+**nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from both public and private databases. At present, the pipeline supports SRA / ENA / DDBJ / GEO / Synapse ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)). 
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.
 
@@ -26,11 +26,19 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 Via a single file of ids, provided one-per-line (see [example input file](https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/public_database_ids.txt)) the pipeline performs the following steps:
 
-1. Resolve database ids back to appropriate experiment-level ids and to be compatible with the [ENA API](https://ena-docs.readthedocs.io/en/latest/retrieval/programmatic-access.html), or appropriate database
-2. Fetch extensive id metadata including direct download links to FastQ files via ENA API or appropriate database
-3. Download FastQ files in parallel and perform `md5sum` check
+**SRA / ENA / DDBJ / GEO Identifiers**
+1. Resolve database ids back to appropriate experiment-level ids and to be compatible with the [ENA API](https://ena-docs.readthedocs.io/en/latest/retrieval/programmatic-access.html)
+2. Fetch extensive id metadata including direct download links to FastQ files via ENA API
+3. Download FastQ files in parallel via `curl` and perform `md5sum` check
 4. Collate id metadata and paths to FastQ files in a single samplesheet
 
+**Synapse Identifiers**
+1. Resolve Synapse directory SynapseIDs to the SynapseIDs of the FastQ files contained, using the `synapse list` command.
+2. Retrieve FastQ file metadata including FastQ file names, md5sums, etags, annotations, and data provenance via the `synapse show` command.
+3. Download FastQ files in parallel via `synapse get` and perform `md5sum` check
+4. Collate paths to FastQ files in a single samplesheet
+
+**Samplesheet Generation**
 The columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core.
 
 ## Quick Start
diff --git a/docs/output.md b/docs/output.md
index 167c1f69..acc1d956 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -4,11 +4,11 @@
 
 This document describes the output produced by the pipeline. The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.
 
-## Pipeline overview
+## SRA / ENA / DDBJ / GEO - Pipeline Overview
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
-* [FastQ download](#fastq-download) - Download FastQ files via SRA / ENA / DDBJ / GEO / Synapse ids
+* [FastQ download](#fastq-download) - Download FastQ files via SRA / ENA / DDBJ / GEO ids
 * [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
 ### FastQ download
@@ -19,18 +19,18 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 * `fastq/`
     * `*.fastq.gz`: Paired-end/single-end reads downloaded from the SRA / ENA / DDBJ / GEO.
 * `fastq/md5/`
-    * `*.md5`: Files containing `md5` sum for FastQ files downloaded from the ENA or appropriate database.
+    * `*.md5`: Files containing `md5` sum for FastQ files downloaded from the ENA.
 * `samplesheet/`
     * `samplesheet.csv`: Auto-created samplesheet with collated metadata and paths to downloaded FastQ files.
     * `id_mappings.csv`: File with selected fields that can be used to rename samples to more informative names; see [`--sample_mapping_fields`](https://nf-co.re/fetchngs/parameters#sample_mapping_fields) parameter to customise this behaviour.
     * `multiqc_config.yml`: [MultiQC](https://multiqc.info/docs/#bulk-sample-renaming) config file that can be passed to most nf-core pipelines via the `--multiqc_config` parameter for bulk renaming of sample names from database ids; [`--sample_mapping_fields`](https://nf-co.re/fetchngs/parameters#sample_mapping_fields) parameter to customise this behaviour.
 * `metadata/`
-    * `*.runinfo_ftp.tsv`: Re-formatted metadata file downloaded from the ENA or appropriate database.
-    * `*.runinfo.tsv`: Original metadata file downloaded from the ENA or appropriate database.
+    * `*.runinfo_ftp.tsv`: Re-formatted metadata file downloaded from the ENA.
+    * `*.runinfo.tsv`: Original metadata file downloaded from the ENA.
 
 </details>
 
-Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introduction) for a list of supported public repository identifiers and how to provide them to the pipeline. The final sample information for `SRA`, `GEO`, `DDBJ`, and `ENA` identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5sums. If download links exist, the files will be downloaded in parallel by FTP otherwise they will NOT be downloaded. This is intentional because the tools such as `parallel-fastq-dump`, `fasterq-dump`, `prefetch` etc require pre-existing configuration files in the users home directory which makes automation tricky across different platforms and containerisation. Sample information for `Synapse` identifiers are downloaded in parallel directly from the [Synapse](https://www.synapse.org/#) platform. A [configuration file](http://python-docs.synapse.org/build/html/Credentials.html#use-synapseconfig) containing valid login credentials is required for Synapse downloads.
+Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introduction) for a list of supported public repository identifiers and how to provide them to the pipeline. The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5sums. If download links exist, the files will be downloaded in parallel by FTP otherwise they will NOT be downloaded. This is intentional because the tools such as `parallel-fastq-dump`, `fasterq-dump`, `prefetch` etc require pre-existing configuration files in the users home directory which makes automation tricky across different platforms and containerisation.
 
 ### Pipeline information
 
@@ -43,4 +43,43 @@ Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introductio
 
 </details>
 
+## Synapse - Pipeline Overview
+
+The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
+
+* [FastQ download](#fastq-Download) - Download FastQ files via Synapse ids
+* [Pipeline information](#pipeline-Information) - Report metrics generated during the workflow execution
+
+### FastQ Download
+
+<details markdown="1">
+<summary>Output files</summary>
+
+* `fastq/`
+    * `*.fastq.gz`: Paired-end/single-end reads downloaded from Synapse.
+* `fastq/md5/`
+    * `*.md5`: Files containing `md5` sum for FastQ files downloaded from the Synapse platform.
+* `samplesheet/`
+    * `samplesheet.csv`: Auto-created samplesheet with collated metadata and paths to downloaded FastQ files.
+* `metadata/`
+    * `*.metadata.txt`: Original metadata file, generated using the `synapse show` command.
+    * `*.list.txt`: Original output of the `synapse list` command, containing the SynapseIDs, file version numbers, file names, and other file-specific data of the Synapse directory ID provided.
+
+</details>
+
+Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introduction) for detailed instructions on how to correctly provide Synapse IDs to the pipeline. FastQ files and corresponding sample information for `Synapse` identifiers are downloaded in parallel directly from the [Synapse](https://www.synapse.org/#) platform. A [configuration file](http://python-docs.synapse.org/build/html/Credentials.html#use-synapseconfig) containing valid login credentials is required for Synapse downloads.
+
+The final sample information for the FastQ files downloaded from `Synapse` is obtained from the file name itself. The file names are parsed according to the glob pattern `*{1,2}*`. This returns the sample name, presumed to be the longest possible string matching the glob pattern, with the fewest number of wildcard insertions. Further information on sample name parsing can be found in the [usage documentation](https://nf-co.re/fetchngs/usage#introduction).
+
+### Pipeline Information
+
+<details markdown="1">
+<summary>Output files</summary>
+
+* `pipeline_info/`
+    * Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
+    * Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.tsv`.
+
+</details>
+
 [Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.
diff --git a/docs/usage.md b/docs/usage.md
index e1a096f4..6e9787ad 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -6,7 +6,7 @@
 
 ## Introduction
 
-The pipeline has been set-up to automatically download and process the raw FastQ files from public repositories. Identifiers can be provided in a file, one-per-line via the `--input` parameter. Currently, the following types of example identifiers are supported:
+The pipeline has been set-up to automatically download and process the raw FastQ files from both public and private repositories. Identifiers can be provided in a file, one-per-line via the `--input` parameter. Currently, the following types of example identifiers are supported:
 
 | `SRA`        | `ENA`        | `DDBJ`       | `GEO`      | `Synapse`   |
 |--------------|--------------|--------------|------------|-------------|
@@ -18,15 +18,13 @@ The pipeline has been set-up to automatically download and process the raw FastQ
 | SRA1068758   | ERA2420837   | DRA008156    |            |             |
 | PRJNA625551  | PRJEB37513   | PRJDB4176    |            |             |
 
+**SRR / ERR / DRR Sample Identifiers**
+
 If `SRR`/`ERR`/`DRR` run ids are provided then these will be resolved back to their appropriate `SRX`/`ERX`/`DRX` ids to be able to merge multiple runs from the same experiment. This is conceptually the same as merging multiple libraries sequenced from the same sample.
 
 The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5 sums. If download links exist, the files will be downloaded in parallel by FTP otherwise they will NOT be downloaded. This is intentional because tools such as `parallel-fastq-dump`, `fasterq-dump`, `prefetch` etc require pre-existing configuration files in the users home directory which makes automation tricky across different platforms and containerisation. We may add this functionality in later releases.
 
-To download data from `Synapse`, the SynapseID of the directory containing all files to be downloaded should be provided. The directory ID will then be resolved to the SynapseIDs of the corresponding FastQ files, which are then downloaded in parellel using the `synapse get` command. In order to download data from Synapse, an account must be created and a user configuration file provided via the parameter `--synapse_config`. All Synapse metadata, annotations and provenance are also downloaded using the `synapse show` command, and are outputted to a separate metadata file. By default, only the md5sums, file sizes, etags, Synapse IDs, file names, and file versions are shown.
-
-As a bonus, the columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core. It is highly recommended that you double-check that all of the identifiers you defined using `--input` are represented in the samplesheet. Also, public databases don't reliably hold information such as strandedness information so you may need to amend these entries too if for example your samplesheet was created by providing `--nf_core_pipeline rnaseq`.
-
-All of the sample metadata obtained from the ENA will be appended as additional columns to help you manually curate the samplesheet before you run the pipeline. You can customise the metadata fields that are appended to the samplesheet via the `--ena_metadata_fields` parameter. The default list of fields used by the pipeline can be found at the top of the [`bin/sra_ids_to_runinfo.py`](https://github.com/nf-core/fetchngs/blob/master/bin/sra_ids_to_runinfo.py) script within the pipeline repo. However, this pipeline requires a minimal set of fields to download FastQ files i.e. `'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'`. A comprehensive list of accepted metadata fields can be obtained from the [ENA API](https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run]).
+All of the sample metadata obtained from the ENA will be appended as additional columns to help you manually curate the generated samplesheet before you run the pipeline. You can customise the metadata fields that are appended to the samplesheet via the `--ena_metadata_fields` parameter. The default list of fields used by the pipeline can be found at the top of the [`bin/sra_ids_to_runinfo.py`](https://github.com/nf-core/fetchngs/blob/master/bin/sra_ids_to_runinfo.py) script within the pipeline repo. However, this pipeline requires a minimal set of fields to download FastQ files i.e. `'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'`. A comprehensive list of accepted metadata fields can be obtained from the [ENA API](https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run]).
 
 If you have a GEO accession (found in the data availability section of published papers) you can directly download a text file containing the appropriate SRA ids to pass to the pipeline:
 
@@ -36,6 +34,29 @@ If you have a GEO accession (found in the data availability section of published
 
 This downloads a text file called `SRR_Acc_List.txt` that can be directly provided to the pipeline e.g. `--input SRR_Acc_List.txt`.
 
+**Synapse Sample Identifiers**
+
+[Synapse](https://www.synapse.org/#) is a collaborative research platform created by [Sage Bionetworks](https://sagebionetworks.org/). Its aim is to promote reproducible research and responsible data sharing throughout the biomedical community. To download data from `Synapse`, the SynapseID of the _directory_ containing all files to be downloaded should be provided. The SynapseID should be an eleven-character identifier, beginning with `syn`.
+
+This SynapseID will then be resolved to the SynapseIDs of the corresponding FastQ files contained within the directory. The individual FastQ files are then downloaded in parellel using the `synapse get` command. All Synapse metadata, annotations and provenance are also downloaded using the `synapse show` command, and are outputted to a separate metadata file. By default, only the md5sums, file sizes, etags, Synapse IDs, file names, and file versions are shown.
+
+In order to download data from Synapse, an account must be created and a user configuration file provided via the parameter `--synapse_config`. For more information about Synapse configuration, please see the [Synapse client configuration](https://help.synapse.org/docs/Client-Configuration.1985446156.html) documentation.
+
+The final sample information for the FastQ files used for samplesheet generation is obtained from the file name itself. The file names are parsed according to the glob pattern `*{1,2}*`, which returns the sample name, presumed to be the longest possible string matching the glob pattern, with the fewest number of wildcard insertions.
+
+<details markdown="1">
+<summary>Supported File Names</summary>
+
+* Files named `SRR493366_1.fastq` and `SRR493366_2.fastq` will have a sample name of `SRR493366`
+* Files named `SRR_493_367_1.fastq` and `SRR_493_367_2.fastq` will have a sample name of `SRR_493_367`
+* Files named `filename12_1.fastq` and `filename12_2.fastq` will have a sample name of `filename12`
+
+</details>
+
+**Samplesheet Generation**
+
+As a bonus, the columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core. It is highly recommended that you double-check that all of the identifiers you defined using `--input` are represented in the samplesheet. Also, public databases don't reliably hold information such as strandedness information so you may need to amend these entries too if for example your samplesheet was created by providing `--nf_core_pipeline rnaseq`.
+
 ## Running the pipeline
 
 The typical command for running the pipeline is as follows:

From 884dafa7b455fe29aa38f44fc5058c7c8a2ddc10 Mon Sep 17 00:00:00 2001
From: Daisy Wenyan Han <60151111+daisyhan97@users.noreply.github.com>
Date: Mon, 18 Oct 2021 16:06:46 -0700
Subject: [PATCH 086/852] Change SampleName function name

---
 lib/WorkflowSynapse.groovy | 2 +-
 workflows/synapse.nf       | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/WorkflowSynapse.groovy b/lib/WorkflowSynapse.groovy
index d36d1e55..557d58bf 100755
--- a/lib/WorkflowSynapse.groovy
+++ b/lib/WorkflowSynapse.groovy
@@ -39,7 +39,7 @@ class WorkflowSynapse {
     //
     // Obtain Sample ID from File Name
     //
-    public static String getSampleID(input_file, pattern) {
+    public static String sampleNameFromFastQ(input_file, pattern) {
 
         def sampleids = ""
 
diff --git a/workflows/synapse.nf b/workflows/synapse.nf
index 1f535f60..82125050 100644
--- a/workflows/synapse.nf
+++ b/workflows/synapse.nf
@@ -101,14 +101,14 @@ workflow SYNAPSE {
     SYNAPSE_GET
         .out
         .fastq
-        .map { meta, fastq -> [ WorkflowSynapse.getSampleID( fastq , "*{1,2}*"), fastq ] }
+        .map { meta, fastq -> [ WorkflowSynapse.sampleNameFromFastQ( fastq , "*{1,2}*"), fastq ] }
         .groupTuple(sort: { it -> it.baseName })
         .set { ch_fastq }
 
     SYNAPSE_GET
         .out
         .fastq
-        .map { meta, fastq -> [ WorkflowSynapse.getSampleID( fastq , "*{1,2}*"), meta.id ] }
+        .map { meta, fastq -> [ WorkflowSynapse.sampleNameFromFastQ( fastq , "*{1,2}*"), meta.id ] }
         .groupTuple()
         .join(ch_fastq)
         .map { id, synids, fastq ->

From fc071ecc4306c87f0b2943b5c1c652002db00d67 Mon Sep 17 00:00:00 2001
From: Daisy Wenyan Han <60151111+daisyhan97@users.noreply.github.com>
Date: Mon, 18 Oct 2021 16:25:26 -0700
Subject: [PATCH 087/852] Fix md

---
 README.md     | 10 ++++++----
 docs/usage.md |  6 +++---
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index 889d4a87..312db468 100644
--- a/README.md
+++ b/README.md
@@ -16,7 +16,7 @@
 
 ## Introduction
 
-**nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from both public and private databases. At present, the pipeline supports SRA / ENA / DDBJ / GEO / Synapse ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)). 
+**nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from both public and private databases. At present, the pipeline supports SRA / ENA / DDBJ / GEO / Synapse ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)).
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.
 
@@ -26,19 +26,21 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 Via a single file of ids, provided one-per-line (see [example input file](https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/public_database_ids.txt)) the pipeline performs the following steps:
 
-**SRA / ENA / DDBJ / GEO Identifiers**
+### SRA / ENA / DDBJ / GEO Identifiers
+
 1. Resolve database ids back to appropriate experiment-level ids and to be compatible with the [ENA API](https://ena-docs.readthedocs.io/en/latest/retrieval/programmatic-access.html)
 2. Fetch extensive id metadata including direct download links to FastQ files via ENA API
 3. Download FastQ files in parallel via `curl` and perform `md5sum` check
 4. Collate id metadata and paths to FastQ files in a single samplesheet
 
-**Synapse Identifiers**
+### Synapse Identifiers
+
 1. Resolve Synapse directory SynapseIDs to the SynapseIDs of the FastQ files contained, using the `synapse list` command.
 2. Retrieve FastQ file metadata including FastQ file names, md5sums, etags, annotations, and data provenance via the `synapse show` command.
 3. Download FastQ files in parallel via `synapse get` and perform `md5sum` check
 4. Collate paths to FastQ files in a single samplesheet
 
-**Samplesheet Generation**
+### Samplesheet Generation
 The columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core.
 
 ## Quick Start
diff --git a/docs/usage.md b/docs/usage.md
index 6e9787ad..0b2bfa44 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -18,7 +18,7 @@ The pipeline has been set-up to automatically download and process the raw FastQ
 | SRA1068758   | ERA2420837   | DRA008156    |            |             |
 | PRJNA625551  | PRJEB37513   | PRJDB4176    |            |             |
 
-**SRR / ERR / DRR Sample Identifiers**
+### SRR / ERR / DRR Sample Identifiers
 
 If `SRR`/`ERR`/`DRR` run ids are provided then these will be resolved back to their appropriate `SRX`/`ERX`/`DRX` ids to be able to merge multiple runs from the same experiment. This is conceptually the same as merging multiple libraries sequenced from the same sample.
 
@@ -34,7 +34,7 @@ If you have a GEO accession (found in the data availability section of published
 
 This downloads a text file called `SRR_Acc_List.txt` that can be directly provided to the pipeline e.g. `--input SRR_Acc_List.txt`.
 
-**Synapse Sample Identifiers**
+### Synapse Sample Identifiers
 
 [Synapse](https://www.synapse.org/#) is a collaborative research platform created by [Sage Bionetworks](https://sagebionetworks.org/). Its aim is to promote reproducible research and responsible data sharing throughout the biomedical community. To download data from `Synapse`, the SynapseID of the _directory_ containing all files to be downloaded should be provided. The SynapseID should be an eleven-character identifier, beginning with `syn`.
 
@@ -53,7 +53,7 @@ The final sample information for the FastQ files used for samplesheet generation
 
 </details>
 
-**Samplesheet Generation**
+### Samplesheet Generation
 
 As a bonus, the columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core. It is highly recommended that you double-check that all of the identifiers you defined using `--input` are represented in the samplesheet. Also, public databases don't reliably hold information such as strandedness information so you may need to amend these entries too if for example your samplesheet was created by providing `--nf_core_pipeline rnaseq`.
 

From 89ae0b7600cd46c53a29af0248867793ba46f09a Mon Sep 17 00:00:00 2001
From: Daisy Wenyan Han <60151111+daisyhan97@users.noreply.github.com>
Date: Mon, 18 Oct 2021 16:27:11 -0700
Subject: [PATCH 088/852] Whitespace whitespace

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 312db468..209a239b 100644
--- a/README.md
+++ b/README.md
@@ -41,6 +41,7 @@ Via a single file of ids, provided one-per-line (see [example input file](https:
 4. Collate paths to FastQ files in a single samplesheet
 
 ### Samplesheet Generation
+
 The columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core.
 
 ## Quick Start

From 3909540c682a1170d88d8e7777130e5a769f50b5 Mon Sep 17 00:00:00 2001
From: Daisy Wenyan Han <60151111+daisyhan97@users.noreply.github.com>
Date: Tue, 19 Oct 2021 08:44:08 -0700
Subject: [PATCH 089/852] Remove md5sum check

---
 lib/WorkflowSynapse.groovy   | 1 +
 modules/local/synapse_get.nf | 3 +--
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/WorkflowSynapse.groovy b/lib/WorkflowSynapse.groovy
index 557d58bf..8a79c6a6 100755
--- a/lib/WorkflowSynapse.groovy
+++ b/lib/WorkflowSynapse.groovy
@@ -20,6 +20,7 @@ class WorkflowSynapse {
             meta["${category}|${entries[0]}"] = entries[1]
         }
         meta.id = meta['properties|id']
+        meta.name = meta['properties|name']
         meta.md5 = meta['File|md5']
         return meta.findAll{ it.value != null }
     }
diff --git a/modules/local/synapse_get.nf b/modules/local/synapse_get.nf
index 1e959296..99985f48 100644
--- a/modules/local/synapse_get.nf
+++ b/modules/local/synapse_get.nf
@@ -36,8 +36,7 @@ process SYNAPSE_GET {
         $options.args \\
         $meta.id
 
-    find ./ -type f -name "*.fastq.gz" -exec echo "${meta.md5} " {} \\; > ${meta.id}.md5
-    md5sum -c ${meta.id}.md5
+    echo "${meta.md5} \t ${meta.name}" > ${meta.id}.md5
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:

From fad83a8ba5d3ed75c334a6d09277fbc23020609e Mon Sep 17 00:00:00 2001
From: Daisy Wenyan Han <60151111+daisyhan97@users.noreply.github.com>
Date: Tue, 19 Oct 2021 11:09:21 -0500
Subject: [PATCH 090/852] Syntax Edits

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 README.md | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 209a239b..9bf7db8f 100644
--- a/README.md
+++ b/README.md
@@ -26,21 +26,21 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 Via a single file of ids, provided one-per-line (see [example input file](https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/public_database_ids.txt)) the pipeline performs the following steps:
 
-### SRA / ENA / DDBJ / GEO Identifiers
+### SRA / ENA / DDBJ / GEO ids
 
 1. Resolve database ids back to appropriate experiment-level ids and to be compatible with the [ENA API](https://ena-docs.readthedocs.io/en/latest/retrieval/programmatic-access.html)
 2. Fetch extensive id metadata including direct download links to FastQ files via ENA API
 3. Download FastQ files in parallel via `curl` and perform `md5sum` check
 4. Collate id metadata and paths to FastQ files in a single samplesheet
 
-### Synapse Identifiers
+### Synapse ids
 
-1. Resolve Synapse directory SynapseIDs to the SynapseIDs of the FastQ files contained, using the `synapse list` command.
-2. Retrieve FastQ file metadata including FastQ file names, md5sums, etags, annotations, and data provenance via the `synapse show` command.
-3. Download FastQ files in parallel via `synapse get` and perform `md5sum` check
+1. Resolve Synapse directory ids to their corresponding FastQ files ids via the `synapse list` command.
+2. Retrieve FastQ file metadata including FastQ file names, md5sums, etags, annotations and other data provenance via the `synapse show` command.
+3. Download FastQ files in parallel via `synapse get`
 4. Collate paths to FastQ files in a single samplesheet
 
-### Samplesheet Generation
+### Samplesheet format
 
 The columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core.
 

From bf020ac1fc4528267e13b9de2f29b7e38893a281 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Tue, 19 Oct 2021 17:21:20 +0100
Subject: [PATCH 091/852] Update output.md

---
 docs/output.md | 34 +++++++++-------------------------
 1 file changed, 9 insertions(+), 25 deletions(-)

diff --git a/docs/output.md b/docs/output.md
index acc1d956..575bd84f 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -4,14 +4,16 @@
 
 This document describes the output produced by the pipeline. The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.
 
-## SRA / ENA / DDBJ / GEO - Pipeline Overview
+## Pipeline Overview
 
-The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
+The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using one of the following workflows:
 
-* [FastQ download](#fastq-download) - Download FastQ files via SRA / ENA / DDBJ / GEO ids
+* Download FastQ files and create samplesheet from:
+  1. [SRA / ENA / DDBJ / GEO ids](#sra-ena-ddbj-geo-ids)
+  2. [Synapse ids](#synapse-ids)
 * [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
-### FastQ download
+### SRA / ENA / DDBJ / GEO ids
 
 <details markdown="1">
 <summary>Output files</summary>
@@ -32,25 +34,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introduction) for a list of supported public repository identifiers and how to provide them to the pipeline. The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5sums. If download links exist, the files will be downloaded in parallel by FTP otherwise they will NOT be downloaded. This is intentional because the tools such as `parallel-fastq-dump`, `fasterq-dump`, `prefetch` etc require pre-existing configuration files in the users home directory which makes automation tricky across different platforms and containerisation.
 
-### Pipeline information
-
-<details markdown="1">
-<summary>Output files</summary>
-
-* `pipeline_info/`
-    * Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
-    * Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.tsv`.
-
-</details>
-
-## Synapse - Pipeline Overview
-
-The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
-
-* [FastQ download](#fastq-Download) - Download FastQ files via Synapse ids
-* [Pipeline information](#pipeline-Information) - Report metrics generated during the workflow execution
-
-### FastQ Download
+### Synapse ids
 
 <details markdown="1">
 <summary>Output files</summary>
@@ -62,8 +46,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 * `samplesheet/`
     * `samplesheet.csv`: Auto-created samplesheet with collated metadata and paths to downloaded FastQ files.
 * `metadata/`
-    * `*.metadata.txt`: Original metadata file, generated using the `synapse show` command.
-    * `*.list.txt`: Original output of the `synapse list` command, containing the SynapseIDs, file version numbers, file names, and other file-specific data of the Synapse directory ID provided.
+    * `*.metadata.txt`: Original metadata file generated using the `synapse show` command.
+    * `*.list.txt`: Original output of the `synapse list` command, containing the Synapse ids, file version numbers, file names, and other file-specific data for the Synapse directory ID provided.
 
 </details>
 

From 522cab37d805fa7afc08ae75071a6b9cf0277e89 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Tue, 19 Oct 2021 17:25:36 +0100
Subject: [PATCH 092/852] Update output.md

---
 docs/output.md | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/docs/output.md b/docs/output.md
index 575bd84f..510edaf0 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -4,15 +4,17 @@
 
 This document describes the output produced by the pipeline. The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.
 
-## Pipeline Overview
+## Pipeline overview
 
-The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using one of the following workflows:
+The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data depending on the type of ids provided:
 
 * Download FastQ files and create samplesheet from:
-  1. [SRA / ENA / DDBJ / GEO ids](#sra-ena-ddbj-geo-ids)
+  1. [SRA / ENA / DDBJ / GEO ids](#sra--ena--ddbj--geo-ids)
   2. [Synapse ids](#synapse-ids)
 * [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
+Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introduction) for a list of supported public repository identifiers and how to provide them to the pipeline.
+
 ### SRA / ENA / DDBJ / GEO ids
 
 <details markdown="1">
@@ -32,7 +34,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 </details>
 
-Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introduction) for a list of supported public repository identifiers and how to provide them to the pipeline. The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5sums. If download links exist, the files will be downloaded in parallel by FTP otherwise they will NOT be downloaded. This is intentional because the tools such as `parallel-fastq-dump`, `fasterq-dump`, `prefetch` etc require pre-existing configuration files in the users home directory which makes automation tricky across different platforms and containerisation.
+The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5sums. If download links exist, the files will be downloaded in parallel by FTP otherwise they will NOT be downloaded. This is intentional because the tools such as `parallel-fastq-dump`, `fasterq-dump`, `prefetch` etc require pre-existing configuration files in the users home directory which makes automation tricky across different platforms and containerisation.
 
 ### Synapse ids
 
@@ -51,7 +53,7 @@ Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introductio
 
 </details>
 
-Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introduction) for detailed instructions on how to correctly provide Synapse IDs to the pipeline. FastQ files and corresponding sample information for `Synapse` identifiers are downloaded in parallel directly from the [Synapse](https://www.synapse.org/#) platform. A [configuration file](http://python-docs.synapse.org/build/html/Credentials.html#use-synapseconfig) containing valid login credentials is required for Synapse downloads.
+FastQ files and corresponding sample information for `Synapse` identifiers are downloaded in parallel directly from the [Synapse](https://www.synapse.org/#) platform. A [configuration file](http://python-docs.synapse.org/build/html/Credentials.html#use-synapseconfig) containing valid login credentials is required for Synapse downloads.
 
 The final sample information for the FastQ files downloaded from `Synapse` is obtained from the file name itself. The file names are parsed according to the glob pattern `*{1,2}*`. This returns the sample name, presumed to be the longest possible string matching the glob pattern, with the fewest number of wildcard insertions. Further information on sample name parsing can be found in the [usage documentation](https://nf-co.re/fetchngs/usage#introduction).
 

From 3b52a76f4bf343582c22d833f6017be1cf21614a Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Tue, 19 Oct 2021 17:32:29 +0100
Subject: [PATCH 093/852] Update usage.md

---
 docs/usage.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/docs/usage.md b/docs/usage.md
index 0b2bfa44..2301a040 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -18,7 +18,7 @@ The pipeline has been set-up to automatically download and process the raw FastQ
 | SRA1068758   | ERA2420837   | DRA008156    |            |             |
 | PRJNA625551  | PRJEB37513   | PRJDB4176    |            |             |
 
-### SRR / ERR / DRR Sample Identifiers
+### SRR / ERR / DRR Sample ids
 
 If `SRR`/`ERR`/`DRR` run ids are provided then these will be resolved back to their appropriate `SRX`/`ERX`/`DRX` ids to be able to merge multiple runs from the same experiment. This is conceptually the same as merging multiple libraries sequenced from the same sample.
 
@@ -34,11 +34,11 @@ If you have a GEO accession (found in the data availability section of published
 
 This downloads a text file called `SRR_Acc_List.txt` that can be directly provided to the pipeline e.g. `--input SRR_Acc_List.txt`.
 
-### Synapse Sample Identifiers
+### Synapse ids
 
-[Synapse](https://www.synapse.org/#) is a collaborative research platform created by [Sage Bionetworks](https://sagebionetworks.org/). Its aim is to promote reproducible research and responsible data sharing throughout the biomedical community. To download data from `Synapse`, the SynapseID of the _directory_ containing all files to be downloaded should be provided. The SynapseID should be an eleven-character identifier, beginning with `syn`.
+[Synapse](https://www.synapse.org/#) is a collaborative research platform created by [Sage Bionetworks](https://sagebionetworks.org/). Its aim is to promote reproducible research and responsible data sharing throughout the biomedical community. To download data from `Synapse`, the Synapse id of the _directory_ containing all files to be downloaded should be provided. The Synapse id should be an eleven-characters beginning with `syn`.
 
-This SynapseID will then be resolved to the SynapseIDs of the corresponding FastQ files contained within the directory. The individual FastQ files are then downloaded in parellel using the `synapse get` command. All Synapse metadata, annotations and provenance are also downloaded using the `synapse show` command, and are outputted to a separate metadata file. By default, only the md5sums, file sizes, etags, Synapse IDs, file names, and file versions are shown.
+This Synapse id will then be resolved to the Synapse id of the corresponding FastQ files contained within the directory. The individual FastQ files are then downloaded in parellel using the `synapse get` command. All Synapse metadata, annotations and data provenance are also downloaded using the `synapse show` command, and are outputted to a separate metadata file. By default, only the md5sums, file sizes, etags, Synapse ids, file names, and file versions are shown.
 
 In order to download data from Synapse, an account must be created and a user configuration file provided via the parameter `--synapse_config`. For more information about Synapse configuration, please see the [Synapse client configuration](https://help.synapse.org/docs/Client-Configuration.1985446156.html) documentation.
 
@@ -53,7 +53,7 @@ The final sample information for the FastQ files used for samplesheet generation
 
 </details>
 
-### Samplesheet Generation
+### Samplesheet format
 
 As a bonus, the columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core. It is highly recommended that you double-check that all of the identifiers you defined using `--input` are represented in the samplesheet. Also, public databases don't reliably hold information such as strandedness information so you may need to amend these entries too if for example your samplesheet was created by providing `--nf_core_pipeline rnaseq`.
 

From 8d4f321ffccce6593c4628a8f383f8bbafced0d3 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Tue, 19 Oct 2021 17:32:53 +0100
Subject: [PATCH 094/852] Update docs/output.md

---
 docs/output.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/output.md b/docs/output.md
index 510edaf0..c292f563 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -57,7 +57,7 @@ FastQ files and corresponding sample information for `Synapse` identifiers are d
 
 The final sample information for the FastQ files downloaded from `Synapse` is obtained from the file name itself. The file names are parsed according to the glob pattern `*{1,2}*`. This returns the sample name, presumed to be the longest possible string matching the glob pattern, with the fewest number of wildcard insertions. Further information on sample name parsing can be found in the [usage documentation](https://nf-co.re/fetchngs/usage#introduction).
 
-### Pipeline Information
+### Pipeline information
 
 <details markdown="1">
 <summary>Output files</summary>

From aa54f0917f49971a44e99a7d057a795bc661ff82 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Tue, 19 Oct 2021 17:36:07 +0100
Subject: [PATCH 095/852] Update docs/usage.md

---
 docs/usage.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/usage.md b/docs/usage.md
index 2301a040..5040552b 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -18,7 +18,7 @@ The pipeline has been set-up to automatically download and process the raw FastQ
 | SRA1068758   | ERA2420837   | DRA008156    |            |             |
 | PRJNA625551  | PRJEB37513   | PRJDB4176    |            |             |
 
-### SRR / ERR / DRR Sample ids
+### SRR / ERR / DRR ids
 
 If `SRR`/`ERR`/`DRR` run ids are provided then these will be resolved back to their appropriate `SRX`/`ERX`/`DRX` ids to be able to merge multiple runs from the same experiment. This is conceptually the same as merging multiple libraries sequenced from the same sample.
 

From e9303e6d4c6bdf3ff5a1b48a6bb73cec76feb61e Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Tue, 19 Oct 2021 17:37:10 +0100
Subject: [PATCH 096/852] Update output.md

---
 docs/output.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/output.md b/docs/output.md
index c292f563..df7fec02 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -9,8 +9,8 @@ This document describes the output produced by the pipeline. The directories lis
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data depending on the type of ids provided:
 
 * Download FastQ files and create samplesheet from:
-  1. [SRA / ENA / DDBJ / GEO ids](#sra--ena--ddbj--geo-ids)
-  2. [Synapse ids](#synapse-ids)
+    1. [SRA / ENA / DDBJ / GEO ids](#sra--ena--ddbj--geo-ids)
+    2. [Synapse ids](#synapse-ids)
 * [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
 Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introduction) for a list of supported public repository identifiers and how to provide them to the pipeline.

From 349224fb3fe2ac6fa7b264cf5f51044d69bf7321 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 20 Oct 2021 09:38:52 +0100
Subject: [PATCH 097/852] Update regex for DDBJ and synapse ids

---
 assets/schema_input.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index 224e5cf7..00c0d47f 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -8,7 +8,7 @@
         "type": "array",
         "items": {
             "type": "string",
-            "pattern": "^[SEPG][RAS][RXSMPAJXE][EN]?[AB]?\\d{4,9}$",
+            "pattern": "^[SEPGDs][RASy][RXSMPAJXEn][END]?[AB]?\\d{4,9}$",
             "errorMessage": "Please provide a valid SRA, ENA, DDBJ or GEO identifier"
         }
     }

From 756b598cd9800bc6c87f52cea06aaa50974420ad Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 20 Oct 2021 09:39:12 +0100
Subject: [PATCH 098/852] Add functions to check if SRA or Synapse ids have
 been provided

---
 lib/WorkflowMain.groovy | 60 ++++++++++++++++++++++++++++++++++-------
 1 file changed, 50 insertions(+), 10 deletions(-)

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index f1804f51..6f1fcb2d 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -78,15 +78,55 @@ class WorkflowMain {
         }
     }
 
-    // Check input type
-    public static String getIdentifierType(workflow, params, log) {
-        def input_type = ""
-        params.input.eachLine { line ->
-        if (line.contains("syn")) {
-            input_type = "Synapse"
-        } else {
-            input_type = "SRA"
-        }}
-        return input_type
+    // Check if input ids are from the SRA
+    public static Boolean isSraId(input, log) {
+        def is_sra = false
+        def total_ids = 0
+        def no_match_ids = []
+        def pattern = /^[SEPGD][RAS][RXSMPAJXE][END]?[AB]?\d{4,9}$/
+        input.eachLine { line ->
+            total_ids += 1
+            def matcher = line =~ pattern
+            if (!matcher) {
+                no_match_ids << line
+            }
+        }
+
+        def num_match = total_ids - no_match_ids.size()
+        if (num_match > 0) {
+            if (num_match == total_ids) {
+                is_sra = true
+            } else {
+                log.error "Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / DDBJ / GEO or Synapse ids!"
+                System.exit(1)
+            }
+        }
+        return is_sra
+    }
+
+    // Check if input ids are from the Synapse platform
+    public static Boolean isSynapseId(input, log) {
+        def is_synapse = false
+        def total_ids = 0
+        def no_match_ids = []
+        def pattern = /^syn\d{8}$/
+        input.eachLine { line ->
+            total_ids += 1
+            def matcher = line =~ pattern
+            if (!matcher) {
+                no_match_ids << line
+            }
+        }
+
+        def num_match = total_ids - no_match_ids.size()
+        if (num_match > 0) {
+            if (num_match == total_ids) {
+                is_synapse = true
+            } else {
+                log.error "Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / DDBJ / GEO or Synapse ids!"
+                System.exit(1)
+            }
+        }
+        return is_synapse
     }
 }

From 68385ddcf173b22b2479c4e8948c87c9b4af65ae Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 20 Oct 2021 09:39:29 +0100
Subject: [PATCH 099/852] Auto-detect id type and invoke relevant workflow

---
 main.nf | 40 ++++++++++++++++++++++++++++++----------
 1 file changed, 30 insertions(+), 10 deletions(-)

diff --git a/main.nf b/main.nf
index 0b76d9da..abb0d5fb 100644
--- a/main.nf
+++ b/main.nf
@@ -18,7 +18,18 @@ nextflow.enable.dsl = 2
 */
 
 WorkflowMain.initialise(workflow, params, log)
-input_type = WorkflowMain.getIdentifierType(workflow, params, log)
+
+// Check if --input file is empty
+ch_input = file(params.input, checkIfExists: true)
+if (ch_input.isEmpty()) {exit 1, "File provided with --input is empty: ${ch_input.getName()}!"}
+
+// Read in ids from --input file
+Channel
+    .from(file(params.input, checkIfExists: true))
+    .splitCsv(header:false, sep:'', strip:true)
+    .map { it[0] }
+    .unique()
+    .set { ch_ids }
 
 /*
 ========================================================================================
@@ -26,10 +37,15 @@ input_type = WorkflowMain.getIdentifierType(workflow, params, log)
 ========================================================================================
 */
 
-if (input_type == 'Synapse') {
+def id_type = ''
+if (WorkflowMain.isSraId(ch_input, log)) {
+    id_type = 'sra'
+    include { SRA } from './workflows/sra'
+} else if (WorkflowMain.isSynapseId(ch_input, log)) {
+    id_type = 'synapse'
     include { SYNAPSE } from './workflows/synapse'
 } else {
-    include { SRA } from './workflows/sra'
+    exit 1, 'Ids provided via --input not recognised please make sure they are either SRA / ENA / DDBJ / GEO or Synapse ids!'
 }
 
 //
@@ -37,14 +53,18 @@ if (input_type == 'Synapse') {
 //
 workflow NFCORE_FETCHNGS {
 
-    // Workflow for SynapseIDs
-    if (input_type == 'Synapse') {
-        SYNAPSE ()
-    } else {
-    // Workflow for SRA/ENA/GEO IDs
-        SRA ()
-    }
+    //
+    // WORKFLOW: Download FastQ files for SRA / ENA / DDBJ / GEO ids
+    //
+    if (id_type == 'sra') {
+        SRA ( ch_ids )
 
+    //
+    // WORKFLOW: Download FastQ files for Synapse ids
+    //
+    } else if (id_type == 'synapse') {
+        SYNAPSE ( ch_ids )
+    }
 }
 
 /*

From fe3c09742de5758fbf645d88ec096810c83f9798 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 20 Oct 2021 09:39:54 +0100
Subject: [PATCH 100/852] Pass input ids as a channel directly to workflows

---
 workflows/sra.nf     | 14 +++++---------
 workflows/synapse.nf | 14 +++++---------
 2 files changed, 10 insertions(+), 18 deletions(-)

diff --git a/workflows/sra.nf b/workflows/sra.nf
index 835bd874..dd8e13df 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -13,14 +13,6 @@ def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
 // Validate input parameters
 WorkflowSra.initialise(params, log, valid_params)
 
-// Read in ids from --input file
-Channel
-    .from(file(params.input, checkIfExists: true))
-    .splitCsv(header:false, sep:'', strip:true)
-    .map { it[0] }
-    .unique()
-    .set { ch_ids }
-
 /*
 ========================================================================================
     IMPORT LOCAL MODULES/SUBWORKFLOWS
@@ -53,13 +45,17 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/
 
 workflow SRA {
 
+    take:
+    ids // channel: [ ids ]
+
+    main:
     ch_versions = Channel.empty()
 
     //
     // MODULE: Get SRA run information for public database ids
     //
     SRA_IDS_TO_RUNINFO (
-        ch_ids,
+        ids,
         params.ena_metadata_fields ?: ''
     )
     ch_versions = ch_versions.mix(SRA_IDS_TO_RUNINFO.out.versions.first())
diff --git a/workflows/synapse.nf b/workflows/synapse.nf
index 3d993789..b308372e 100644
--- a/workflows/synapse.nf
+++ b/workflows/synapse.nf
@@ -6,14 +6,6 @@
 
 def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
 
-// Read in ids from --input file
-Channel
-    .from(file(params.input, checkIfExists: true))
-    .splitCsv(header:false, sep:'', strip:true)
-    .map { it[0] }
-    .unique()
-    .set { ch_ids }
-
 // Create channel for synapse config
 if (params.synapse_config) {
     ch_synapse_config = file(params.synapse_config, checkIfExists: true)
@@ -52,13 +44,17 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/
 
 workflow SYNAPSE {
 
+    take:
+    ids // channel: [ ids ]
+
+    main:
     ch_versions = Channel.empty()
 
     //
     // MODULE: Expand synapse ids for individual FastQ files
     //
     SYNAPSE_LIST (
-        ch_ids,
+        ids,
         ch_synapse_config
     )
     ch_versions = ch_versions.mix(SYNAPSE_LIST.out.versions.first())

From 153d1ab92e342c75501ae04c5719af4e889c5b76 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 20 Oct 2021 09:41:33 +0100
Subject: [PATCH 101/852] Tweak comments

---
 main.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index abb0d5fb..98b25cb1 100644
--- a/main.nf
+++ b/main.nf
@@ -37,6 +37,7 @@ Channel
 ========================================================================================
 */
 
+// Auto-detect id type
 def id_type = ''
 if (WorkflowMain.isSraId(ch_input, log)) {
     id_type = 'sra'
@@ -49,7 +50,7 @@ if (WorkflowMain.isSraId(ch_input, log)) {
 }
 
 //
-// WORKFLOW: Run main nf-core/fetchngs analysis pipeline, depending on type of dentifier provided
+// WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided
 //
 workflow NFCORE_FETCHNGS {
 

From b7a86fd8b066ecd2313a95e2fe76c44e3c014b14 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Mon, 18 Oct 2021 13:33:49 +0200
Subject: [PATCH 102/852] refactor: make curl retry with exponential back-off

---
 modules/local/sra_fastq_ftp.nf | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/modules/local/sra_fastq_ftp.nf b/modules/local/sra_fastq_ftp.nf
index 39d3659d..713a9f81 100644
--- a/modules/local/sra_fastq_ftp.nf
+++ b/modules/local/sra_fastq_ftp.nf
@@ -30,7 +30,10 @@ process SRA_FASTQ_FTP {
     script:
     if (meta.single_end) {
         """
-        bash -c 'until curl $options.args -L ${fastq[0]} -o ${meta.id}.fastq.gz; do sleep 1; done';
+        curl $options.args \\
+            --retry 5 \\
+            -L ${fastq[0]} \\
+            -o ${meta.id}.fastq.gz
 
         echo "${meta.md5_1} ${meta.id}.fastq.gz" > ${meta.id}.fastq.gz.md5
         md5sum -c ${meta.id}.fastq.gz.md5
@@ -42,12 +45,18 @@ process SRA_FASTQ_FTP {
         """
     } else {
         """
-        bash -c 'until curl $options.args -L ${fastq[0]} -o ${meta.id}_1.fastq.gz; do sleep 1; done';
+        curl $options.args \\
+            --retry 5 \\
+            -L ${fastq[0]} \\
+            -o ${meta.id}_1.fastq.gz
 
         echo "${meta.md5_1} ${meta.id}_1.fastq.gz" > ${meta.id}_1.fastq.gz.md5
         md5sum -c ${meta.id}_1.fastq.gz.md5
 
-        bash -c 'until curl $options.args -L ${fastq[1]} -o ${meta.id}_2.fastq.gz; do sleep 1; done';
+        curl $options.args \\
+            --retry 5 \\
+            -L ${fastq[1]} \\
+            -o ${meta.id}_2.fastq.gz
 
         echo "${meta.md5_2} ${meta.id}_2.fastq.gz" > ${meta.id}_2.fastq.gz.md5
         md5sum -c ${meta.id}_2.fastq.gz.md5

From fc5200ceb5be32de249608e05210ea86b759736a Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Mon, 18 Oct 2021 15:27:50 +0200
Subject: [PATCH 103/852] refactor: report curl version instead of sed

---
 modules/local/sra_fastq_ftp.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/sra_fastq_ftp.nf b/modules/local/sra_fastq_ftp.nf
index 713a9f81..ce08d602 100644
--- a/modules/local/sra_fastq_ftp.nf
+++ b/modules/local/sra_fastq_ftp.nf
@@ -40,7 +40,7 @@ process SRA_FASTQ_FTP {
 
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
-            sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
+            curl: \$(echo \$(curl --version | head -n 1 | sed 's/^curl //; s/ .*\$//'))
         END_VERSIONS
         """
     } else {
@@ -63,7 +63,7 @@ process SRA_FASTQ_FTP {
 
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
-            sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
+            curl: \$(echo \$(curl --version | head -n 1 | sed 's/^curl //; s/ .*\$//'))
         END_VERSIONS
         """
     }

From 1336b06ce12aad19a50535fe51fa0779dddd5bb2 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Fri, 22 Oct 2021 21:50:31 +0200
Subject: [PATCH 104/852] refactor: move retry to module options args

---
 conf/modules.config            | 2 +-
 modules/local/sra_fastq_ftp.nf | 3 ---
 2 files changed, 1 insertion(+), 4 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 0d44e9ee..5824a876 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -33,7 +33,7 @@ params {
         'sra_fastq_ftp' {
             publish_dir     = 'fastq'
             publish_files   = ['fastq.gz':'', 'md5':'md5']
-            args            = '-C - --max-time 1200'
+            args            = '--retry 5 --continue-at - --max-time 1200'
         }
         'sra_to_samplesheet' {
             publish_dir     = 'samplesheet'
diff --git a/modules/local/sra_fastq_ftp.nf b/modules/local/sra_fastq_ftp.nf
index ce08d602..8d5adc2f 100644
--- a/modules/local/sra_fastq_ftp.nf
+++ b/modules/local/sra_fastq_ftp.nf
@@ -31,7 +31,6 @@ process SRA_FASTQ_FTP {
     if (meta.single_end) {
         """
         curl $options.args \\
-            --retry 5 \\
             -L ${fastq[0]} \\
             -o ${meta.id}.fastq.gz
 
@@ -46,7 +45,6 @@ process SRA_FASTQ_FTP {
     } else {
         """
         curl $options.args \\
-            --retry 5 \\
             -L ${fastq[0]} \\
             -o ${meta.id}_1.fastq.gz
 
@@ -54,7 +52,6 @@ process SRA_FASTQ_FTP {
         md5sum -c ${meta.id}_1.fastq.gz.md5
 
         curl $options.args \\
-            --retry 5 \\
             -L ${fastq[1]} \\
             -o ${meta.id}_2.fastq.gz
 

From 1acd7ea2f15e91da33c56195204758ca44866b9f Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Sun, 24 Oct 2021 01:41:42 +0100
Subject: [PATCH 105/852] Apply suggestions from code review

---
 modules/local/sra_fastq_ftp.nf | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/modules/local/sra_fastq_ftp.nf b/modules/local/sra_fastq_ftp.nf
index 8d5adc2f..cccdd8ac 100644
--- a/modules/local/sra_fastq_ftp.nf
+++ b/modules/local/sra_fastq_ftp.nf
@@ -30,7 +30,8 @@ process SRA_FASTQ_FTP {
     script:
     if (meta.single_end) {
         """
-        curl $options.args \\
+        curl \\
+            $options.args \\
             -L ${fastq[0]} \\
             -o ${meta.id}.fastq.gz
 
@@ -44,14 +45,16 @@ process SRA_FASTQ_FTP {
         """
     } else {
         """
-        curl $options.args \\
+        curl \\
+            $options.args \\
             -L ${fastq[0]} \\
             -o ${meta.id}_1.fastq.gz
 
         echo "${meta.md5_1} ${meta.id}_1.fastq.gz" > ${meta.id}_1.fastq.gz.md5
         md5sum -c ${meta.id}_1.fastq.gz.md5
 
-        curl $options.args \\
+        curl \\
+            $options.args \\
             -L ${fastq[1]} \\
             -o ${meta.id}_2.fastq.gz
 

From e4e1d4f6d4910083e684ab07680547d4b7950c2c Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 24 Oct 2021 01:48:25 +0100
Subject: [PATCH 106/852] Change contributors section

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 9bf7db8f..43dcf30d 100644
--- a/README.md
+++ b/README.md
@@ -72,7 +72,7 @@ The nf-core/fetchngs pipeline comes with documentation about the pipeline [usage
 
 ## Credits
 
-nf-core/fetchngs was originally written by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [The Bioinformatics & Biostatistics Group](https://www.crick.ac.uk/research/science-technology-platforms/bioinformatics-and-biostatistics/) at [The Francis Crick Institute, London](https://www.crick.ac.uk/) and Jose Espinosa-Carrasco ([@JoseEspinosa](https://github.com/JoseEspinosa)) from [The Comparative Bioinformatics Group](https://www.crg.eu/en/cedric_notredame) at [The Centre for Genomic Regulation, Spain](https://www.crg.eu/).
+nf-core/fetchngs was originally written by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [Seqera Labs, Spain](https://seqera.io/) and Jose Espinosa-Carrasco ([@JoseEspinosa](https://github.com/JoseEspinosa)) from [The Comparative Bioinformatics Group](https://www.crg.eu/en/cedric_notredame) at [The Centre for Genomic Regulation, Spain](https://www.crg.eu/).
 
 ## Contributions and Support
 

From 1a01b8ccd846e6e010920b46f54032637dcc97ff Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 24 Oct 2021 01:50:44 +0100
Subject: [PATCH 107/852] Simplify matcher logic

---
 lib/WorkflowMain.groovy | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index 6f1fcb2d..d5814c09 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -86,8 +86,7 @@ class WorkflowMain {
         def pattern = /^[SEPGD][RAS][RXSMPAJXE][END]?[AB]?\d{4,9}$/
         input.eachLine { line ->
             total_ids += 1
-            def matcher = line =~ pattern
-            if (!matcher) {
+            if (!(line =~ pattern)) {
                 no_match_ids << line
             }
         }
@@ -112,8 +111,7 @@ class WorkflowMain {
         def pattern = /^syn\d{8}$/
         input.eachLine { line ->
             total_ids += 1
-            def matcher = line =~ pattern
-            if (!matcher) {
+            if (!(line =~ pattern)) {
                 no_match_ids << line
             }
         }

From c133d36a27c7bbe697da50fa56fb0ad6f9cf27db Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 24 Oct 2021 01:59:32 +0100
Subject: [PATCH 108/852] Use better and more concise regex for ids

---
 assets/schema_input.json | 2 +-
 lib/WorkflowMain.groovy  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index 00c0d47f..25006d9b 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -8,7 +8,7 @@
         "type": "array",
         "items": {
             "type": "string",
-            "pattern": "^[SEPGDs][RASy][RXSMPAJXEn][END]?[AB]?\\d{4,9}$",
+            "pattern":"^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM])|(syn))(\\d+)$",
             "errorMessage": "Please provide a valid SRA, ENA, DDBJ or GEO identifier"
         }
     }
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index d5814c09..09264303 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -83,7 +83,7 @@ class WorkflowMain {
         def is_sra = false
         def total_ids = 0
         def no_match_ids = []
-        def pattern = /^[SEPGD][RAS][RXSMPAJXE][END]?[AB]?\d{4,9}$/
+        def pattern = /^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM]))(\d+)$/
         input.eachLine { line ->
             total_ids += 1
             if (!(line =~ pattern)) {

From b8398ef6983a8ccd4cc09c79afb8561c6eea869b Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Sat, 16 Oct 2021 14:19:59 +0200
Subject: [PATCH 109/852] chore: install prefetch module

---
 modules.json                                  |  3 +
 .../modules/sratools/prefetch/functions.nf    | 78 +++++++++++++++++++
 .../nf-core/modules/sratools/prefetch/main.nf | 50 ++++++++++++
 .../modules/sratools/prefetch/meta.yml        | 43 ++++++++++
 4 files changed, 174 insertions(+)
 create mode 100644 modules/nf-core/modules/sratools/prefetch/functions.nf
 create mode 100644 modules/nf-core/modules/sratools/prefetch/main.nf
 create mode 100644 modules/nf-core/modules/sratools/prefetch/meta.yml

diff --git a/modules.json b/modules.json
index ff841d00..38d23a23 100644
--- a/modules.json
+++ b/modules.json
@@ -5,6 +5,9 @@
         "nf-core/modules": {
             "custom/dumpsoftwareversions": {
                 "git_sha": "84f2302920078b0cf7716b2a2e5fcc0be5c4531d"
+            },
+            "sratools/prefetch": {
+                "git_sha": "07c0830057cc655de113d84499c7c1499460bb55"
             }
         }
     }
diff --git a/modules/nf-core/modules/sratools/prefetch/functions.nf b/modules/nf-core/modules/sratools/prefetch/functions.nf
new file mode 100644
index 00000000..85628ee0
--- /dev/null
+++ b/modules/nf-core/modules/sratools/prefetch/functions.nf
@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}
diff --git a/modules/nf-core/modules/sratools/prefetch/main.nf b/modules/nf-core/modules/sratools/prefetch/main.nf
new file mode 100644
index 00000000..207d1e10
--- /dev/null
+++ b/modules/nf-core/modules/sratools/prefetch/main.nf
@@ -0,0 +1,50 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process SRATOOLS_PREFETCH {
+    tag "$id"
+    label 'process_low'
+    label 'error_retry'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container 'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5262h314213e_0'
+    } else {
+        container 'quay.io/biocontainers/sra-tools:2.11.0--pl5262h314213e_0'
+    }
+
+    input:
+    tuple val(meta), val(id)
+
+    output:
+    tuple val(meta), path("$id"), emit: sra
+    path "versions.yml"         , emit: versions
+
+    script:
+    def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
+    """
+    eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
+    if [[ ! -f "\${NCBI_SETTINGS}" ]]; then
+        mkdir -p "\$(dirname "\${NCBI_SETTINGS}")"
+        printf '${config}' > "\${NCBI_SETTINGS}"
+    fi
+
+    prefetch \\
+        $options.args \\
+        --progress \\
+        $id
+
+    vdb-validate $id
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/modules/sratools/prefetch/meta.yml b/modules/nf-core/modules/sratools/prefetch/meta.yml
new file mode 100644
index 00000000..ab0a5ce5
--- /dev/null
+++ b/modules/nf-core/modules/sratools/prefetch/meta.yml
@@ -0,0 +1,43 @@
+name: sratools_prefetch
+description: Download sequencing data from the NCBI Sequence Read Archive (SRA).
+keywords:
+  - sequencing
+  - fastq
+  - prefetch
+tools:
+  - sratools:
+      description: SRA Toolkit and SDK from NCBI
+      homepage: https://github.com/ncbi/sra-tools
+      documentation: https://github.com/ncbi/sra-tools/wiki
+      tool_dev_url: https://github.com/ncbi/sra-tools
+      licence: ['Public Domain']
+
+input:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - id:
+      type: val
+      description: >
+        A string denoting an SRA id.
+
+output:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - sra:
+      type: directory
+      description: >
+        Directory containing the ETL data for the given SRA id.
+      pattern: "*/*.sra"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@Midnighter"

From 8f665946b54633e4fc3024306152444c552e7954 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Sat, 16 Oct 2021 14:23:14 +0200
Subject: [PATCH 110/852] chore: install fasterqdump module

---
 conf/modules.config                           |  3 +
 modules.json                                  |  3 +
 .../modules/sratools/fasterqdump/functions.nf | 78 +++++++++++++++++++
 .../modules/sratools/fasterqdump/main.nf      | 58 ++++++++++++++
 .../modules/sratools/fasterqdump/meta.yml     | 42 ++++++++++
 5 files changed, 184 insertions(+)
 create mode 100644 modules/nf-core/modules/sratools/fasterqdump/functions.nf
 create mode 100644 modules/nf-core/modules/sratools/fasterqdump/main.nf
 create mode 100644 modules/nf-core/modules/sratools/fasterqdump/meta.yml

diff --git a/conf/modules.config b/conf/modules.config
index 5824a876..434a5c59 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -35,6 +35,9 @@ params {
             publish_files   = ['fastq.gz':'', 'md5':'md5']
             args            = '--retry 5 --continue-at - --max-time 1200'
         }
+        'sratools/fasterqdump' {
+            publish_dir     = 'fastq'
+        }
         'sra_to_samplesheet' {
             publish_dir     = 'samplesheet'
             publish_files   = false
diff --git a/modules.json b/modules.json
index 38d23a23..f004808d 100644
--- a/modules.json
+++ b/modules.json
@@ -6,6 +6,9 @@
             "custom/dumpsoftwareversions": {
                 "git_sha": "84f2302920078b0cf7716b2a2e5fcc0be5c4531d"
             },
+            "sratools/fasterqdump": {
+                "git_sha": "de997825de788fe2210db16d9426f10342a1ba1d"
+            },
             "sratools/prefetch": {
                 "git_sha": "07c0830057cc655de113d84499c7c1499460bb55"
             }
diff --git a/modules/nf-core/modules/sratools/fasterqdump/functions.nf b/modules/nf-core/modules/sratools/fasterqdump/functions.nf
new file mode 100644
index 00000000..85628ee0
--- /dev/null
+++ b/modules/nf-core/modules/sratools/fasterqdump/functions.nf
@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}
diff --git a/modules/nf-core/modules/sratools/fasterqdump/main.nf b/modules/nf-core/modules/sratools/fasterqdump/main.nf
new file mode 100644
index 00000000..08ef9045
--- /dev/null
+++ b/modules/nf-core/modules/sratools/fasterqdump/main.nf
@@ -0,0 +1,58 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process SRATOOLS_FASTERQDUMP {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0 conda-forge::pigz=2.6' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container 'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0'
+    } else {
+        container 'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0'
+    }
+
+    input:
+    tuple val(meta), path(sra)
+
+    output:
+    tuple val(meta), path(output), emit: reads
+    path "versions.yml"          , emit: versions
+
+    script:
+    def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
+    // Paired-end data extracted by fasterq-dump (--split-3 the default) always creates
+    // *_1.fastq *_2.fastq files but sometimes also an additional *.fastq file
+    // for unpaired reads which we ignore here.
+    output = meta.single_end ? '*.fastq.gz' : '*_{1,2}.fastq.gz'
+    """
+    eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
+    if [[ ! -f "\${NCBI_SETTINGS}" ]]; then
+        mkdir -p "\$(dirname "\${NCBI_SETTINGS}")"
+        printf '${config}' > "\${NCBI_SETTINGS}"
+    fi
+
+    fasterq-dump \\
+        ${options.args} \\
+        --threads $task.cpus \\
+        ${sra.name}
+
+    pigz \\
+        ${options.args2} \\
+        --no-name \\
+        --processes $task.cpus \\
+        *.fastq
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(fasterq-dump --version 2>&1 | grep -Eo '[0-9.]+')
+        pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/modules/sratools/fasterqdump/meta.yml b/modules/nf-core/modules/sratools/fasterqdump/meta.yml
new file mode 100644
index 00000000..ac61e71f
--- /dev/null
+++ b/modules/nf-core/modules/sratools/fasterqdump/meta.yml
@@ -0,0 +1,42 @@
+name: sratools_fasterqdump
+description: Extract sequencing reads in FASTQ format from a given NCBI Sequence Read Archive (SRA).
+keywords:
+  - sequencing
+  - FASTQ
+  - dump
+tools:
+  - sratools:
+      description: SRA Toolkit and SDK from NCBI
+      homepage: https://github.com/ncbi/sra-tools
+      documentation: https://github.com/ncbi/sra-tools/wiki
+      tool_dev_url: https://github.com/ncbi/sra-tools
+      licence: ['Public Domain']
+
+input:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - sra:
+      type: directory
+      description: Directory containing ETL data for the given SRA.
+      pattern: "*/*.sra"
+
+output:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - reads:
+      type: file
+      description: Extracted FASTQ file or files if the sequencing reads are paired-end.
+      pattern: "*.fastq.gz"
+
+authors:
+  - "@Midnighter"

From d999b7f7487b82d0c06fe6587c8d0b8aaaaa2818 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Sat, 16 Oct 2021 14:44:26 +0200
Subject: [PATCH 111/852] feat: add sra-tools subworkflow

---
 conf/modules.config                          |  3 ++
 subworkflows/local/sra_fastq/main.nf         | 34 ++++++++++++++++++
 subworkflows/local/sra_fastq/meta.yml        | 36 ++++++++++++++++++++
 subworkflows/local/sra_fastq/nextflow.config |  2 ++
 workflows/sra.nf                             | 18 +++++-----
 5 files changed, 83 insertions(+), 10 deletions(-)
 create mode 100644 subworkflows/local/sra_fastq/main.nf
 create mode 100644 subworkflows/local/sra_fastq/meta.yml
 create mode 100644 subworkflows/local/sra_fastq/nextflow.config

diff --git a/conf/modules.config b/conf/modules.config
index 434a5c59..e253262e 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -35,6 +35,9 @@ params {
             publish_files   = ['fastq.gz':'', 'md5':'md5']
             args            = '--retry 5 --continue-at - --max-time 1200'
         }
+        'sratools/prefetch' {
+            publish_dir     = 'sra'
+        }
         'sratools/fasterqdump' {
             publish_dir     = 'fastq'
         }
diff --git a/subworkflows/local/sra_fastq/main.nf b/subworkflows/local/sra_fastq/main.nf
new file mode 100644
index 00000000..c6590b59
--- /dev/null
+++ b/subworkflows/local/sra_fastq/main.nf
@@ -0,0 +1,34 @@
+//
+// Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
+//
+
+params.prefetch_options    = [:]
+params.fasterqdump_options = [:]
+
+include { SRATOOLS_PREFETCH    } from '../../../modules/nf-core/modules/sratools/prefetch/main'    addParams( options: params.prefetch_options    )
+include { SRATOOLS_FASTERQDUMP } from '../../../modules/nf-core/modules/sratools/fasterqdump/main' addParams( options: params.fasterqdump_options )
+
+workflow SRA_FASTQ {
+    take:
+    sra_ids  // channel: [ val(meta), val(id) ]
+
+    main:
+
+    ch_versions = Channel.empty()
+
+    //
+    // Prefetch sequencing reads in SRA format.
+    //
+    SRATOOLS_PREFETCH ( sra_ids )
+    ch_versions = ch_versions.mix( SRATOOLS_PREFETCH.out.versions.first() )
+
+    //
+    // Convert the SRA format into one or more compressed FASTQ files.
+    //
+    SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra )
+    ch_versions = ch_versions.mix( SRATOOLS_FASTERQDUMP.out.versions.first() )
+
+    emit:
+    reads    = SRATOOLS_FASTERQDUMP.out.reads  // channel: [ val(meta), [ reads ] ]
+    versions = ch_versions                     // channel: [ versions.yml ]
+}
diff --git a/subworkflows/local/sra_fastq/meta.yml b/subworkflows/local/sra_fastq/meta.yml
new file mode 100644
index 00000000..146176ee
--- /dev/null
+++ b/subworkflows/local/sra_fastq/meta.yml
@@ -0,0 +1,36 @@
+name: sra_fastq
+description: Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
+keywords:
+  - sequencing
+  - FASTQ
+  - prefetch
+  - dump
+modules:
+  - sratools/prefetch
+  - sratools/fasterqdump
+input:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - id:
+      type: string
+      description: >
+        SRA identifier.
+output:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: Extracted FASTQ file or files if the sequencing reads are paired-end.
+      pattern: "*.fastq.gz"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - '@Midnighter'
diff --git a/subworkflows/local/sra_fastq/nextflow.config b/subworkflows/local/sra_fastq/nextflow.config
new file mode 100644
index 00000000..07448834
--- /dev/null
+++ b/subworkflows/local/sra_fastq/nextflow.config
@@ -0,0 +1,2 @@
+params.prefetch_options    = [:]
+params.fasterqdump_options = [:]
diff --git a/workflows/sra.nf b/workflows/sra.nf
index dd8e13df..efc08482 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -25,6 +25,7 @@ def modules = params.modules.clone()
 include { SRA_IDS_TO_RUNINFO      } from '../modules/local/sra_ids_to_runinfo'      addParams( options: modules['sra_ids_to_runinfo']      )
 include { SRA_RUNINFO_TO_FTP      } from '../modules/local/sra_runinfo_to_ftp'      addParams( options: modules['sra_runinfo_to_ftp']      )
 include { SRA_FASTQ_FTP           } from '../modules/local/sra_fastq_ftp'           addParams( options: modules['sra_fastq_ftp']           )
+include { SRA_FASTQ               } from '../subworkflows/local/sra_fastq/main'     addParams( prefetch_options: modules['sratools/prefetch'], fasterqdump_options: modules['sratools/fasterqdump'] )
 include { SRA_TO_SAMPLESHEET      } from '../modules/local/sra_to_samplesheet'      addParams( options: modules['sra_to_samplesheet'], results_dir: modules['sra_fastq_ftp'].publish_dir )
 include { SRA_MERGE_SAMPLESHEET   } from '../modules/local/sra_merge_samplesheet'   addParams( options: modules['sra_merge_samplesheet']   )
 include { MULTIQC_MAPPINGS_CONFIG } from '../modules/local/multiqc_mappings_config' addParams( options: modules['multiqc_mappings_config'] )
@@ -90,11 +91,17 @@ workflow SRA {
         )
         ch_versions = ch_versions.mix(SRA_FASTQ_FTP.out.versions.first())
 
+        // SUBWORKFLOW: Download sequencing reads without FTP links using sra-tools.
+        SRA_FASTQ (
+            ch_sra_reads.map { meta, reads -> if (!meta.fastq_1) [meta, meta.run_accession] }
+        )
+        ch_versions = ch_versions.mix(SRA_FASTQ.out.versions.first())
+
         //
         // MODULE: Stage FastQ files downloaded by SRA together and auto-create a samplesheet
         //
         SRA_TO_SAMPLESHEET (
-            SRA_FASTQ_FTP.out.fastq,
+            SRA_FASTQ_FTP.out.fastq.mix(SRA_FASTQ.out.reads),
             params.nf_core_pipeline ?: '',
             params.sample_mapping_fields
         )
@@ -117,15 +124,6 @@ workflow SRA {
             )
             ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions)
         }
-
-        //
-        // If ids don't have a direct FTP download link write them to file for download outside of the pipeline
-        //
-        def no_ids_file = ["${params.outdir}", "${modules['sra_fastq_ftp'].publish_dir}", "IDS_NOT_DOWNLOADED.txt" ].join(File.separator)
-        ch_sra_reads
-            .map { meta, reads -> if (!meta.fastq_1) "${meta.id.split('_')[0..-2].join('_')}" }
-            .unique()
-            .collectFile(name: no_ids_file, sort: true, newLine: true)
     }
 
     //

From b37bf865e6f2a2d02d502403261eb3a20e50ee96 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Fri, 22 Oct 2021 22:03:28 +0200
Subject: [PATCH 112/852] refactor: rename module options keys

---
 conf/modules.config | 4 ++--
 workflows/sra.nf    | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index e253262e..534b8249 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -35,10 +35,10 @@ params {
             publish_files   = ['fastq.gz':'', 'md5':'md5']
             args            = '--retry 5 --continue-at - --max-time 1200'
         }
-        'sratools/prefetch' {
+        'sratools_prefetch' {
             publish_dir     = 'sra'
         }
-        'sratools/fasterqdump' {
+        'sratools_fasterqdump' {
             publish_dir     = 'fastq'
         }
         'sra_to_samplesheet' {
diff --git a/workflows/sra.nf b/workflows/sra.nf
index efc08482..b3d357e4 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -25,7 +25,7 @@ def modules = params.modules.clone()
 include { SRA_IDS_TO_RUNINFO      } from '../modules/local/sra_ids_to_runinfo'      addParams( options: modules['sra_ids_to_runinfo']      )
 include { SRA_RUNINFO_TO_FTP      } from '../modules/local/sra_runinfo_to_ftp'      addParams( options: modules['sra_runinfo_to_ftp']      )
 include { SRA_FASTQ_FTP           } from '../modules/local/sra_fastq_ftp'           addParams( options: modules['sra_fastq_ftp']           )
-include { SRA_FASTQ               } from '../subworkflows/local/sra_fastq/main'     addParams( prefetch_options: modules['sratools/prefetch'], fasterqdump_options: modules['sratools/fasterqdump'] )
+include { SRA_FASTQ               } from '../subworkflows/local/sra_fastq/main'     addParams( prefetch_options: modules['sratools_prefetch'], fasterqdump_options: modules['sratools_fasterqdump'] )
 include { SRA_TO_SAMPLESHEET      } from '../modules/local/sra_to_samplesheet'      addParams( options: modules['sra_to_samplesheet'], results_dir: modules['sra_fastq_ftp'].publish_dir )
 include { SRA_MERGE_SAMPLESHEET   } from '../modules/local/sra_merge_samplesheet'   addParams( options: modules['sra_merge_samplesheet']   )
 include { MULTIQC_MAPPINGS_CONFIG } from '../modules/local/multiqc_mappings_config' addParams( options: modules['multiqc_mappings_config'] )

From 0d0ba2445ef918a5564f2f8b37fdf83b39cd62f6 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Mon, 25 Oct 2021 16:11:49 +0200
Subject: [PATCH 113/852] refactor: make script accept missing fastq_ftp

---
 bin/sra_runinfo_to_ftp.py | 236 +++++++++++++++++++++++++-------------
 1 file changed, 154 insertions(+), 82 deletions(-)

diff --git a/bin/sra_runinfo_to_ftp.py b/bin/sra_runinfo_to_ftp.py
index a6f02136..130007b6 100755
--- a/bin/sra_runinfo_to_ftp.py
+++ b/bin/sra_runinfo_to_ftp.py
@@ -1,107 +1,179 @@
 #!/usr/bin/env python
 
-import os
-import sys
-import errno
+
 import argparse
-import collections
+import csv
+import logging
+import sys
+from itertools import chain
+from pathlib import Path
+
+
+logger = logging.getLogger()
+
 
 def parse_args(args=None):
     Description = "Create samplesheet with FTP download links and md5ums from sample information obtained via 'sra_ids_to_runinfo.py' script."
-    Epilog = 'Example usage: python sra_runinfo_to_ftp.py <FILES_IN> <FILE_OUT>'
+    Epilog = "Example usage: python sra_runinfo_to_ftp.py <FILES_IN> <FILE_OUT>"
 
     parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
-    parser.add_argument('FILES_IN', help="Comma-separated list of metadata file created from 'sra_ids_to_runinfo.py' script.")
-    parser.add_argument('FILE_OUT', help="Output file containing paths to download FastQ files along with their associated md5sums.")
+    parser.add_argument(
+        "files_in",
+        metavar="FILES_IN",
+        help="Comma-separated list of metadata file created from 'sra_ids_to_runinfo.py' script.",
+    )
+    parser.add_argument(
+        "file_out",
+        metavar="FILE_OUT",
+        type=Path,
+        help="Output file containing paths to download FastQ files along with their associated md5sums.",
+    )
+    parser.add_argument(
+        "-l",
+        "--log-level",
+        help="The desired log level (default WARNING).",
+        choices=("CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"),
+        default="WARNING",
+    )
     return parser.parse_args(args)
 
-def make_dir(path):
-    if not len(path) == 0:
-        try:
-            os.makedirs(path)
-        except OSError as exception:
-            if exception.errno != errno.EEXIST:
-                raise
+
+def valid_fastq_extension(fastq):
+    return fastq.endswith("fastq.gz")
+
 
 def parse_sra_runinfo(file_in):
-    runinfo_dict = {}
-    with open(file_in, "r") as fin:
-        header = fin.readline().strip().split('\t')
-        for line in fin:
-            line_dict   = dict(zip(header,line.strip().split('\t')))
-            line_dict   = collections.OrderedDict(list(line_dict.items()))
-            run_id      = line_dict['run_accession']
-            exp_id      = line_dict['experiment_accession']
-            library     = line_dict['library_layout']
-            fastq_files = line_dict['fastq_ftp']
-            fastq_md5   = line_dict['fastq_md5']
-
-            db_id = exp_id
-            sample_dict = collections.OrderedDict()
-            if library == 'SINGLE':
-                sample_dict = collections.OrderedDict([('fastq_1',''), ('fastq_2',''), ('md5_1',''), ('md5_2',''), ('single_end','true')])
-                if fastq_files:
-                    sample_dict['fastq_1']  = fastq_files
-                    sample_dict['md5_1']    = fastq_md5
+    runinfo = {}
+    columns = [
+        "run_accession",
+        "experiment_accession",
+        "library_layout",
+        "fastq_ftp",
+        "fastq_md5",
+    ]
+    extensions = [
+        "fastq_1",
+        "fastq_2",
+        "md5_1",
+        "md5_2",
+        "single_end",
+    ]
+    with open(file_in, "r", newline="") as fin:
+        reader = csv.DictReader(fin, delimiter="\t", skipinitialspace=True)
+        header = list(reader.fieldnames)
+        if missing := frozenset(columns).difference(frozenset(header)):
+            logger.critical(
+                f"The following expected columns are missing from {file_in}: "
+                f"{', '.join(missing)}."
+            )
+            sys.exit(1)
+        for row in reader:
+            db_id = row["experiment_accession"]
+            if row["fastq_ftp"]:
+                fq_files = row["fastq_ftp"].split(";")[-2:]
+                fq_md5 = row["fastq_md5"].split(";")[-2:]
+                if len(fq_files) == 1:
+                    assert fq_files[0].endswith(
+                        ".fastq.gz"
+                    ), f"Unexpected FastQ file format {file_in.name}."
+                    if row["library_layout"] != "SINGLE":
+                        logger.warning(
+                            f"The library layout '{row['library_layout']}' should be "
+                            f"'SINGLE'."
+                        )
+                    sample = {
+                        "fastq_1": fq_files[0],
+                        "fastq_2": None,
+                        "md5_1": fq_md5[0],
+                        "md5_2": None,
+                        "single_end": "true",
+                    }
+                elif len(fq_files) == 2:
+                    assert fq_files[0].endswith(
+                        "_1.fastq.gz"
+                    ), f"Unexpected FastQ file format {file_in.name}."
+                    assert fq_files[1].endswith(
+                        "_2.fastq.gz"
+                    ), f"Unexpected FastQ file format {file_in.name}."
+                    if row["library_layout"] != "PAIRED":
+                        logger.warning(
+                            f"The library layout '{row['library_layout']}' should be "
+                            f"'PAIRED'."
+                        )
+                    sample = {
+                        "fastq_1": fq_files[0],
+                        "fastq_2": fq_files[1],
+                        "md5_1": fq_md5[0],
+                        "md5_2": fq_md5[1],
+                        "single_end": "false",
+                    }
                 else:
-                    ## In some instances FTP links don't exist for FastQ files
-                    ## These have to be downloaded via fastq-dump / fasterq-dump / parallel-fastq-dump via the run id
-                    db_id = run_id
-
-            elif library == 'PAIRED':
-                sample_dict = collections.OrderedDict([('fastq_1',''), ('fastq_2',''), ('md5_1',''), ('md5_2',''), ('single_end','false')])
-                if fastq_files:
-                    fq_files = fastq_files.split(';')[-2:]
-                    fq_md5   = fastq_md5.split(';')[-2:]
-                    if len(fq_files) == 2:
-                        if fq_files[0].find('_1.fastq.gz') != -1 and fq_files[1].find('_2.fastq.gz') != -1:
-                            sample_dict['fastq_1'] = fq_files[0]
-                            sample_dict['fastq_2'] = fq_files[1]
-                            sample_dict['md5_1']   = fq_md5[0]
-                            sample_dict['md5_2']   = fq_md5[1]
-                        else:
-                            print("Invalid FastQ files found for database id:'{}'!.".format(run_id))
-                    else:
-                        print("Invalid number of FastQ files ({}) found for paired-end database id:'{}'!.".format(len(fq_files), run_id))
-                else:
-                    db_id = run_id
+                    raise RuntimeError(f"Unexpected number of FastQ files: {fq_files}.")
+            else:
+                # In some instances, FTP links don't exist for FastQ files.
+                # These have to be downloaded with the run accession using sra-tools.
+                db_id = row["run_accession"]
+                sample = dict.fromkeys(extensions, None)
+                if row["library_layout"] == "SINGLE":
+                    sample["single_end"] = "true"
+                elif row["library_layout"] == "PAIRED":
+                    sample["single_end"] = "false"
 
-            if sample_dict:
-                sample_dict.update(line_dict)
-                if db_id not in runinfo_dict:
-                    runinfo_dict[db_id] = [sample_dict]
+            sample.update(row)
+            if db_id not in runinfo:
+                runinfo[db_id] = [sample]
+            else:
+                if sample in runinfo[db_id]:
+                    logger.error(
+                        f"Input run info file contains duplicate rows!\n"
+                        f"{', '.join([row[col] for col in header])}"
+                    )
                 else:
-                    if sample_dict in runinfo_dict[db_id]:
-                        print("Input run info file contains duplicate rows!\nLine: '{}'".format(line))
-                    else:
-                        runinfo_dict[db_id].append(sample_dict)
+                    runinfo[db_id].append(sample)
+
+    return runinfo, header + extensions
 
-    return runinfo_dict
 
 def sra_runinfo_to_ftp(files_in, file_out):
-    samplesheet_dict = {}
+    samplesheet = {}
+    header = []
     for file_in in files_in:
-        runinfo_dict = parse_sra_runinfo(file_in)
-        for db_id in runinfo_dict.keys():
-            if db_id not in samplesheet_dict:
-                samplesheet_dict[db_id] = runinfo_dict[db_id]
+        runinfo, sample_header = parse_sra_runinfo(file_in)
+        header.append(sample_header)
+        for db_id, rows in runinfo.items():
+            if db_id not in samplesheet:
+                samplesheet[db_id] = rows
             else:
-                print("Duplicate sample identifier found!\nID: '{}'".format(db_id))
-
-    ## Write samplesheet with paths to FastQ files and md5 sums
-    if samplesheet_dict:
-        out_dir = os.path.dirname(file_out)
-        make_dir(out_dir)
-        with open(file_out, "w") as fout:
-            header = ['id'] + list(samplesheet_dict[list(samplesheet_dict.keys())[0]][0].keys())
-            fout.write("\t".join(header) + "\n")
-            for db_id in sorted(samplesheet_dict.keys()):
-                for idx,val in enumerate(samplesheet_dict[db_id]):
-                    fout.write('\t'.join(["{}_T{}".format(db_id,idx+1)] + [val[x] for x in header[1:]]) + '\n')
+                logger.warning(f"Duplicate sample identifier found!\nID: '{db_id}'")
+
+    # Create a combined header from all input files.
+    combined_header = header[0] + list(
+        set().union(chain.from_iterable(header)).difference(header[0])
+    )
+    combined_header.insert(0, "id")
+
+    # Write samplesheet with paths to FastQ files and md5 sums.
+    if samplesheet:
+        with file_out.open("w", newline="") as fout:
+            writer = csv.DictWriter(fout, fieldnames=combined_header, delimiter="\t")
+            writer.writeheader()
+            for db_id in sorted(samplesheet):
+                for idx, row in enumerate(samplesheet[db_id], start=1):
+                    row["id"] = f"{db_id}_T{idx}"
+                    writer.writerow(row)
+
 
 def main(args=None):
     args = parse_args(args)
-    sra_runinfo_to_ftp([x.strip() for x in args.FILES_IN.split(',')], args.FILE_OUT)
+    logging.basicConfig(level=args.log_level, format="[%(levelname)s] %(message)s")
+    files = [Path(x.strip()) for x in args.files_in.split(",")]
+    for path in files:
+        if not path.is_file():
+            logger.critical(f"The given input file {path} was not found!")
+            sys.exit(1)
+    args.file_out.parent.mkdir(parents=True, exist_ok=True)
+    sra_runinfo_to_ftp(files, args.file_out)
+
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     sys.exit(main())

From 8b5847a6a1e2e85c760c2f32c4307b3a4316ef9e Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Mon, 25 Oct 2021 16:21:31 +0200
Subject: [PATCH 114/852] feat: include SRA subworkflow

---
 workflows/sra.nf | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/workflows/sra.nf b/workflows/sra.nf
index b3d357e4..530bf91a 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -69,6 +69,8 @@ workflow SRA {
     )
     ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first())
 
+
+
     SRA_RUNINFO_TO_FTP
         .out
         .tsv
@@ -79,6 +81,10 @@ workflow SRA {
                 [ meta, [ meta.fastq_1, meta.fastq_2 ] ]
         }
         .unique()
+        .branch {
+            ftp: it[0].fastq_1
+            raw: !it[0].fastq_1
+        }
         .set { ch_sra_reads }
     ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first())
 
@@ -87,13 +93,13 @@ workflow SRA {
         // MODULE: If FTP link is provided in run information then download FastQ directly via FTP and validate with md5sums
         //
         SRA_FASTQ_FTP (
-            ch_sra_reads.map { meta, reads -> if (meta.fastq_1)  [ meta, reads ] }
+            ch_sra_reads.ftp
         )
         ch_versions = ch_versions.mix(SRA_FASTQ_FTP.out.versions.first())
 
         // SUBWORKFLOW: Download sequencing reads without FTP links using sra-tools.
         SRA_FASTQ (
-            ch_sra_reads.map { meta, reads -> if (!meta.fastq_1) [meta, meta.run_accession] }
+            ch_sra_reads.raw.map { meta, reads -> [ meta, meta.run_accession ] }
         )
         ch_versions = ch_versions.mix(SRA_FASTQ.out.versions.first())
 

From 8deb5f18e287e7f7082315b699462570166c4b96 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Mon, 25 Oct 2021 16:35:20 +0200
Subject: [PATCH 115/852] docs: add credits and usage

---
 README.md     | 4 ++--
 docs/usage.md | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 43dcf30d..b51867ed 100644
--- a/README.md
+++ b/README.md
@@ -30,7 +30,7 @@ Via a single file of ids, provided one-per-line (see [example input file](https:
 
 1. Resolve database ids back to appropriate experiment-level ids and to be compatible with the [ENA API](https://ena-docs.readthedocs.io/en/latest/retrieval/programmatic-access.html)
 2. Fetch extensive id metadata including direct download links to FastQ files via ENA API
-3. Download FastQ files in parallel via `curl` and perform `md5sum` check
+3. Download FastQ files in parallel via `curl` if available from FTP and perform `md5sum` check. Otherwise use sra-tools to download SRAs and convert them to FastQ.
 4. Collate id metadata and paths to FastQ files in a single samplesheet
 
 ### Synapse ids
@@ -72,7 +72,7 @@ The nf-core/fetchngs pipeline comes with documentation about the pipeline [usage
 
 ## Credits
 
-nf-core/fetchngs was originally written by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [Seqera Labs, Spain](https://seqera.io/) and Jose Espinosa-Carrasco ([@JoseEspinosa](https://github.com/JoseEspinosa)) from [The Comparative Bioinformatics Group](https://www.crg.eu/en/cedric_notredame) at [The Centre for Genomic Regulation, Spain](https://www.crg.eu/).
+nf-core/fetchngs was originally written by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [Seqera Labs, Spain](https://seqera.io/) and Jose Espinosa-Carrasco ([@JoseEspinosa](https://github.com/JoseEspinosa)) from [The Comparative Bioinformatics Group](https://www.crg.eu/en/cedric_notredame) at [The Centre for Genomic Regulation, Spain](https://www.crg.eu/). Support for download of sequencing reads without FTP links via sra-tools was added by Moritz E. Beber ([@Midnighter](https://github.com/Midnighter)) from [Unseen Bio ApS, Denmark](https://unseenbio.com).
 
 ## Contributions and Support
 
diff --git a/docs/usage.md b/docs/usage.md
index 5040552b..6af310a6 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -22,7 +22,7 @@ The pipeline has been set-up to automatically download and process the raw FastQ
 
 If `SRR`/`ERR`/`DRR` run ids are provided then these will be resolved back to their appropriate `SRX`/`ERX`/`DRX` ids to be able to merge multiple runs from the same experiment. This is conceptually the same as merging multiple libraries sequenced from the same sample.
 
-The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5 sums. If download links exist, the files will be downloaded in parallel by FTP otherwise they will NOT be downloaded. This is intentional because tools such as `parallel-fastq-dump`, `fasterq-dump`, `prefetch` etc require pre-existing configuration files in the users home directory which makes automation tricky across different platforms and containerisation. We may add this functionality in later releases.
+The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5 sums. If download links exist, the files will be downloaded in parallel by FTP. Otherwise they are downloaded using sra-tools.
 
 All of the sample metadata obtained from the ENA will be appended as additional columns to help you manually curate the generated samplesheet before you run the pipeline. You can customise the metadata fields that are appended to the samplesheet via the `--ena_metadata_fields` parameter. The default list of fields used by the pipeline can be found at the top of the [`bin/sra_ids_to_runinfo.py`](https://github.com/nf-core/fetchngs/blob/master/bin/sra_ids_to_runinfo.py) script within the pipeline repo. However, this pipeline requires a minimal set of fields to download FastQ files i.e. `'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'`. A comprehensive list of accepted metadata fields can be obtained from the [ENA API](https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run]).
 

From 36753b3d91469c81926ed0cc5d89d84abc85e0bc Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Mon, 25 Oct 2021 16:37:03 +0200
Subject: [PATCH 116/852] chore: add changelog entry

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9e9a0cb2..5c2178bf 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unpublished Version / DEV]
 
+* Add support for run accessions not available on FTP via sra-tools.
+
 ### Enhancements & fixes
 
 * Added a workflow to download FastQ files and to create samplesheets for ids from the [Synapse platform](https://www.synapse.org/) hosted by [Sage Bionetworks](https://sagebionetworks.org/).

From 408f1bc0add9ce4d8c0aa987cbe8f5a6adf3fdf1 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 25 Oct 2021 16:49:30 +0100
Subject: [PATCH 117/852] Fix #46

---
 CHANGELOG.md              | 1 +
 bin/sra_ids_to_runinfo.py | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9e9a0cb2..a03c0774 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 * Added a workflow to download FastQ files and to create samplesheets for ids from the [Synapse platform](https://www.synapse.org/) hosted by [Sage Bionetworks](https://sagebionetworks.org/).
 * Handle SRA identifiers that do **not** return metadata, for example, due to being private.
+* [[#46](https://github.com/nf-core/fetchngs/issues/46)] - Bug in sra_ids_to_runinfo.py
 * Added support for [DDBJ ids](https://www.ddbj.nig.ac.jp/index-e.html). See examples below:
 
 | `DDBJ`        |
diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index 0f81c125..bbd1e6f0 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -269,7 +269,7 @@ def _gse_to_srx(cls, identifier):
         gsm_ids = [
             line.split("=")[1].strip()
             for line in response.text().splitlines()
-            if line.startswith("GSM")
+            if line.split('=')[1].strip().startswith('GSM')
         ]
         for gsm_id in gsm_ids:
             ids += cls._id_to_srx(gsm_id)

From 0d82d986b699ce9c30b2c3e1b4407a53d58aa7c2 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 25 Oct 2021 17:21:31 +0100
Subject: [PATCH 118/852] Change default process requirements for
 sra_fastq_ftp.nf

---
 modules/local/sra_fastq_ftp.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/sra_fastq_ftp.nf b/modules/local/sra_fastq_ftp.nf
index cccdd8ac..23ea5dd5 100644
--- a/modules/local/sra_fastq_ftp.nf
+++ b/modules/local/sra_fastq_ftp.nf
@@ -6,7 +6,7 @@ options        = initOptions(params.options)
 
 process SRA_FASTQ_FTP {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_low'
     label 'error_retry'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,

From 8c6231ca0a5364514e79673cb447f96320de39d8 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 25 Oct 2021 22:58:47 +0100
Subject: [PATCH 119/852] Update CHANGELOG

---
 CHANGELOG.md | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 49d2c5f1..0153327e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,14 +3,13 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unpublished Version / DEV]
-
-* Add support for run accessions not available on FTP via sra-tools.
+## [[1.4](https://github.com/nf-core/fetchngs/releases/tag/1.4)] - 2021-10-25
 
 ### Enhancements & fixes
 
 * Added a workflow to download FastQ files and to create samplesheets for ids from the [Synapse platform](https://www.synapse.org/) hosted by [Sage Bionetworks](https://sagebionetworks.org/).
-* Handle SRA identifiers that do **not** return metadata, for example, due to being private.
+* SRA identifiers not available for direct download via the ENA FTP will now be downloaded via sra-tools.
+* Correctly handle errors from SRA identifiers that do **not** return metadata, for example, due to being private.
 * [[#46](https://github.com/nf-core/fetchngs/issues/46)] - Bug in sra_ids_to_runinfo.py
 * Added support for [DDBJ ids](https://www.ddbj.nig.ac.jp/index-e.html). See examples below:
 

From 5c910777374498f92fdaa5dd826893b804fe08db Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 25 Oct 2021 22:59:02 +0100
Subject: [PATCH 120/852] Update listing in README

---
 README.md | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index b51867ed..ff3829ef 100644
--- a/README.md
+++ b/README.md
@@ -29,8 +29,10 @@ Via a single file of ids, provided one-per-line (see [example input file](https:
 ### SRA / ENA / DDBJ / GEO ids
 
 1. Resolve database ids back to appropriate experiment-level ids and to be compatible with the [ENA API](https://ena-docs.readthedocs.io/en/latest/retrieval/programmatic-access.html)
-2. Fetch extensive id metadata including direct download links to FastQ files via ENA API
-3. Download FastQ files in parallel via `curl` if available from FTP and perform `md5sum` check. Otherwise use sra-tools to download SRAs and convert them to FastQ.
+2. Fetch extensive id metadata via ENA API
+3. Download FastQ files:
+  - If direct download links are available from the ENA API, fetch in parallel via `curl` and perform `md5sum` check
+  - Otherwise use `sra-tools` to download `.sra` files and convert them to FastQ
 4. Collate id metadata and paths to FastQ files in a single samplesheet
 
 ### Synapse ids

From 97e8c32ca447a0be7e02cdcfb47f05f760dc6cc2 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 25 Oct 2021 22:59:18 +0100
Subject: [PATCH 121/852] Don't publish .sra files by default

---
 conf/modules.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conf/modules.config b/conf/modules.config
index 534b8249..2a2bcca5 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -37,6 +37,7 @@ params {
         }
         'sratools_prefetch' {
             publish_dir     = 'sra'
+            publish_files   = false
         }
         'sratools_fasterqdump' {
             publish_dir     = 'fastq'

From 2fcce24cbbd49bc0f3ee335887627322c3bcff45 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 25 Oct 2021 22:59:31 +0100
Subject: [PATCH 122/852] Bump pipeline version to 1.4

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 45dfb946..066fb0b3 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -149,7 +149,7 @@ manifest {
     description     = 'Pipeline to fetch metadata and raw FastQ files from public databases'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.04.0'
-    version         = '1.4dev'
+    version         = '1.4'
 }
 
 // Function to ensure that resource requirements don't go beyond

From ef931d38e8fba8a8db26e0cdc621458cc30da2cb Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 25 Oct 2021 23:10:11 +0100
Subject: [PATCH 123/852] Update output docs with sra-tools functionality

---
 docs/output.md   | 2 +-
 workflows/sra.nf | 6 ++----
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/docs/output.md b/docs/output.md
index df7fec02..6e6c610b 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -34,7 +34,7 @@ Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introductio
 
 </details>
 
-The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5sums. If download links exist, the files will be downloaded in parallel by FTP otherwise they will NOT be downloaded. This is intentional because the tools such as `parallel-fastq-dump`, `fasterq-dump`, `prefetch` etc require pre-existing configuration files in the users home directory which makes automation tricky across different platforms and containerisation.
+The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5 sums. If download links exist, the files will be downloaded in parallel by FTP. Otherwise they are downloaded using sra-tools.
 
 ### Synapse ids
 
diff --git a/workflows/sra.nf b/workflows/sra.nf
index 530bf91a..4fb41ccd 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -69,8 +69,6 @@ workflow SRA {
     )
     ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first())
 
-
-
     SRA_RUNINFO_TO_FTP
         .out
         .tsv
@@ -83,7 +81,7 @@ workflow SRA {
         .unique()
         .branch {
             ftp: it[0].fastq_1
-            raw: !it[0].fastq_1
+            sra: !it[0].fastq_1
         }
         .set { ch_sra_reads }
     ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first())
@@ -99,7 +97,7 @@ workflow SRA {
 
         // SUBWORKFLOW: Download sequencing reads without FTP links using sra-tools.
         SRA_FASTQ (
-            ch_sra_reads.raw.map { meta, reads -> [ meta, meta.run_accession ] }
+            ch_sra_reads.sra.map { meta, reads -> [ meta, meta.run_accession ] }
         )
         ch_versions = ch_versions.mix(SRA_FASTQ.out.versions.first())
 

From 78c55d9f6a505771c50eb9d3c021379399c81681 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 25 Oct 2021 23:34:27 +0100
Subject: [PATCH 124/852] Fix markdownlint

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index ff3829ef..e21a94a9 100644
--- a/README.md
+++ b/README.md
@@ -31,8 +31,8 @@ Via a single file of ids, provided one-per-line (see [example input file](https:
 1. Resolve database ids back to appropriate experiment-level ids and to be compatible with the [ENA API](https://ena-docs.readthedocs.io/en/latest/retrieval/programmatic-access.html)
 2. Fetch extensive id metadata via ENA API
 3. Download FastQ files:
-  - If direct download links are available from the ENA API, fetch in parallel via `curl` and perform `md5sum` check
-  - Otherwise use `sra-tools` to download `.sra` files and convert them to FastQ
+    - If direct download links are available from the ENA API, fetch in parallel via `curl` and perform `md5sum` check
+    - Otherwise use `sra-tools` to download `.sra` files and convert them to FastQ
 4. Collate id metadata and paths to FastQ files in a single samplesheet
 
 ### Synapse ids

From 767f02e6007372a5d2c05057b4051024aaa3ab29 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 25 Oct 2021 23:37:01 +0100
Subject: [PATCH 125/852] Replace asterix with dashes for markdownling

---
 README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index e21a94a9..636ba12f 100644
--- a/README.md
+++ b/README.md
@@ -58,9 +58,9 @@ The columns in the auto-created samplesheet can be tailored to be accepted out-o
     nextflow run nf-core/fetchngs -profile test,<docker/singularity/podman/shifter/charliecloud/conda/institute>
     ```
 
-    > * Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
-    > * If you are using `singularity` then the pipeline will auto-detect this and attempt to download the Singularity images directly as opposed to performing a conversion from Docker images. If you are persistently observing issues downloading Singularity images directly due to timeout or network issues then please use the `--singularity_pull_docker_container` parameter to pull and convert the Docker image instead. Alternatively, it is highly recommended to use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to pre-download all of the required containers before running the pipeline and to set the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options to be able to store and re-use the images from a central location for future pipeline runs.
-    > * If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
+    > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
+    > - If you are using `singularity` then the pipeline will auto-detect this and attempt to download the Singularity images directly as opposed to performing a conversion from Docker images. If you are persistently observing issues downloading Singularity images directly due to timeout or network issues then please use the `--singularity_pull_docker_container` parameter to pull and convert the Docker image instead. Alternatively, it is highly recommended to use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to pre-download all of the required containers before running the pipeline and to set the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options to be able to store and re-use the images from a central location for future pipeline runs.
+    > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
 
 4. Start running your own analysis!
 

From d739f3718be5f92e5f10e165c4fe75ee9ca9fea4 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Tue, 26 Oct 2021 11:26:40 +0200
Subject: [PATCH 126/852] feat: add bash script to retry prefetch

---
 bin/retry_with_backoff.sh                     | 100 ++++++++++++++++++
 .../nf-core/modules/sratools/prefetch/main.nf |   2 +-
 2 files changed, 101 insertions(+), 1 deletion(-)
 create mode 100755 bin/retry_with_backoff.sh

diff --git a/bin/retry_with_backoff.sh b/bin/retry_with_backoff.sh
new file mode 100755
index 00000000..4bdbf1e0
--- /dev/null
+++ b/bin/retry_with_backoff.sh
@@ -0,0 +1,100 @@
+#!/usr/bin/env bash
+
+set -u
+
+retry_with_backoff() {
+    local max_attempts=${1}
+    local delay=${2}
+    local max_time=${3}
+    local attempt=1
+    local output=
+    local status=
+
+    shift 3
+
+    while [ ${attempt} -le ${max_attempts} ]; do
+        output=$("${@}")
+        status=${?}
+
+        if [ ${status} -eq 0 ]; then
+            break
+        fi
+
+        if [ ${attempt} -lt ${max_attempts} ]; then
+            echo "Failed attempt ${attempt} of ${max_attempts}. Retrying in ${delay} s." >&2
+            sleep ${delay}
+        elif [ ${attempt} -eq ${max_attempts} ]; then
+            echo "Failed after ${attempt} attempts." >&2
+            return ${status}
+        fi
+
+        attempt=$(( ${attempt} + 1 ))
+        delay=$(( ${delay} * 2 ))
+        if [ ${delay} -ge ${max_time} ]; then
+            delay=${max_time}
+        fi
+    done
+
+    echo "${output}"
+}
+
+RETRY=5
+DELAY=1
+MAX_TIME=60
+
+usage() {
+    echo "Usage:" >&2
+    echo "$(basename ${0}) [-h] [-r NUM] [-d NUM] [-m NUM] COMMAND" >&2
+    echo "Call the given command with retries and exponential backoff." >&2
+    echo "" >&2
+    echo "  -r NUM  Set the number of retry attempts (default ${RETRY})." >&2
+    echo "  -d NUM  Set the base number of seconds to delay (default ${DELAY})." >&2
+    echo "  -m NUM  Set the maximum delay in seconds (default ${MAX_TIME})." >&2
+    echo "" >&2
+}
+
+check_numeric() {
+    local arg=${1}
+    if [[ ! ${arg} =~ ^[0-9]+$ ]]; then
+        echo "Illegal argument: ${arg}" >&2
+        echo "Expected a number." >&2
+        echo "" >&2
+        usage
+        exit 2
+    fi
+}
+
+while getopts ":hr:d:m:" arg; do
+    case ${arg} in
+        h)
+            usage
+            exit 0
+            ;;
+        r)
+            check_numeric ${OPTARG}
+            RETRY=${OPTARG}
+            ;;
+        d)
+            check_numeric ${OPTARG}
+            DELAY=${OPTARG}
+            ;;
+        m)
+            check_numeric ${OPTARG}
+            MAX_TIME=${OPTARG}
+            ;;
+        ?)
+            echo "Invalid option: -${OPTARG}" >&2
+            echo "" >&2
+            usage
+            exit 2
+            ;;
+        :)
+            echo "Missing argument for: -${OPTARG}" >&2
+            echo "" >&2
+            usage
+            exit 2
+            ;;
+    esac
+done
+
+retry_with_backoff ${RETRY} ${DELAY} ${MAX_TIME} ${@:OPTIND}
diff --git a/modules/nf-core/modules/sratools/prefetch/main.nf b/modules/nf-core/modules/sratools/prefetch/main.nf
index 207d1e10..c57255f5 100644
--- a/modules/nf-core/modules/sratools/prefetch/main.nf
+++ b/modules/nf-core/modules/sratools/prefetch/main.nf
@@ -35,7 +35,7 @@ process SRATOOLS_PREFETCH {
         printf '${config}' > "\${NCBI_SETTINGS}"
     fi
 
-    prefetch \\
+    retry_with_backoff.sh prefetch \\
         $options.args \\
         --progress \\
         $id

From 753e7e2d795a6d8f3c8736b2fe9490f9d85a2ffd Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Tue, 26 Oct 2021 11:32:20 +0200
Subject: [PATCH 127/852] chore: note change

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 49d2c5f1..6e417235 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [Unpublished Version / DEV]
 
 * Add support for run accessions not available on FTP via sra-tools.
+* Resume interrupted downloads with prefetch.
 
 ### Enhancements & fixes
 

From c973452f56967e8061736935a03d3cf11b163cd9 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Tue, 26 Oct 2021 11:37:43 +0200
Subject: [PATCH 128/852] chore: reword changelog

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6e417235..7dc6402a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,7 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [Unpublished Version / DEV]
 
 * Add support for run accessions not available on FTP via sra-tools.
-* Resume interrupted downloads with prefetch.
+* Retry an error in prefetch via bash script in order to allow it to resume interrupted downloads.
 
 ### Enhancements & fixes
 

From 01cc0fbe6a588f5a55cc0afd09ee65b9f4ec8092 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 26 Oct 2021 10:50:08 +0100
Subject: [PATCH 129/852] Update test_full data and credits for synapse

---
 README.md             | 2 +-
 conf/test_full.config | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 636ba12f..a5ffb8a6 100644
--- a/README.md
+++ b/README.md
@@ -74,7 +74,7 @@ The nf-core/fetchngs pipeline comes with documentation about the pipeline [usage
 
 ## Credits
 
-nf-core/fetchngs was originally written by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [Seqera Labs, Spain](https://seqera.io/) and Jose Espinosa-Carrasco ([@JoseEspinosa](https://github.com/JoseEspinosa)) from [The Comparative Bioinformatics Group](https://www.crg.eu/en/cedric_notredame) at [The Centre for Genomic Regulation, Spain](https://www.crg.eu/). Support for download of sequencing reads without FTP links via sra-tools was added by Moritz E. Beber ([@Midnighter](https://github.com/Midnighter)) from [Unseen Bio ApS, Denmark](https://unseenbio.com).
+nf-core/fetchngs was originally written by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [Seqera Labs, Spain](https://seqera.io/) and Jose Espinosa-Carrasco ([@JoseEspinosa](https://github.com/JoseEspinosa)) from [The Comparative Bioinformatics Group](https://www.crg.eu/en/cedric_notredame) at [The Centre for Genomic Regulation, Spain](https://www.crg.eu/). Support for download of sequencing reads without FTP links via sra-tools was added by Moritz E. Beber ([@Midnighter](https://github.com/Midnighter)) from [Unseen Bio ApS, Denmark](https://unseenbio.com). The Synapse workflow was added by Daisy Han [@daisyhan97](https://github.com/daisyhan97) and Bruno Grande [@BrunoGrandePhD](https://github.com/BrunoGrandePhD) from [Sage Bionetworks, Seattle](https://sagebionetworks.org/).
 
 ## Contributions and Support
 
diff --git a/conf/test_full.config b/conf/test_full.config
index a5aea2dc..16398e23 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -15,5 +15,5 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/public_database_ids.txt'
+    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.txt'
 }

From cf374eab1187b8f35426f8807ed0fd10112eb33a Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 3 Nov 2021 15:23:59 +0000
Subject: [PATCH 130/852] Port pipeline to new DSL2 syntax

---
 conf/modules.config                           | 200 ++++++++++++------
 modules.json                                  |  14 +-
 .../main.nf => local/dumpsoftwareversions.nf} |  20 +-
 modules/local/functions.nf                    |  78 -------
 modules/local/multiqc_mappings_config.nf      |  17 +-
 modules/local/sra_fastq_ftp.nf                |  27 +--
 modules/local/sra_ids_to_runinfo.nf           |  17 +-
 modules/local/sra_merge_samplesheet.nf        |  17 +-
 modules/local/sra_runinfo_to_ftp.nf           |  17 +-
 modules/local/sra_to_samplesheet.nf           |   6 -
 .../main.nf => local/sratools_fasterqdump.nf} |  26 +--
 modules/local/sratools_prefetch.nf            |  41 ++++
 modules/local/synapse_get.nf                  |  23 +-
 modules/local/synapse_list.nf                 |  26 +--
 modules/local/synapse_merge_samplesheet.nf    |  17 +-
 modules/local/synapse_show.nf                 |  26 +--
 modules/local/synapse_to_samplesheet.nf       |   7 -
 .../custom/dumpsoftwareversions/functions.nf  |  78 -------
 .../custom/dumpsoftwareversions/meta.yml      |  33 ---
 .../modules/sratools/fasterqdump/functions.nf |  78 -------
 .../modules/sratools/fasterqdump/meta.yml     |  42 ----
 .../modules/sratools/prefetch/functions.nf    |  78 -------
 .../nf-core/modules/sratools/prefetch/main.nf |  50 -----
 .../modules/sratools/prefetch/meta.yml        |  43 ----
 nextflow.config                               |  10 +-
 subworkflows/local/sra_fastq/main.nf          |   7 +-
 workflows/sra.nf                              |  27 +--
 workflows/synapse.nf                          |  23 +-
 28 files changed, 269 insertions(+), 779 deletions(-)
 rename modules/{nf-core/modules/custom/dumpsoftwareversions/main.nf => local/dumpsoftwareversions.nf} (79%)
 delete mode 100644 modules/local/functions.nf
 rename modules/{nf-core/modules/sratools/fasterqdump/main.nf => local/sratools_fasterqdump.nf} (54%)
 create mode 100644 modules/local/sratools_prefetch.nf
 delete mode 100644 modules/nf-core/modules/custom/dumpsoftwareversions/functions.nf
 delete mode 100644 modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml
 delete mode 100644 modules/nf-core/modules/sratools/fasterqdump/functions.nf
 delete mode 100644 modules/nf-core/modules/sratools/fasterqdump/meta.yml
 delete mode 100644 modules/nf-core/modules/sratools/prefetch/functions.nf
 delete mode 100644 modules/nf-core/modules/sratools/prefetch/main.nf
 delete mode 100644 modules/nf-core/modules/sratools/prefetch/meta.yml

diff --git a/conf/modules.config b/conf/modules.config
index 2a2bcca5..88a1a72b 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -1,74 +1,144 @@
 /*
 ========================================================================================
-    Config file for defining DSL2 per module options
+    Config file for defining DSL2 per module options and publishing paths
 ========================================================================================
     Available keys to override module options:
-        args            = Additional arguments appended to command in module.
-        args2           = Second set of arguments appended to command in module (multi-tool modules).
-        args3           = Third set of arguments appended to command in module (multi-tool modules).
-        publish_dir     = Directory to publish results.
-        publish_by_meta = Groovy list of keys available in meta map to append as directories to "publish_dir" path
-                            If publish_by_meta = true                 - Value of ${meta['id']} is appended as a directory to "publish_dir" path
-                            If publish_by_meta = ['id', 'custompath'] - If "id" is in meta map and "custompath" isn't then "${meta['id']}/custompath/"
-                                                                        is appended as a directory to "publish_dir" path
-                            If publish_by_meta = false / null         - No directories are appended to "publish_dir" path
-        publish_files   = Groovy map where key = "file_ext" and value = "directory" to publish results for that file extension
-                            The value of "directory" is appended to the standard "publish_dir" path as defined above.
-                            If publish_files = null (unspecified)     - All files are published.
-                            If publish_files = false                  - No files are published.
-        suffix          = File name suffix for output files.
+        ext.args            = Additional arguments appended to command in module.
+        ext.args2           = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3           = Third set of arguments appended to command in module (multi-tool modules).
+        ext.suffix          = File name suffix for output files.
 ----------------------------------------------------------------------------------------
 */
 
-params {
-    modules {
-        'sra_ids_to_runinfo' {
-            publish_dir     = 'metadata'
-            publish_files   = false
-        }
-        'sra_runinfo_to_ftp' {
-            publish_dir     = 'metadata'
-            publish_files   = ['tsv':'']
-        }
-        'sra_fastq_ftp' {
-            publish_dir     = 'fastq'
-            publish_files   = ['fastq.gz':'', 'md5':'md5']
-            args            = '--retry 5 --continue-at - --max-time 1200'
-        }
-        'sratools_prefetch' {
-            publish_dir     = 'sra'
-            publish_files   = false
-        }
-        'sratools_fasterqdump' {
-            publish_dir     = 'fastq'
-        }
-        'sra_to_samplesheet' {
-            publish_dir     = 'samplesheet'
-            publish_files   = false
-        }
-        'sra_merge_samplesheet' {
-            publish_dir     = 'samplesheet'
-        }
-        'synapse_list' {
-            args            = '--long'
-            publish_dir     = 'metadata'
-        }
-        'synapse_get' {
-            publish_dir     = 'fastq'
-            publish_files   = ['fastq.gz':'', 'md5':'md5']
-        }
-        'synapse_show' {
-            publish_dir     = 'metadata'
-        }
-        'synapse_to_samplesheet' {
-            publish_dir     = 'samplesheet'
-            publish_files   = false
-        }
-        'synapse_merge_samplesheet' {
-            publish_dir     = 'samplesheet'
-        }
-        'multiqc_mappings_config' {
-            publish_dir     = 'samplesheet'
-        }
+process {
+
+    publishDir = [
+        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+    ]
+
+    withName: SRA_IDS_TO_RUNINFO {
+        publishDir = [
+            path: { "${params.outdir}/metadata" },
+            enabled: false
+        ]
+    }
+
+    withName: SRA_RUNINFO_TO_FTP {
+        publishDir = [
+            path: { "${params.outdir}/metadata" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: SRA_FASTQ_FTP {
+        ext.args = '--retry 5 --continue-at - --max-time 1200'
+        publishDir = [
+            [
+                path: { "${params.outdir}/fastq" },
+                mode: params.publish_dir_mode,
+                pattern: "*gz"
+            ],
+            [
+                path: { "${params.outdir}/fastq/md5" },
+                mode: params.publish_dir_mode,
+                pattern: "*.md5"
+            ]
+        ]
+    }
+
+    withName: SRATOOLS_PREFETCH {
+        publishDir = [
+            path: { "${params.outdir}/sra" },
+            enabled: false
+        ]
+    }
+
+    withName: SRATOOLS_FASTERQDUMP {
+        publishDir = [
+            path: { "${params.outdir}/fastq" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: SRA_TO_SAMPLESHEET {
+        publishDir = [
+            path: { "${params.outdir}/samplesheet" },
+            enabled: false
+        ]
+    }
+
+    withName: SRA_MERGE_SAMPLESHEET {
+        publishDir = [
+            path: { "${params.outdir}/samplesheet" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: SYNAPSE_LIST {
+        ext.args = '--long'
+        publishDir = [
+            path: { "${params.outdir}/metadata" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: SYNAPSE_GET {
+        publishDir = [
+            [
+                path: { "${params.outdir}/fastq" },
+                mode: params.publish_dir_mode,
+                pattern: "*gz"
+            ],
+            [
+                path: { "${params.outdir}/fastq/md5" },
+                mode: params.publish_dir_mode,
+                pattern: "*.md5"
+            ]
+        ]
+    }
+
+    withName: SYNAPSE_SHOW {
+        publishDir = [
+            path: { "${params.outdir}/metadata" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: SYNAPSE_TO_SAMPLESHEET {
+        publishDir = [
+            path: { "${params.outdir}/samplesheet" },
+            enabled: false
+        ]
+    }
+
+    withName: SYNAPSE_MERGE_SAMPLESHEET {
+        publishDir = [
+            path: { "${params.outdir}/samplesheet" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: MULTIQC_MAPPINGS_CONFIG {
+        publishDir = [
+            path: { "${params.outdir}/samplesheet" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: DUMPSOFTWAREVERSIONS {
+        publishDir = [
+            path: { "${params.outdir}/pipeline_info" },
+            mode: params.publish_dir_mode,
+            pattern: '*_versions.yml'
+        ]
     }
 }
diff --git a/modules.json b/modules.json
index f004808d..0e4143ef 100644
--- a/modules.json
+++ b/modules.json
@@ -1,17 +1,5 @@
 {
     "name": "nf-core/fetchngs",
     "homePage": "https://github.com/nf-core/fetchngs",
-    "repos": {
-        "nf-core/modules": {
-            "custom/dumpsoftwareversions": {
-                "git_sha": "84f2302920078b0cf7716b2a2e5fcc0be5c4531d"
-            },
-            "sratools/fasterqdump": {
-                "git_sha": "de997825de788fe2210db16d9426f10342a1ba1d"
-            },
-            "sratools/prefetch": {
-                "git_sha": "07c0830057cc655de113d84499c7c1499460bb55"
-            }
-        }
-    }
+    "repos": {}
 }
\ No newline at end of file
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf b/modules/local/dumpsoftwareversions.nf
similarity index 79%
rename from modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
rename to modules/local/dumpsoftwareversions.nf
index faf2073f..69ebcbaa 100644
--- a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
+++ b/modules/local/dumpsoftwareversions.nf
@@ -1,22 +1,12 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
-params.options = [:]
-options        = initOptions(params.options)
-
-process CUSTOM_DUMPSOFTWAREVERSIONS {
+process DUMPSOFTWAREVERSIONS {
     label 'process_low'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', meta:[:], publish_by_meta:[]) }
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
     conda (params.enable_conda ? "bioconda::multiqc=1.11" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0"
-    } else {
-        container "quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0"
-    }
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }"
 
     input:
     path versions
@@ -73,7 +63,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
         return "\\n".join(html)
 
     module_versions = {}
-    module_versions["${getProcessName(task.process)}"] = {
+    module_versions["${task.process.tokenize(':').last()}"] = {
         'python': platform.python_version(),
         'yaml': yaml.__version__
     }
diff --git a/modules/local/functions.nf b/modules/local/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/local/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-//  Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}
diff --git a/modules/local/multiqc_mappings_config.nf b/modules/local/multiqc_mappings_config.nf
index 857c859c..15c30846 100644
--- a/modules/local/multiqc_mappings_config.nf
+++ b/modules/local/multiqc_mappings_config.nf
@@ -1,19 +1,10 @@
-// Import generic module functions
-include { saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
 
 process MULTIQC_MAPPINGS_CONFIG {
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/python:3.9--1"
-    } else {
-        container "quay.io/biocontainers/python:3.9--1"
-    }
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/python:3.9--1' :
+        'quay.io/biocontainers/python:3.9--1' }"
 
     input:
     path csv
@@ -29,7 +20,7 @@ process MULTIQC_MAPPINGS_CONFIG {
         multiqc_config.yml
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    ${task.process.tokenize(':').last()}:
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """
diff --git a/modules/local/sra_fastq_ftp.nf b/modules/local/sra_fastq_ftp.nf
index 23ea5dd5..a775849c 100644
--- a/modules/local/sra_fastq_ftp.nf
+++ b/modules/local/sra_fastq_ftp.nf
@@ -1,23 +1,13 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
 
 process SRA_FASTQ_FTP {
     tag "$meta.id"
     label 'process_low'
     label 'error_retry'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
-    } else {
-        container "biocontainers/biocontainers:v1.2.0_cv1"
-    }
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
+        'biocontainers/biocontainers:v1.2.0_cv1' }"
 
     input:
     tuple val(meta), val(fastq)
@@ -28,10 +18,11 @@ process SRA_FASTQ_FTP {
     path "versions.yml"               , emit: versions
 
     script:
+    def args = task.ext.args ?: ''
     if (meta.single_end) {
         """
         curl \\
-            $options.args \\
+            $args \\
             -L ${fastq[0]} \\
             -o ${meta.id}.fastq.gz
 
@@ -39,14 +30,14 @@ process SRA_FASTQ_FTP {
         md5sum -c ${meta.id}.fastq.gz.md5
 
         cat <<-END_VERSIONS > versions.yml
-        ${getProcessName(task.process)}:
+        ${task.process.tokenize(':').last()}:
             curl: \$(echo \$(curl --version | head -n 1 | sed 's/^curl //; s/ .*\$//'))
         END_VERSIONS
         """
     } else {
         """
         curl \\
-            $options.args \\
+            $args \\
             -L ${fastq[0]} \\
             -o ${meta.id}_1.fastq.gz
 
@@ -54,7 +45,7 @@ process SRA_FASTQ_FTP {
         md5sum -c ${meta.id}_1.fastq.gz.md5
 
         curl \\
-            $options.args \\
+            $args \\
             -L ${fastq[1]} \\
             -o ${meta.id}_2.fastq.gz
 
@@ -62,7 +53,7 @@ process SRA_FASTQ_FTP {
         md5sum -c ${meta.id}_2.fastq.gz.md5
 
         cat <<-END_VERSIONS > versions.yml
-        ${getProcessName(task.process)}:
+        ${task.process.tokenize(':').last()}:
             curl: \$(echo \$(curl --version | head -n 1 | sed 's/^curl //; s/ .*\$//'))
         END_VERSIONS
         """
diff --git a/modules/local/sra_ids_to_runinfo.nf b/modules/local/sra_ids_to_runinfo.nf
index 8200271e..c8209690 100644
--- a/modules/local/sra_ids_to_runinfo.nf
+++ b/modules/local/sra_ids_to_runinfo.nf
@@ -1,21 +1,12 @@
-// Import generic module functions
-include { saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
 
 process SRA_IDS_TO_RUNINFO {
     tag "$id"
     label 'error_retry'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/python:3.9--1"
-    } else {
-        container "quay.io/biocontainers/python:3.9--1"
-    }
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/python:3.9--1' :
+        'quay.io/biocontainers/python:3.9--1' }"
 
     input:
     val id
@@ -35,7 +26,7 @@ process SRA_IDS_TO_RUNINFO {
         $metadata_fields
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    ${task.process.tokenize(':').last()}:
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """
diff --git a/modules/local/sra_merge_samplesheet.nf b/modules/local/sra_merge_samplesheet.nf
index 914bac00..be3f1087 100644
--- a/modules/local/sra_merge_samplesheet.nf
+++ b/modules/local/sra_merge_samplesheet.nf
@@ -1,19 +1,10 @@
-// Import generic module functions
-include { saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
 
 process SRA_MERGE_SAMPLESHEET {
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
-    } else {
-        container "biocontainers/biocontainers:v1.2.0_cv1"
-    }
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
+        'biocontainers/biocontainers:v1.2.0_cv1' }"
 
     input:
     path ('samplesheets/*')
@@ -37,7 +28,7 @@ process SRA_MERGE_SAMPLESHEET {
     done
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    ${task.process.tokenize(':').last()}:
         sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
     END_VERSIONS
     """
diff --git a/modules/local/sra_runinfo_to_ftp.nf b/modules/local/sra_runinfo_to_ftp.nf
index 80028705..a6b6a829 100644
--- a/modules/local/sra_runinfo_to_ftp.nf
+++ b/modules/local/sra_runinfo_to_ftp.nf
@@ -1,19 +1,10 @@
-// Import generic module functions
-include { saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
 
 process SRA_RUNINFO_TO_FTP {
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/python:3.9--1"
-    } else {
-        container "quay.io/biocontainers/python:3.9--1"
-    }
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/python:3.9--1' :
+        'quay.io/biocontainers/python:3.9--1' }"
 
     input:
     path runinfo
@@ -29,7 +20,7 @@ process SRA_RUNINFO_TO_FTP {
         ${runinfo.toString().tokenize(".")[0]}.runinfo_ftp.tsv
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    ${task.process.tokenize(':').last()}:
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """
diff --git a/modules/local/sra_to_samplesheet.nf b/modules/local/sra_to_samplesheet.nf
index c4fc9af7..230ba4ca 100644
--- a/modules/local/sra_to_samplesheet.nf
+++ b/modules/local/sra_to_samplesheet.nf
@@ -1,14 +1,8 @@
-// Import generic module functions
-include { saveFiles; getSoftwareName } from './functions'
 
-params.options     = [:]
 params.results_dir = ''
 
 process SRA_TO_SAMPLESHEET {
     tag "$meta.id"
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     memory 100.MB
 
diff --git a/modules/nf-core/modules/sratools/fasterqdump/main.nf b/modules/local/sratools_fasterqdump.nf
similarity index 54%
rename from modules/nf-core/modules/sratools/fasterqdump/main.nf
rename to modules/local/sratools_fasterqdump.nf
index 08ef9045..cc8fb6fa 100644
--- a/modules/nf-core/modules/sratools/fasterqdump/main.nf
+++ b/modules/local/sratools_fasterqdump.nf
@@ -1,22 +1,12 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
 
 process SRATOOLS_FASTERQDUMP {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0 conda-forge::pigz=2.6' : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container 'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0'
-    } else {
-        container 'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0'
-    }
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' :
+        'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' }"
 
     input:
     tuple val(meta), path(sra)
@@ -26,6 +16,8 @@ process SRATOOLS_FASTERQDUMP {
     path "versions.yml"          , emit: versions
 
     script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
     def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
     // Paired-end data extracted by fasterq-dump (--split-3 the default) always creates
     // *_1.fastq *_2.fastq files but sometimes also an additional *.fastq file
@@ -39,19 +31,19 @@ process SRATOOLS_FASTERQDUMP {
     fi
 
     fasterq-dump \\
-        ${options.args} \\
+        $args \\
         --threads $task.cpus \\
         ${sra.name}
 
     pigz \\
-        ${options.args2} \\
+        $args2 \\
         --no-name \\
         --processes $task.cpus \\
         *.fastq
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(fasterq-dump --version 2>&1 | grep -Eo '[0-9.]+')
+    ${task.process.tokenize(':').last()}:
+        sratools: \$(fasterq-dump --version 2>&1 | grep -Eo '[0-9.]+')
         pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
     END_VERSIONS
     """
diff --git a/modules/local/sratools_prefetch.nf b/modules/local/sratools_prefetch.nf
new file mode 100644
index 00000000..07be740b
--- /dev/null
+++ b/modules/local/sratools_prefetch.nf
@@ -0,0 +1,41 @@
+
+process SRATOOLS_PREFETCH {
+    tag "$id"
+    label 'process_low'
+    label 'error_retry'
+
+    conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5262h314213e_0' :
+        'quay.io/biocontainers/sra-tools:2.11.0--pl5262h314213e_0' }"
+
+    input:
+    tuple val(meta), val(id)
+
+    output:
+    tuple val(meta), path("$id"), emit: sra
+    path "versions.yml"         , emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
+    """
+    eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
+    if [[ ! -f "\${NCBI_SETTINGS}" ]]; then
+        mkdir -p "\$(dirname "\${NCBI_SETTINGS}")"
+        printf '${config}' > "\${NCBI_SETTINGS}"
+    fi
+
+    prefetch \\
+        $args \\
+        --progress \\
+        $id
+
+    vdb-validate $id
+
+    cat <<-END_VERSIONS > versions.yml
+    ${task.process.tokenize(':').last()}:
+        sratools: \$(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/synapse_get.nf b/modules/local/synapse_get.nf
index 99985f48..5269286c 100644
--- a/modules/local/synapse_get.nf
+++ b/modules/local/synapse_get.nf
@@ -1,23 +1,13 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
 
 process SYNAPSE_GET {
     tag "$meta.id"
     label 'process_low'
     label 'error_retry'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::synapseclient=2.4.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/synapseclient:2.4.0--pyh5e36f6f_0"
-    } else {
-        container "quay.io/biocontainers/synapseclient:2.4.0--pyh5e36f6f_0"
-    }
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/synapseclient:2.4.0--pyh5e36f6f_0' :
+        'quay.io/biocontainers/synapseclient:2.4.0--pyh5e36f6f_0' }"
 
     input:
     val meta
@@ -29,18 +19,19 @@ process SYNAPSE_GET {
     path "versions.yml"                , emit: versions
 
     script:
+    def args = task.ext.args ?: ''
     """
     synapse \\
         -c $config \\
         get \\
-        $options.args \\
+        $args \\
         $meta.id
 
     echo "${meta.md5} \t ${meta.name}" > ${meta.id}.md5
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(synapse --version | sed -e "s/Synapse Client //g")
+    ${task.process.tokenize(':').last()}:
+        synapse: \$(synapse --version | sed -e "s/Synapse Client //g")
     END_VERSIONS
     """
 }
diff --git a/modules/local/synapse_list.nf b/modules/local/synapse_list.nf
index 20275de2..f001a186 100644
--- a/modules/local/synapse_list.nf
+++ b/modules/local/synapse_list.nf
@@ -1,22 +1,12 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
 
 process SYNAPSE_LIST {
     tag "$id"
     label 'process_low'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "bioconda::synapseclient=2.4.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/synapseclient:2.4.0--pyh5e36f6f_0"
-    } else {
-        container "quay.io/biocontainers/synapseclient:2.4.0--pyh5e36f6f_0"
-    }
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/synapseclient:2.4.0--pyh5e36f6f_0' :
+        'quay.io/biocontainers/synapseclient:2.4.0--pyh5e36f6f_0' }"
 
     input:
     val id
@@ -27,18 +17,20 @@ process SYNAPSE_LIST {
     path "versions.yml", emit: versions
 
     script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
     """
     synapse \\
         -c $config \\
         list \\
-        $options.args \\
+        $args \\
         $id \\
-        $options.args2 \\
+        $args2 \\
         > ${id}.list.txt
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(synapse --version | sed -e "s/Synapse Client //g")
+    ${task.process.tokenize(':').last()}:
+        syanpse: \$(synapse --version | sed -e "s/Synapse Client //g")
     END_VERSIONS
     """
 }
diff --git a/modules/local/synapse_merge_samplesheet.nf b/modules/local/synapse_merge_samplesheet.nf
index 8027818c..e3f97fa8 100644
--- a/modules/local/synapse_merge_samplesheet.nf
+++ b/modules/local/synapse_merge_samplesheet.nf
@@ -1,19 +1,10 @@
-// Import generic module functions
-include { saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
 
 process SYNAPSE_MERGE_SAMPLESHEET {
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
-    } else {
-        container "biocontainers/biocontainers:v1.2.0_cv1"
-    }
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
+        'biocontainers/biocontainers:v1.2.0_cv1' }"
 
     input:
     path ('samplesheets/*')
@@ -30,7 +21,7 @@ process SYNAPSE_MERGE_SAMPLESHEET {
     done
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    ${task.process.tokenize(':').last()}:
         sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
     END_VERSIONS
     """
diff --git a/modules/local/synapse_show.nf b/modules/local/synapse_show.nf
index 4edc4207..78593861 100644
--- a/modules/local/synapse_show.nf
+++ b/modules/local/synapse_show.nf
@@ -1,22 +1,12 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
 
 process SYNAPSE_SHOW {
     tag "$id"
     label 'process_low'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "bioconda::synapseclient=2.4.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/synapseclient:2.4.0--pyh5e36f6f_0"
-    } else {
-        container "quay.io/biocontainers/synapseclient:2.4.0--pyh5e36f6f_0"
-    }
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/synapseclient:2.4.0--pyh5e36f6f_0' :
+        'quay.io/biocontainers/synapseclient:2.4.0--pyh5e36f6f_0' }"
 
     input:
     val id
@@ -27,18 +17,20 @@ process SYNAPSE_SHOW {
     path "versions.yml", emit: versions
 
     script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
     """
     synapse \\
         -c $config \\
         show \\
-        $options.args \\
+        $args \\
         $id \\
-        $options.args2 \\
+        $args2 \\
         > ${id}.metadata.txt
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(synapse --version | sed -e "s/Synapse Client //g")
+    ${task.process.tokenize(':').last()}:
+        synapse: \$(synapse --version | sed -e "s/Synapse Client //g")
     END_VERSIONS
     """
 }
diff --git a/modules/local/synapse_to_samplesheet.nf b/modules/local/synapse_to_samplesheet.nf
index 28571005..976d7ad7 100644
--- a/modules/local/synapse_to_samplesheet.nf
+++ b/modules/local/synapse_to_samplesheet.nf
@@ -1,14 +1,7 @@
-// Import generic module functions
-include { saveFiles; getSoftwareName } from './functions'
-
-params.options     = [:]
 params.results_dir = ''
 
 process SYNAPSE_TO_SAMPLESHEET {
     tag "$meta.id"
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     memory 100.MB
 
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/functions.nf b/modules/nf-core/modules/custom/dumpsoftwareversions/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/nf-core/modules/custom/dumpsoftwareversions/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-//  Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml
deleted file mode 100644
index 8d4a6ed4..00000000
--- a/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml
+++ /dev/null
@@ -1,33 +0,0 @@
-name: custom_dumpsoftwareversions
-description: Custom module used to dump software versions within the nf-core pipeline template
-keywords:
-  - custom
-  - version
-tools:
-  - custom:
-      description: Custom module used to dump software versions within the nf-core pipeline template
-      homepage: https://github.com/nf-core/tools
-      documentation: https://github.com/nf-core/tools
-
-input:
-  - versions:
-      type: file
-      description: YML file containing software versions
-      pattern: "*.yml"
-
-output:
-  - yml:
-      type: file
-      description: Standard YML file containing software versions
-      pattern: "software_versions.yml"
-  - mqc_yml:
-      type: file
-      description: MultiQC custom content YML file containing software versions
-      pattern: "software_versions_mqc.yml"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-
-authors:
-  - "@drpatelh"
diff --git a/modules/nf-core/modules/sratools/fasterqdump/functions.nf b/modules/nf-core/modules/sratools/fasterqdump/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/nf-core/modules/sratools/fasterqdump/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-//  Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}
diff --git a/modules/nf-core/modules/sratools/fasterqdump/meta.yml b/modules/nf-core/modules/sratools/fasterqdump/meta.yml
deleted file mode 100644
index ac61e71f..00000000
--- a/modules/nf-core/modules/sratools/fasterqdump/meta.yml
+++ /dev/null
@@ -1,42 +0,0 @@
-name: sratools_fasterqdump
-description: Extract sequencing reads in FASTQ format from a given NCBI Sequence Read Archive (SRA).
-keywords:
-  - sequencing
-  - FASTQ
-  - dump
-tools:
-  - sratools:
-      description: SRA Toolkit and SDK from NCBI
-      homepage: https://github.com/ncbi/sra-tools
-      documentation: https://github.com/ncbi/sra-tools/wiki
-      tool_dev_url: https://github.com/ncbi/sra-tools
-      licence: ['Public Domain']
-
-input:
-  - meta:
-      type: map
-      description: >
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - sra:
-      type: directory
-      description: Directory containing ETL data for the given SRA.
-      pattern: "*/*.sra"
-
-output:
-  - meta:
-      type: map
-      description: >
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-  - reads:
-      type: file
-      description: Extracted FASTQ file or files if the sequencing reads are paired-end.
-      pattern: "*.fastq.gz"
-
-authors:
-  - "@Midnighter"
diff --git a/modules/nf-core/modules/sratools/prefetch/functions.nf b/modules/nf-core/modules/sratools/prefetch/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/nf-core/modules/sratools/prefetch/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-//  Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
-    return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    def ioptions  = initOptions(args.options)
-    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
-    // Do not publish versions.yml unless running from pytest workflow
-    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
-        return null
-    }
-    if (ioptions.publish_by_meta) {
-        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-        for (key in key_list) {
-            if (args.meta && key instanceof String) {
-                def path = key
-                if (args.meta.containsKey(key)) {
-                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                }
-                path = path instanceof String ? path : ''
-                path_list.add(path)
-            }
-        }
-    }
-    if (ioptions.publish_files instanceof Map) {
-        for (ext in ioptions.publish_files) {
-            if (args.filename.endsWith(ext.key)) {
-                def ext_list = path_list.collect()
-                ext_list.add(ext.value)
-                return "${getPathFromList(ext_list)}/$args.filename"
-            }
-        }
-    } else if (ioptions.publish_files == null) {
-        return "${getPathFromList(path_list)}/$args.filename"
-    }
-}
diff --git a/modules/nf-core/modules/sratools/prefetch/main.nf b/modules/nf-core/modules/sratools/prefetch/main.nf
deleted file mode 100644
index 207d1e10..00000000
--- a/modules/nf-core/modules/sratools/prefetch/main.nf
+++ /dev/null
@@ -1,50 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
-process SRATOOLS_PREFETCH {
-    tag "$id"
-    label 'process_low'
-    label 'error_retry'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
-
-    conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container 'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5262h314213e_0'
-    } else {
-        container 'quay.io/biocontainers/sra-tools:2.11.0--pl5262h314213e_0'
-    }
-
-    input:
-    tuple val(meta), val(id)
-
-    output:
-    tuple val(meta), path("$id"), emit: sra
-    path "versions.yml"         , emit: versions
-
-    script:
-    def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
-    """
-    eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
-    if [[ ! -f "\${NCBI_SETTINGS}" ]]; then
-        mkdir -p "\$(dirname "\${NCBI_SETTINGS}")"
-        printf '${config}' > "\${NCBI_SETTINGS}"
-    fi
-
-    prefetch \\
-        $options.args \\
-        --progress \\
-        $id
-
-    vdb-validate $id
-
-    cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/modules/sratools/prefetch/meta.yml b/modules/nf-core/modules/sratools/prefetch/meta.yml
deleted file mode 100644
index ab0a5ce5..00000000
--- a/modules/nf-core/modules/sratools/prefetch/meta.yml
+++ /dev/null
@@ -1,43 +0,0 @@
-name: sratools_prefetch
-description: Download sequencing data from the NCBI Sequence Read Archive (SRA).
-keywords:
-  - sequencing
-  - fastq
-  - prefetch
-tools:
-  - sratools:
-      description: SRA Toolkit and SDK from NCBI
-      homepage: https://github.com/ncbi/sra-tools
-      documentation: https://github.com/ncbi/sra-tools/wiki
-      tool_dev_url: https://github.com/ncbi/sra-tools
-      licence: ['Public Domain']
-
-input:
-  - meta:
-      type: map
-      description: >
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - id:
-      type: val
-      description: >
-        A string denoting an SRA id.
-
-output:
-  - meta:
-      type: map
-      description: >
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - sra:
-      type: directory
-      description: >
-        Directory containing the ETL data for the given SRA id.
-      pattern: "*/*.sra"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-
-authors:
-  - "@Midnighter"
diff --git a/nextflow.config b/nextflow.config
index 066fb0b3..cd5e3891 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -28,14 +28,12 @@ params {
     help                       = false
     validate_params            = true
     show_hidden_params         = false
-    schema_ignore_params       = 'modules,igenomes_base'
+    schema_ignore_params       = 'igenomes_base'
     enable_conda               = false
-    singularity_pull_docker_container = false
 
     // Config options
     custom_config_version      = 'master'
     custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
-    hostnames                  = [:]
     config_profile_description = null
     config_profile_contact     = null
     config_profile_url         = null
@@ -52,9 +50,6 @@ params {
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
-
 // Load nf-core custom profiles from different Institutions
 try {
     includeConfig "${params.custom_config_base}/nfcore_custom.config"
@@ -152,6 +147,9 @@ manifest {
     version         = '1.4'
 }
 
+// Load modules.config for DSL2 module specific options
+includeConfig 'conf/modules.config'
+
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit
 def check_max(obj, type) {
diff --git a/subworkflows/local/sra_fastq/main.nf b/subworkflows/local/sra_fastq/main.nf
index c6590b59..84db4b77 100644
--- a/subworkflows/local/sra_fastq/main.nf
+++ b/subworkflows/local/sra_fastq/main.nf
@@ -2,11 +2,8 @@
 // Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
 //
 
-params.prefetch_options    = [:]
-params.fasterqdump_options = [:]
-
-include { SRATOOLS_PREFETCH    } from '../../../modules/nf-core/modules/sratools/prefetch/main'    addParams( options: params.prefetch_options    )
-include { SRATOOLS_FASTERQDUMP } from '../../../modules/nf-core/modules/sratools/fasterqdump/main' addParams( options: params.fasterqdump_options )
+include { SRATOOLS_PREFETCH    } from '../../../modules/local/sratools_prefetch.nf'
+include { SRATOOLS_FASTERQDUMP } from '../../../modules/local/sratools_fasterqdump.nf'
 
 workflow SRA_FASTQ {
     take:
diff --git a/workflows/sra.nf b/workflows/sra.nf
index 4fb41ccd..40eeab9d 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -20,23 +20,16 @@ WorkflowSra.initialise(params, log, valid_params)
 */
 
 // Don't overwrite global params.modules, create a copy instead and use that within the main script.
-def modules = params.modules.clone()
+//def modules = params.modules.clone()
 
-include { SRA_IDS_TO_RUNINFO      } from '../modules/local/sra_ids_to_runinfo'      addParams( options: modules['sra_ids_to_runinfo']      )
-include { SRA_RUNINFO_TO_FTP      } from '../modules/local/sra_runinfo_to_ftp'      addParams( options: modules['sra_runinfo_to_ftp']      )
-include { SRA_FASTQ_FTP           } from '../modules/local/sra_fastq_ftp'           addParams( options: modules['sra_fastq_ftp']           )
-include { SRA_FASTQ               } from '../subworkflows/local/sra_fastq/main'     addParams( prefetch_options: modules['sratools_prefetch'], fasterqdump_options: modules['sratools_fasterqdump'] )
-include { SRA_TO_SAMPLESHEET      } from '../modules/local/sra_to_samplesheet'      addParams( options: modules['sra_to_samplesheet'], results_dir: modules['sra_fastq_ftp'].publish_dir )
-include { SRA_MERGE_SAMPLESHEET   } from '../modules/local/sra_merge_samplesheet'   addParams( options: modules['sra_merge_samplesheet']   )
-include { MULTIQC_MAPPINGS_CONFIG } from '../modules/local/multiqc_mappings_config' addParams( options: modules['multiqc_mappings_config'] )
-
-/*
-========================================================================================
-    IMPORT NF-CORE MODULES/SUBWORKFLOWS
-========================================================================================
-*/
-
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main' addParams( options: [publish_files : ['_versions.yml':'']] )
+include { SRA_IDS_TO_RUNINFO      } from '../modules/local/sra_ids_to_runinfo'
+include { SRA_RUNINFO_TO_FTP      } from '../modules/local/sra_runinfo_to_ftp'
+include { SRA_FASTQ_FTP           } from '../modules/local/sra_fastq_ftp'
+include { SRA_FASTQ               } from '../subworkflows/local/sra_fastq/main'
+include { SRA_TO_SAMPLESHEET      } from '../modules/local/sra_to_samplesheet'      // addParams( results_dir: modules['sra_fastq_ftp'].publish_dir )
+include { SRA_MERGE_SAMPLESHEET   } from '../modules/local/sra_merge_samplesheet'
+include { MULTIQC_MAPPINGS_CONFIG } from '../modules/local/multiqc_mappings_config'
+include { DUMPSOFTWAREVERSIONS    } from '../modules/local/dumpsoftwareversions'
 
 /*
 ========================================================================================
@@ -133,7 +126,7 @@ workflow SRA {
     //
     // MODULE: Dump software versions for all tools used in the workflow
     //
-    CUSTOM_DUMPSOFTWAREVERSIONS (
+    DUMPSOFTWAREVERSIONS (
         ch_versions.unique().collectFile(name: 'collated_versions.yml')
     )
 }
diff --git a/workflows/synapse.nf b/workflows/synapse.nf
index 2fc3cf69..06ce6319 100644
--- a/workflows/synapse.nf
+++ b/workflows/synapse.nf
@@ -20,21 +20,14 @@ if (params.synapse_config) {
 */
 
 // Don't overwrite global params.modules, create a copy instead and use that within the main script.
-def modules = params.modules.clone()
+//def modules = params.modules.clone()
 
-include { SYNAPSE_LIST              } from '../modules/local/synapse_list'              addParams( options: modules['synapse_list']              )
-include { SYNAPSE_SHOW              } from '../modules/local/synapse_show'              addParams( options: modules['synapse_show']              )
-include { SYNAPSE_GET               } from '../modules/local/synapse_get'               addParams( options: modules['synapse_get']               )
-include { SYNAPSE_TO_SAMPLESHEET    } from '../modules/local/synapse_to_samplesheet'    addParams( options: modules['synapse_to_samplesheet'], results_dir: modules['synapse_get'].publish_dir )
-include { SYNAPSE_MERGE_SAMPLESHEET } from '../modules/local/synapse_merge_samplesheet' addParams( options: modules['synapse_merge_samplesheet'] )
-
-/*
-========================================================================================
-    IMPORT NF-CORE MODULES/SUBWORKFLOWS
-========================================================================================
-*/
-
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main' addParams( options: [publish_files : ['_versions.yml':'']] )
+include { SYNAPSE_LIST              } from '../modules/local/synapse_list'
+include { SYNAPSE_SHOW              } from '../modules/local/synapse_show'
+include { SYNAPSE_GET               } from '../modules/local/synapse_get'
+include { SYNAPSE_TO_SAMPLESHEET    } from '../modules/local/synapse_to_samplesheet'    // addParams( results_dir: modules['synapse_get'].publish_dir )
+include { SYNAPSE_MERGE_SAMPLESHEET } from '../modules/local/synapse_merge_samplesheet'
+include { DUMPSOFTWAREVERSIONS      } from '../modules/local/dumpsoftwareversions'
 
 /*
 ========================================================================================
@@ -132,7 +125,7 @@ workflow SYNAPSE {
     //
     // MODULE: Dump software versions for all tools used in the workflow
     //
-    CUSTOM_DUMPSOFTWAREVERSIONS (
+    DUMPSOFTWAREVERSIONS (
         ch_versions.unique().collectFile(name: 'collated_versions.yml')
     )
 }

From 44844e3be78d15848dfe41bc77c380bf3c6cfb17 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 3 Nov 2021 15:24:28 +0000
Subject: [PATCH 131/852] Run CI for pipeline NXF and latest edge version

---
 .github/workflows/ci.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 08ac1cfb..6b67751c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -18,12 +18,11 @@ jobs:
     if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}
     runs-on: ubuntu-latest
     env:
-      NXF_VER: ${{ matrix.nxf_ver }}
       NXF_ANSI_LOG: false
     strategy:
       matrix:
-        # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ["21.04.0", ""]
+        # Nextflow versions: check pipeline minimum and latest edge version
+        nxf_ver: ["NXF_VER=21.04.0", "NXF_EDGE=1"]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -34,6 +33,8 @@ jobs:
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
+          export ${{ matrix.nxf_ver }}
+          nextflow self-update
 
       - name: Run pipeline with SRA test data
         run: |

From fa4be0b9cd8551b179d8e281d08cd4d9830884de Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 3 Nov 2021 15:24:49 +0000
Subject: [PATCH 132/852] Remove params.hostnames

---
 lib/NfcoreSchema.groovy   |  3 +--
 lib/NfcoreTemplate.groovy | 30 +++++++++---------------------
 lib/WorkflowMain.groovy   |  6 +++---
 nextflow_schema.json      | 13 -------------
 4 files changed, 13 insertions(+), 39 deletions(-)

diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy
index 8d6920dd..dcb39c83 100755
--- a/lib/NfcoreSchema.groovy
+++ b/lib/NfcoreSchema.groovy
@@ -260,13 +260,12 @@ class NfcoreSchema {
 
         // Get pipeline parameters defined in JSON Schema
         def Map params_summary = [:]
-        def blacklist  = ['hostnames']
         def params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename))
         for (group in params_map.keySet()) {
             def sub_params = new LinkedHashMap()
             def group_params = params_map.get(group)  // This gets the parameters of that particular group
             for (param in group_params.keySet()) {
-                if (params.containsKey(param) && !blacklist.contains(param)) {
+                if (params.containsKey(param)) {
                     def params_value = params.get(param)
                     def schema_value = group_params.get(param).default
                     def param_type   = group_params.get(param).type
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
index 3dd46e64..4592007f 100755
--- a/lib/NfcoreTemplate.groovy
+++ b/lib/NfcoreTemplate.groovy
@@ -19,27 +19,16 @@ class NfcoreTemplate {
     }
 
     //
-    // Check params.hostnames
+    //  Warn if a -profile or Nextflow config has not been provided to run the pipeline
     //
-    public static void hostName(workflow, params, log) {
-        Map colors = logColours(params.monochrome_logs)
-        if (params.hostnames) {
-            try {
-                def hostname = "hostname".execute().text.trim()
-                params.hostnames.each { prof, hnames ->
-                    hnames.each { hname ->
-                        if (hostname.contains(hname) && !workflow.profile.contains(prof)) {
-                            log.info "=${colors.yellow}====================================================${colors.reset}=\n" +
-                                "${colors.yellow}WARN: You are running with `-profile $workflow.profile`\n" +
-                                "      but your machine hostname is ${colors.white}'$hostname'${colors.reset}.\n" +
-                                "      ${colors.yellow_bold}Please use `-profile $prof${colors.reset}`\n" +
-                                "=${colors.yellow}====================================================${colors.reset}="
-                        }
-                    }
-                }
-            } catch (Exception e) {
-                log.warn "[$workflow.manifest.name] Could not determine 'hostname' - skipping check. Reason: ${e.message}."
-            }
+    public static void checkConfigProvided(workflow, log) {
+        if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
+            log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
+                    "This will be dependent on your local compute enviroment but can be acheived via one or more of the following:\n" +
+                    "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
+                    "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
+                    "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
+                    "Please refer to the quick start section and usage docs for the pipeline.\n "
         }
     }
 
@@ -146,7 +135,6 @@ class NfcoreTemplate {
                 log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
             }
         } else {
-            hostName(workflow, params, log)
             log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
         }
     }
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index 09264303..e8f3c20d 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -60,6 +60,9 @@ class WorkflowMain {
         // Print parameter summary log to screen
         log.info paramsSummaryLog(workflow, params, log)
 
+        // Check that a -profile or Nextflow config has been provided to run the pipeline
+        NfcoreTemplate.checkConfigProvided(workflow, log)
+
         // Check that conda channels are set-up correctly
         if (params.enable_conda) {
             Utils.checkCondaChannels(log)
@@ -68,9 +71,6 @@ class WorkflowMain {
         // Check AWS batch settings
         NfcoreTemplate.awsBatch(workflow, params)
 
-        // Check the hostnames against configured profiles
-        NfcoreTemplate.hostName(workflow, params, log)
-
         // Check input has been provided
         if (!params.input) {
             log.error "Please provide an input file containing ids to the pipeline - one per line e.g. '--input ids.txt'"
diff --git a/nextflow_schema.json b/nextflow_schema.json
index b2f26972..be10a344 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -88,12 +88,6 @@
                     "help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
                     "fa_icon": "fas fa-users-cog"
                 },
-                "hostnames": {
-                    "type": "string",
-                    "description": "Institutional configs hostname.",
-                    "hidden": true,
-                    "fa_icon": "fas fa-users-cog"
-                },
                 "config_profile_name": {
                     "type": "string",
                     "description": "Institutional config name.",
@@ -230,13 +224,6 @@
                     "description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
                     "hidden": true,
                     "fa_icon": "fas fa-bacon"
-                },
-                "singularity_pull_docker_container": {
-                    "type": "boolean",
-                    "description": "Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.",
-                    "hidden": true,
-                    "fa_icon": "fas fa-toolbox",
-                    "help_text": "This may be useful for example if you are unable to directly pull Singularity containers to run the pipeline due to http/https proxy issues."
                 }
             }
         }

From ef640c724e1b69466829576844f885e77104b619 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 3 Nov 2021 15:55:13 +0000
Subject: [PATCH 133/852] Fix nf-core lint

---
 .nf-core.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.nf-core.yml b/.nf-core.yml
index 92e07317..b8e4d216 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -2,7 +2,9 @@ lint:
   files_unchanged:
     - .github/CONTRIBUTING.md
     - assets/sendmail_template.txt
+    - lib/NfcoreSchema.groovy
     - lib/NfcoreTemplate.groovy
   files_exist:
     - bin/scrape_software_versions.py
     - modules/local/get_software_versions.nf
+  actions_ci: False

From c7cbd2f9dcf3212f7483c26a709054c01e00e801 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 4 Nov 2021 11:49:52 +0000
Subject: [PATCH 134/852] Add params.input_type to split out config options for
 each workflow

---
 conf/modules.config      | 224 ++++++++++++++++++++++-----------------
 conf/test_synapse.config |   3 +-
 lib/WorkflowMain.groovy  |   8 ++
 main.nf                  |  24 +++--
 nextflow.config          |   1 +
 nextflow_schema.json     |  10 ++
 6 files changed, 162 insertions(+), 108 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 88a1a72b..0f6c8138 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -10,6 +10,9 @@
 ----------------------------------------------------------------------------------------
 */
 
+//
+// Generic process options for all workflows
+//
 process {
 
     publishDir = [
@@ -18,127 +21,150 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-    withName: SRA_IDS_TO_RUNINFO {
-        publishDir = [
-            path: { "${params.outdir}/metadata" },
-            enabled: false
-        ]
-    }
-
-    withName: SRA_RUNINFO_TO_FTP {
+    withName: DUMPSOFTWAREVERSIONS {
         publishDir = [
-            path: { "${params.outdir}/metadata" },
+            path: { "${params.outdir}/pipeline_info" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            pattern: '*_versions.yml'
         ]
     }
 
-    withName: SRA_FASTQ_FTP {
-        ext.args = '--retry 5 --continue-at - --max-time 1200'
-        publishDir = [
-            [
+}
+
+//
+//  Process options for the SRA workflow
+//
+if (params.input_type == 'sra') {
+
+    process {
+
+        withName: SRA_IDS_TO_RUNINFO {
+            publishDir = [
+                path: { "${params.outdir}/metadata" },
+                enabled: false
+            ]
+        }
+
+        withName: SRA_RUNINFO_TO_FTP {
+            publishDir = [
+                path: { "${params.outdir}/metadata" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+        withName: SRA_FASTQ_FTP {
+            ext.args = '--retry 5 --continue-at - --max-time 1200'
+            publishDir = [
+                [
+                    path: { "${params.outdir}/fastq" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*gz"
+                ],
+                [
+                    path: { "${params.outdir}/fastq/md5" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.md5"
+                ]
+            ]
+        }
+
+        withName: SRATOOLS_PREFETCH {
+            publishDir = [
+                path: { "${params.outdir}/sra" },
+                enabled: false
+            ]
+        }
+
+        withName: SRATOOLS_FASTERQDUMP {
+            publishDir = [
                 path: { "${params.outdir}/fastq" },
                 mode: params.publish_dir_mode,
-                pattern: "*gz"
-            ],
-            [
-                path: { "${params.outdir}/fastq/md5" },
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+        withName: SRA_TO_SAMPLESHEET {
+            publishDir = [
+                path: { "${params.outdir}/samplesheet" },
+                enabled: false
+            ]
+        }
+
+        withName: SRA_MERGE_SAMPLESHEET {
+            publishDir = [
+                path: { "${params.outdir}/samplesheet" },
                 mode: params.publish_dir_mode,
-                pattern: "*.md5"
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
-        ]
-    }
+        }
 
-    withName: SRATOOLS_PREFETCH {
-        publishDir = [
-            path: { "${params.outdir}/sra" },
-            enabled: false
-        ]
-    }
+        withName: MULTIQC_MAPPINGS_CONFIG {
+            publishDir = [
+                path: { "${params.outdir}/samplesheet" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
 
-    withName: SRATOOLS_FASTERQDUMP {
-        publishDir = [
-            path: { "${params.outdir}/fastq" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
     }
 
-    withName: SRA_TO_SAMPLESHEET {
-        publishDir = [
-            path: { "${params.outdir}/samplesheet" },
-            enabled: false
-        ]
-    }
+}
 
-    withName: SRA_MERGE_SAMPLESHEET {
-        publishDir = [
-            path: { "${params.outdir}/samplesheet" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
+//
+//  Process options for the Synapse workflow
+//
+if (params.input_type == 'synapse') {
 
-    withName: SYNAPSE_LIST {
-        ext.args = '--long'
-        publishDir = [
-            path: { "${params.outdir}/metadata" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
+    process {
 
-    withName: SYNAPSE_GET {
-        publishDir = [
-            [
-                path: { "${params.outdir}/fastq" },
-                mode: params.publish_dir_mode,
-                pattern: "*gz"
-            ],
-            [
-                path: { "${params.outdir}/fastq/md5" },
+        withName: SYNAPSE_LIST {
+            ext.args = '--long'
+            publishDir = [
+                path: { "${params.outdir}/metadata" },
                 mode: params.publish_dir_mode,
-                pattern: "*.md5"
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
-        ]
-    }
+        }
+
+        withName: SYNAPSE_GET {
+            publishDir = [
+                [
+                    path: { "${params.outdir}/fastq" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*gz"
+                ],
+                [
+                    path: { "${params.outdir}/fastq/md5" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.md5"
+                ]
+            ]
+        }
 
-    withName: SYNAPSE_SHOW {
-        publishDir = [
-            path: { "${params.outdir}/metadata" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
+        withName: SYNAPSE_SHOW {
+            publishDir = [
+                path: { "${params.outdir}/metadata" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
 
-    withName: SYNAPSE_TO_SAMPLESHEET {
-        publishDir = [
-            path: { "${params.outdir}/samplesheet" },
-            enabled: false
-        ]
-    }
+        withName: SYNAPSE_TO_SAMPLESHEET {
+            publishDir = [
+                path: { "${params.outdir}/samplesheet" },
+                enabled: false
+            ]
+        }
 
-    withName: SYNAPSE_MERGE_SAMPLESHEET {
-        publishDir = [
-            path: { "${params.outdir}/samplesheet" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
+        withName: SYNAPSE_MERGE_SAMPLESHEET {
+            publishDir = [
+                path: { "${params.outdir}/samplesheet" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
 
-    withName: MULTIQC_MAPPINGS_CONFIG {
-        publishDir = [
-            path: { "${params.outdir}/samplesheet" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
     }
 
-    withName: DUMPSOFTWAREVERSIONS {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            pattern: '*_versions.yml'
-        ]
-    }
 }
diff --git a/conf/test_synapse.config b/conf/test_synapse.config
index d68d4098..d9433493 100644
--- a/conf/test_synapse.config
+++ b/conf/test_synapse.config
@@ -20,5 +20,6 @@ params {
     max_time   = 6.h
 
     // Input data
-    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/synapse_ids_test.txt'
+    input      = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/synapse_ids_test.txt'
+    input_type = 'synapse'
 }
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index e8f3c20d..f64fa80f 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -46,6 +46,7 @@ class WorkflowMain {
     // Validate parameters and print summary to screen
     //
     public static void initialise(workflow, params, log) {
+
         // Print help to screen if required
         if (params.help) {
             log.info help(workflow, params, log)
@@ -76,6 +77,13 @@ class WorkflowMain {
             log.error "Please provide an input file containing ids to the pipeline - one per line e.g. '--input ids.txt'"
             System.exit(1)
         }
+
+        // Check valid input_type has been provided
+        def input_types = ['sra', 'synapse']
+        if (!input_types.contains(params.input_type)) {
+            log.error "Invalid option: '${params.input_type}'. Valid options for '--input_type': ${input_types.join(', ')}."
+            System.exit(1)
+        }
     }
 
     // Check if input ids are from the SRA
diff --git a/main.nf b/main.nf
index 98b25cb1..a2ae62f1 100644
--- a/main.nf
+++ b/main.nf
@@ -37,18 +37,26 @@ Channel
 ========================================================================================
 */
 
-// Auto-detect id type
-def id_type = ''
+// Auto-detect input id type
+def input_type = ''
 if (WorkflowMain.isSraId(ch_input, log)) {
-    id_type = 'sra'
-    include { SRA } from './workflows/sra'
+    input_type = 'sra'
 } else if (WorkflowMain.isSynapseId(ch_input, log)) {
-    id_type = 'synapse'
-    include { SYNAPSE } from './workflows/synapse'
+    input_type = 'synapse'
 } else {
     exit 1, 'Ids provided via --input not recognised please make sure they are either SRA / ENA / DDBJ / GEO or Synapse ids!'
 }
 
+if (params.input_type == input_type) {
+    if (params.input_type == 'sra') {
+        include { SRA } from './workflows/sra'
+    } else if (params.input_type == 'synapse') {
+        include { SYNAPSE } from './workflows/synapse'
+    }
+} else {
+    exit 1, "Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!"
+}
+
 //
 // WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided
 //
@@ -57,13 +65,13 @@ workflow NFCORE_FETCHNGS {
     //
     // WORKFLOW: Download FastQ files for SRA / ENA / DDBJ / GEO ids
     //
-    if (id_type == 'sra') {
+    if (params.input_type == 'sra') {
         SRA ( ch_ids )
 
     //
     // WORKFLOW: Download FastQ files for Synapse ids
     //
-    } else if (id_type == 'synapse') {
+    } else if (params.input_type == 'synapse') {
         SYNAPSE ( ch_ids )
     }
 }
diff --git a/nextflow.config b/nextflow.config
index cd5e3891..6ae6a8da 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -11,6 +11,7 @@ params {
 
     // Input options
     input                      = null
+    input_type                 = 'sra'
     nf_core_pipeline           = null
     ena_metadata_fields        = null
     sample_mapping_fields      = 'run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description,description'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index be10a344..1f923f28 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -23,6 +23,16 @@
                     "fa_icon": "fas fa-file-excel",
                     "description": "File containing SRA/ENA/DDBJ/GEO identifiers one per line to download their associated metadata and FastQ files."
                 },
+                "input_type": {
+                    "type": "string",
+                    "default": "sra",
+                    "description": "Specifies the type of identifier provided via `--input` - available options are 'sra' and 'synapse'.",
+                    "fa_icon": "fas fa-keyboard",
+                    "enum": [
+                        "sra",
+                        "synapse"
+                    ]
+                },
                 "ena_metadata_fields": {
                     "type": "string",
                     "fa_icon": "fas fa-columns",

From 107e3e5dc96ae9394f058385d51342041be8ffbc Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 4 Nov 2021 12:26:14 +0000
Subject: [PATCH 135/852] Refactor sra_fastq subworkflow to be local

---
 .../local/{sra_fastq/main.nf => sra_fastq.nf} |  4 +--
 subworkflows/local/sra_fastq/meta.yml         | 36 -------------------
 subworkflows/local/sra_fastq/nextflow.config  |  2 --
 workflows/sra.nf                              |  2 +-
 4 files changed, 3 insertions(+), 41 deletions(-)
 rename subworkflows/local/{sra_fastq/main.nf => sra_fastq.nf} (82%)
 delete mode 100644 subworkflows/local/sra_fastq/meta.yml
 delete mode 100644 subworkflows/local/sra_fastq/nextflow.config

diff --git a/subworkflows/local/sra_fastq/main.nf b/subworkflows/local/sra_fastq.nf
similarity index 82%
rename from subworkflows/local/sra_fastq/main.nf
rename to subworkflows/local/sra_fastq.nf
index 84db4b77..04039f79 100644
--- a/subworkflows/local/sra_fastq/main.nf
+++ b/subworkflows/local/sra_fastq.nf
@@ -2,8 +2,8 @@
 // Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
 //
 
-include { SRATOOLS_PREFETCH    } from '../../../modules/local/sratools_prefetch.nf'
-include { SRATOOLS_FASTERQDUMP } from '../../../modules/local/sratools_fasterqdump.nf'
+include { SRATOOLS_PREFETCH    } from '../../modules/local/sratools_prefetch.nf'
+include { SRATOOLS_FASTERQDUMP } from '../../modules/local/sratools_fasterqdump.nf'
 
 workflow SRA_FASTQ {
     take:
diff --git a/subworkflows/local/sra_fastq/meta.yml b/subworkflows/local/sra_fastq/meta.yml
deleted file mode 100644
index 146176ee..00000000
--- a/subworkflows/local/sra_fastq/meta.yml
+++ /dev/null
@@ -1,36 +0,0 @@
-name: sra_fastq
-description: Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
-keywords:
-  - sequencing
-  - FASTQ
-  - prefetch
-  - dump
-modules:
-  - sratools/prefetch
-  - sratools/fasterqdump
-input:
-  - meta:
-      type: map
-      description: >
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - id:
-      type: string
-      description: >
-        SRA identifier.
-output:
-  - meta:
-      type: map
-      description: >
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: Extracted FASTQ file or files if the sequencing reads are paired-end.
-      pattern: "*.fastq.gz"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-authors:
-  - '@Midnighter'
diff --git a/subworkflows/local/sra_fastq/nextflow.config b/subworkflows/local/sra_fastq/nextflow.config
deleted file mode 100644
index 07448834..00000000
--- a/subworkflows/local/sra_fastq/nextflow.config
+++ /dev/null
@@ -1,2 +0,0 @@
-params.prefetch_options    = [:]
-params.fasterqdump_options = [:]
diff --git a/workflows/sra.nf b/workflows/sra.nf
index 40eeab9d..e23d968e 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -25,7 +25,7 @@ WorkflowSra.initialise(params, log, valid_params)
 include { SRA_IDS_TO_RUNINFO      } from '../modules/local/sra_ids_to_runinfo'
 include { SRA_RUNINFO_TO_FTP      } from '../modules/local/sra_runinfo_to_ftp'
 include { SRA_FASTQ_FTP           } from '../modules/local/sra_fastq_ftp'
-include { SRA_FASTQ               } from '../subworkflows/local/sra_fastq/main'
+include { SRA_FASTQ               } from '../subworkflows/local/sra_fastq'
 include { SRA_TO_SAMPLESHEET      } from '../modules/local/sra_to_samplesheet'      // addParams( results_dir: modules['sra_fastq_ftp'].publish_dir )
 include { SRA_MERGE_SAMPLESHEET   } from '../modules/local/sra_merge_samplesheet'
 include { MULTIQC_MAPPINGS_CONFIG } from '../modules/local/multiqc_mappings_config'

From 4be83f200d661a24ec074752702cffd9ab7bb329 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 4 Nov 2021 12:51:55 +0000
Subject: [PATCH 136/852] Remove last remaining addParams call

---
 modules/local/sra_to_samplesheet.nf     | 6 ++----
 modules/local/synapse_to_samplesheet.nf | 7 +++----
 workflows/sra.nf                        | 5 +----
 workflows/synapse.nf                    | 5 +----
 4 files changed, 7 insertions(+), 16 deletions(-)

diff --git a/modules/local/sra_to_samplesheet.nf b/modules/local/sra_to_samplesheet.nf
index 230ba4ca..dbbc6613 100644
--- a/modules/local/sra_to_samplesheet.nf
+++ b/modules/local/sra_to_samplesheet.nf
@@ -1,6 +1,4 @@
 
-params.results_dir = ''
-
 process SRA_TO_SAMPLESHEET {
     tag "$meta.id"
 
@@ -32,8 +30,8 @@ process SRA_TO_SAMPLESHEET {
     // Add relevant fields to the beginning of the map
     pipeline_map = [
         sample  : "${meta.id.split('_')[0..-2].join('_')}",
-        fastq_1 : "${params.outdir}/${params.results_dir}/${fastq[0]}",
-        fastq_2 : meta.single_end ? '' : "${params.outdir}/${params.results_dir}/${fastq[1]}"
+        fastq_1 : "${params.outdir}/fastq/${fastq[0]}",
+        fastq_2 : meta.single_end ? '' : "${params.outdir}/fastq/${fastq[1]}"
     ]
 
     // Add nf-core pipeline specific entries
diff --git a/modules/local/synapse_to_samplesheet.nf b/modules/local/synapse_to_samplesheet.nf
index 976d7ad7..40519ec0 100644
--- a/modules/local/synapse_to_samplesheet.nf
+++ b/modules/local/synapse_to_samplesheet.nf
@@ -1,4 +1,3 @@
-params.results_dir = ''
 
 process SYNAPSE_TO_SAMPLESHEET {
     tag "$meta.id"
@@ -18,11 +17,11 @@ process SYNAPSE_TO_SAMPLESHEET {
     def meta_map = meta.clone()
     meta_map.remove("id")
 
-    def fastq_1 = "${params.outdir}/${params.results_dir}/${fastq}"
+    def fastq_1 = "${params.outdir}/fastq/${fastq}"
     def fastq_2 = ''
     if (fastq instanceof List && fastq.size() == 2) {
-        fastq_1 = "${params.outdir}/${params.results_dir}/${fastq[0]}"
-        fastq_2 = "${params.outdir}/${params.results_dir}/${fastq[1]}"
+        fastq_1 = "${params.outdir}/fastq/${fastq[0]}"
+        fastq_2 = "${params.outdir}/fastq/${fastq[1]}"
     }
 
     // Add relevant fields to the beginning of the map
diff --git a/workflows/sra.nf b/workflows/sra.nf
index e23d968e..c108812f 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -19,14 +19,11 @@ WorkflowSra.initialise(params, log, valid_params)
 ========================================================================================
 */
 
-// Don't overwrite global params.modules, create a copy instead and use that within the main script.
-//def modules = params.modules.clone()
-
 include { SRA_IDS_TO_RUNINFO      } from '../modules/local/sra_ids_to_runinfo'
 include { SRA_RUNINFO_TO_FTP      } from '../modules/local/sra_runinfo_to_ftp'
 include { SRA_FASTQ_FTP           } from '../modules/local/sra_fastq_ftp'
 include { SRA_FASTQ               } from '../subworkflows/local/sra_fastq'
-include { SRA_TO_SAMPLESHEET      } from '../modules/local/sra_to_samplesheet'      // addParams( results_dir: modules['sra_fastq_ftp'].publish_dir )
+include { SRA_TO_SAMPLESHEET      } from '../modules/local/sra_to_samplesheet'
 include { SRA_MERGE_SAMPLESHEET   } from '../modules/local/sra_merge_samplesheet'
 include { MULTIQC_MAPPINGS_CONFIG } from '../modules/local/multiqc_mappings_config'
 include { DUMPSOFTWAREVERSIONS    } from '../modules/local/dumpsoftwareversions'
diff --git a/workflows/synapse.nf b/workflows/synapse.nf
index 06ce6319..5a7e3fe7 100644
--- a/workflows/synapse.nf
+++ b/workflows/synapse.nf
@@ -19,13 +19,10 @@ if (params.synapse_config) {
 ========================================================================================
 */
 
-// Don't overwrite global params.modules, create a copy instead and use that within the main script.
-//def modules = params.modules.clone()
-
 include { SYNAPSE_LIST              } from '../modules/local/synapse_list'
 include { SYNAPSE_SHOW              } from '../modules/local/synapse_show'
 include { SYNAPSE_GET               } from '../modules/local/synapse_get'
-include { SYNAPSE_TO_SAMPLESHEET    } from '../modules/local/synapse_to_samplesheet'    // addParams( results_dir: modules['synapse_get'].publish_dir )
+include { SYNAPSE_TO_SAMPLESHEET    } from '../modules/local/synapse_to_samplesheet'
 include { SYNAPSE_MERGE_SAMPLESHEET } from '../modules/local/synapse_merge_samplesheet'
 include { DUMPSOFTWAREVERSIONS      } from '../modules/local/dumpsoftwareversions'
 

From eb5816e9c1e5a9f55a8369fdaba66f2c2d7f592d Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 4 Nov 2021 12:55:00 +0000
Subject: [PATCH 137/852] Update CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0153327e..65d06ea6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+* Convert pipeline to updated Nextflow DSL2 syntax for future adoption across nf-core
 * Added a workflow to download FastQ files and to create samplesheets for ids from the [Synapse platform](https://www.synapse.org/) hosted by [Sage Bionetworks](https://sagebionetworks.org/).
 * SRA identifiers not available for direct download via the ENA FTP will now be downloaded via sra-tools.
 * Correctly handle errors from SRA identifiers that do **not** return metadata, for example, due to being private.

From ddcb96d7ca0c89b9276b5b2b1ce3f6a86b0c9e72 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 4 Nov 2021 15:39:54 +0000
Subject: [PATCH 138/852] Fix assignment alignment

---
 modules/local/sratools_fasterqdump.nf | 4 ++--
 modules/local/sratools_prefetch.nf    | 2 +-
 modules/local/synapse_list.nf         | 2 +-
 modules/local/synapse_show.nf         | 2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/local/sratools_fasterqdump.nf b/modules/local/sratools_fasterqdump.nf
index cc8fb6fa..ae69b5e6 100644
--- a/modules/local/sratools_fasterqdump.nf
+++ b/modules/local/sratools_fasterqdump.nf
@@ -16,8 +16,8 @@ process SRATOOLS_FASTERQDUMP {
     path "versions.yml"          , emit: versions
 
     script:
-    def args = task.ext.args ?: ''
-    def args2 = task.ext.args2 ?: ''
+    def args   = task.ext.args  ?: ''
+    def args2  = task.ext.args2 ?: ''
     def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
     // Paired-end data extracted by fasterq-dump (--split-3 the default) always creates
     // *_1.fastq *_2.fastq files but sometimes also an additional *.fastq file
diff --git a/modules/local/sratools_prefetch.nf b/modules/local/sratools_prefetch.nf
index 07be740b..033aeedf 100644
--- a/modules/local/sratools_prefetch.nf
+++ b/modules/local/sratools_prefetch.nf
@@ -17,7 +17,7 @@ process SRATOOLS_PREFETCH {
     path "versions.yml"         , emit: versions
 
     script:
-    def args = task.ext.args ?: ''
+    def args   = task.ext.args ?: ''
     def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
     """
     eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
diff --git a/modules/local/synapse_list.nf b/modules/local/synapse_list.nf
index f001a186..0255c925 100644
--- a/modules/local/synapse_list.nf
+++ b/modules/local/synapse_list.nf
@@ -17,7 +17,7 @@ process SYNAPSE_LIST {
     path "versions.yml", emit: versions
 
     script:
-    def args = task.ext.args ?: ''
+    def args  = task.ext.args  ?: ''
     def args2 = task.ext.args2 ?: ''
     """
     synapse \\
diff --git a/modules/local/synapse_show.nf b/modules/local/synapse_show.nf
index 78593861..9a81493a 100644
--- a/modules/local/synapse_show.nf
+++ b/modules/local/synapse_show.nf
@@ -17,7 +17,7 @@ process SYNAPSE_SHOW {
     path "versions.yml", emit: versions
 
     script:
-    def args = task.ext.args ?: ''
+    def args  = task.ext.args  ?: ''
     def args2 = task.ext.args2 ?: ''
     """
     synapse \\

From 4b2e0f82775d0475c0fb51948ee0405fa3d69605 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Mon, 8 Nov 2021 11:23:21 +0000
Subject: [PATCH 139/852] Update main.nf

---
 modules/nf-core/modules/sratools/prefetch/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/modules/sratools/prefetch/main.nf b/modules/nf-core/modules/sratools/prefetch/main.nf
index c57255f5..207d1e10 100644
--- a/modules/nf-core/modules/sratools/prefetch/main.nf
+++ b/modules/nf-core/modules/sratools/prefetch/main.nf
@@ -35,7 +35,7 @@ process SRATOOLS_PREFETCH {
         printf '${config}' > "\${NCBI_SETTINGS}"
     fi
 
-    retry_with_backoff.sh prefetch \\
+    prefetch \\
         $options.args \\
         --progress \\
         $id

From 0238704dce66dd698f2c85168f9684b3e529d1e4 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Nov 2021 12:38:52 +0000
Subject: [PATCH 140/852] Name output files with EXPID_RUNID_T1

---
 bin/sra_runinfo_to_ftp.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/bin/sra_runinfo_to_ftp.py b/bin/sra_runinfo_to_ftp.py
index 130007b6..094782f8 100755
--- a/bin/sra_runinfo_to_ftp.py
+++ b/bin/sra_runinfo_to_ftp.py
@@ -112,7 +112,6 @@ def parse_sra_runinfo(file_in):
             else:
                 # In some instances, FTP links don't exist for FastQ files.
                 # These have to be downloaded with the run accession using sra-tools.
-                db_id = row["run_accession"]
                 sample = dict.fromkeys(extensions, None)
                 if row["library_layout"] == "SINGLE":
                     sample["single_end"] = "true"
@@ -160,6 +159,8 @@ def sra_runinfo_to_ftp(files_in, file_out):
             for db_id in sorted(samplesheet):
                 for idx, row in enumerate(samplesheet[db_id], start=1):
                     row["id"] = f"{db_id}_T{idx}"
+                    if 'run_accession' in row:
+                        row["id"] = f"{db_id}_{row['run_accession']}_T{idx}"
                     writer.writerow(row)
 
 

From 5909b7587842a6ce4fe0ce074c7382b7e779847c Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Nov 2021 12:39:09 +0000
Subject: [PATCH 141/852] Output md5sums for fasterqdump

---
 conf/modules.config | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 0f6c8138..753ab27d 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -78,9 +78,16 @@ if (params.input_type == 'sra') {
 
         withName: SRATOOLS_FASTERQDUMP {
             publishDir = [
-                path: { "${params.outdir}/fastq" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                [
+                    path: { "${params.outdir}/fastq" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*gz"
+                ],
+                [
+                    path: { "${params.outdir}/fastq/md5" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.md5"
+                ]
             ]
         }
 

From a9b05fd83681123e230553d402605750180fddb9 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Nov 2021 12:39:27 +0000
Subject: [PATCH 142/852] Rename FastQs by meta.id and output md5sums for
 fasterqdump

---
 modules/local/sratools_fasterqdump.nf | 24 +++++++++++++++++++++---
 1 file changed, 21 insertions(+), 3 deletions(-)

diff --git a/modules/local/sratools_fasterqdump.nf b/modules/local/sratools_fasterqdump.nf
index ae69b5e6..f834eb8b 100644
--- a/modules/local/sratools_fasterqdump.nf
+++ b/modules/local/sratools_fasterqdump.nf
@@ -12,8 +12,9 @@ process SRATOOLS_FASTERQDUMP {
     tuple val(meta), path(sra)
 
     output:
-    tuple val(meta), path(output), emit: reads
-    path "versions.yml"          , emit: versions
+    tuple val(meta), path(fastq_output), emit: reads
+    tuple val(meta), path(md5_output)  , emit: md5
+    path "versions.yml"                , emit: versions
 
     script:
     def args   = task.ext.args  ?: ''
@@ -22,7 +23,8 @@ process SRATOOLS_FASTERQDUMP {
     // Paired-end data extracted by fasterq-dump (--split-3 the default) always creates
     // *_1.fastq *_2.fastq files but sometimes also an additional *.fastq file
     // for unpaired reads which we ignore here.
-    output = meta.single_end ? '*.fastq.gz' : '*_{1,2}.fastq.gz'
+    fastq_output = meta.single_end ? '*.fastq.gz'     : '*_{1,2}.fastq.gz'
+    md5_output   = meta.single_end ? '*.fastq.gz.md5' : '*_{1,2}.fastq.gz.md5'
     """
     eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
     if [[ ! -f "\${NCBI_SETTINGS}" ]]; then
@@ -41,6 +43,22 @@ process SRATOOLS_FASTERQDUMP {
         --processes $task.cpus \\
         *.fastq
 
+    ## Rename FastQ files by meta.id
+    if [ -f  ${sra.name}.fastq.gz ]; then
+        mv ${sra.name}.fastq.gz ${meta.id}.fastq.gz
+        md5sum ${meta.id}.fastq.gz > ${meta.id}.fastq.gz.md5
+    fi
+
+    if [ -f  ${sra.name}_1.fastq.gz ]; then
+        mv ${sra.name}_1.fastq.gz ${meta.id}_1.fastq.gz
+        md5sum ${meta.id}_1.fastq.gz > ${meta.id}_1.fastq.gz.md5
+    fi
+
+    if [ -f  ${sra.name}_2.fastq.gz ]; then
+        mv ${sra.name}_2.fastq.gz ${meta.id}_2.fastq.gz
+        md5sum ${meta.id}_2.fastq.gz > ${meta.id}_2.fastq.gz.md5
+    fi
+
     cat <<-END_VERSIONS > versions.yml
     ${task.process.tokenize(':').last()}:
         sratools: \$(fasterq-dump --version 2>&1 | grep -Eo '[0-9.]+')

From e4384a3a759ebae2d423610dc2c57b72d649c35b Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Nov 2021 12:40:02 +0000
Subject: [PATCH 143/852] Run custom bash script for retry with prefetch

---
 modules/local/sratools_prefetch.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/sratools_prefetch.nf b/modules/local/sratools_prefetch.nf
index 033aeedf..1edb16a3 100644
--- a/modules/local/sratools_prefetch.nf
+++ b/modules/local/sratools_prefetch.nf
@@ -26,7 +26,7 @@ process SRATOOLS_PREFETCH {
         printf '${config}' > "\${NCBI_SETTINGS}"
     fi
 
-    prefetch \\
+    retry_with_backoff.sh prefetch \\
         $args \\
         --progress \\
         $id

From 8c895a47cbcd39f60ac689084f3cdbdf655d45c6 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Nov 2021 12:57:12 +0000
Subject: [PATCH 144/852] Dump experiment accession by default in mappings
 files

---
 nextflow.config      | 2 +-
 nextflow_schema.json | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 6ae6a8da..9e9e2c16 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -14,7 +14,7 @@ params {
     input_type                 = 'sra'
     nf_core_pipeline           = null
     ena_metadata_fields        = null
-    sample_mapping_fields      = 'run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description,description'
+    sample_mapping_fields      = 'experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description,description'
     synapse_config             = null
     skip_fastq_download        = false
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 1f923f28..c033f6c4 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -43,7 +43,7 @@
                     "type": "string",
                     "fa_icon": "fas fa-globe-americas",
                     "description": "Comma-separated list of ENA metadata fields used to create a separate 'id_mappings.csv' and 'multiqc_config.yml' with selected fields that can be used to rename samples in general and in MultiQC.",
-                    "default": "run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description,description"
+                    "default": "experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description,description"
                 },
                 "nf_core_pipeline": {
                     "type": "string",

From 4b0c836744613f7f6ee6da80474937fede8079eb Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Nov 2021 13:05:40 +0000
Subject: [PATCH 145/852] Update CHANGELOG and add links to sra-tools

---
 CHANGELOG.md | 2 +-
 CITATIONS.md | 2 ++
 README.md    | 2 +-
 3 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 327cd99b..dde659d5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 * Convert pipeline to updated Nextflow DSL2 syntax for future adoption across nf-core
 * Added a workflow to download FastQ files and to create samplesheets for ids from the [Synapse platform](https://www.synapse.org/) hosted by [Sage Bionetworks](https://sagebionetworks.org/).
-* SRA identifiers not available for direct download via the ENA FTP will now be downloaded via sra-tools.
+* SRA identifiers not available for direct download via the ENA FTP will now be downloaded via [`sra-tools`](https://github.com/ncbi/sra-tools).
 * Correctly handle errors from SRA identifiers that do **not** return metadata, for example, due to being private.
 * Retry an error in prefetch via bash script in order to allow it to resume interrupted downloads.
 * [[#46](https://github.com/nf-core/fetchngs/issues/46)] - Bug in sra_ids_to_runinfo.py
diff --git a/CITATIONS.md b/CITATIONS.md
index 01819d3e..88db364c 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -28,6 +28,8 @@
 * [GEO](https://pubmed.ncbi.nlm.nih.gov/23193258/)
     > Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A. NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5. doi: 10.1093/nar/gks1193. Epub 2012 Nov 27. PubMed PMID: 23193258; PubMed Central PMCID: PMC3531084.
 
+* [sra-tools](https://github.com/ncbi/sra-tools)
+
 * [Synapse](https://pubmed.ncbi.nlm.nih.gov/24071850/)
     > Omberg L, Ellrott K, Yuan Y, Kandoth C, Wong C, Kellen MR, Friend SH, Stuart J, Liang H, Margolin AA. Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas. Nat Genet. 2013 Oct;45(10):1121-6. doi: 10.1038/ng.2761. PMID: 24071850; PMCID: PMC3950337.
 
diff --git a/README.md b/README.md
index a5ffb8a6..cb694fd5 100644
--- a/README.md
+++ b/README.md
@@ -32,7 +32,7 @@ Via a single file of ids, provided one-per-line (see [example input file](https:
 2. Fetch extensive id metadata via ENA API
 3. Download FastQ files:
     - If direct download links are available from the ENA API, fetch in parallel via `curl` and perform `md5sum` check
-    - Otherwise use `sra-tools` to download `.sra` files and convert them to FastQ
+    - Otherwise use [`sra-tools`](https://github.com/ncbi/sra-tools) to download `.sra` files and convert them to FastQ
 4. Collate id metadata and paths to FastQ files in a single samplesheet
 
 ### Synapse ids

From b9f954766aadadcd927717d788205e12819f211b Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Nov 2021 13:08:19 +0000
Subject: [PATCH 146/852] Move sra-tools citation

---
 CITATIONS.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CITATIONS.md b/CITATIONS.md
index 88db364c..a1d9d91b 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -14,6 +14,8 @@
 
 * [Requests](https://docs.python-requests.org/)
 
+* [sra-tools](https://github.com/ncbi/sra-tools)
+
 ## Pipeline resources
 
 * [ENA](https://pubmed.ncbi.nlm.nih.gov/33175160/)
@@ -28,8 +30,6 @@
 * [GEO](https://pubmed.ncbi.nlm.nih.gov/23193258/)
     > Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A. NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5. doi: 10.1093/nar/gks1193. Epub 2012 Nov 27. PubMed PMID: 23193258; PubMed Central PMCID: PMC3531084.
 
-* [sra-tools](https://github.com/ncbi/sra-tools)
-
 * [Synapse](https://pubmed.ncbi.nlm.nih.gov/24071850/)
     > Omberg L, Ellrott K, Yuan Y, Kandoth C, Wong C, Kellen MR, Friend SH, Stuart J, Liang H, Margolin AA. Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas. Nat Genet. 2013 Oct;45(10):1121-6. doi: 10.1038/ng.2761. PMID: 24071850; PMCID: PMC3950337.
 

From 7d582eeca51b1e9f224e6ca8f28d25dc0b1df1cf Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Nov 2021 13:12:34 +0000
Subject: [PATCH 147/852] Update CHANLGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index dde659d5..ff5301b4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * SRA identifiers not available for direct download via the ENA FTP will now be downloaded via [`sra-tools`](https://github.com/ncbi/sra-tools).
 * Correctly handle errors from SRA identifiers that do **not** return metadata, for example, due to being private.
 * Retry an error in prefetch via bash script in order to allow it to resume interrupted downloads.
+* Rename output FastQ files using `{EXP_ACC}_{RUN_ACC}_T1*fastq.gz` convention for run id provenance
 * [[#46](https://github.com/nf-core/fetchngs/issues/46)] - Bug in sra_ids_to_runinfo.py
 * Added support for [DDBJ ids](https://www.ddbj.nig.ac.jp/index-e.html). See examples below:
 

From 6675b96ca282bf2c0d102048793ca85b652b1ec9 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Nov 2021 14:42:25 +0000
Subject: [PATCH 148/852] Replace *_T* suffix with run accession

---
 bin/sra_runinfo_to_ftp.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bin/sra_runinfo_to_ftp.py b/bin/sra_runinfo_to_ftp.py
index 094782f8..d9400b2f 100755
--- a/bin/sra_runinfo_to_ftp.py
+++ b/bin/sra_runinfo_to_ftp.py
@@ -158,9 +158,9 @@ def sra_runinfo_to_ftp(files_in, file_out):
             writer.writeheader()
             for db_id in sorted(samplesheet):
                 for idx, row in enumerate(samplesheet[db_id], start=1):
-                    row["id"] = f"{db_id}_T{idx}"
+                    row["id"] = f"{db_id}"
                     if 'run_accession' in row:
-                        row["id"] = f"{db_id}_{row['run_accession']}_T{idx}"
+                        row["id"] = f"{db_id}_{row['run_accession']}"
                     writer.writerow(row)
 
 

From d11da5602fe65f2c37a43e5d4be418c4408f5fae Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Nov 2021 14:42:46 +0000
Subject: [PATCH 149/852] Fix bug in md5sum output format

---
 modules/local/sra_fastq_ftp.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/local/sra_fastq_ftp.nf b/modules/local/sra_fastq_ftp.nf
index a775849c..dfbe72dd 100644
--- a/modules/local/sra_fastq_ftp.nf
+++ b/modules/local/sra_fastq_ftp.nf
@@ -26,7 +26,7 @@ process SRA_FASTQ_FTP {
             -L ${fastq[0]} \\
             -o ${meta.id}.fastq.gz
 
-        echo "${meta.md5_1} ${meta.id}.fastq.gz" > ${meta.id}.fastq.gz.md5
+        echo "${meta.md5_1}  ${meta.id}.fastq.gz" > ${meta.id}.fastq.gz.md5
         md5sum -c ${meta.id}.fastq.gz.md5
 
         cat <<-END_VERSIONS > versions.yml
@@ -41,7 +41,7 @@ process SRA_FASTQ_FTP {
             -L ${fastq[0]} \\
             -o ${meta.id}_1.fastq.gz
 
-        echo "${meta.md5_1} ${meta.id}_1.fastq.gz" > ${meta.id}_1.fastq.gz.md5
+        echo "${meta.md5_1}  ${meta.id}_1.fastq.gz" > ${meta.id}_1.fastq.gz.md5
         md5sum -c ${meta.id}_1.fastq.gz.md5
 
         curl \\
@@ -49,7 +49,7 @@ process SRA_FASTQ_FTP {
             -L ${fastq[1]} \\
             -o ${meta.id}_2.fastq.gz
 
-        echo "${meta.md5_2} ${meta.id}_2.fastq.gz" > ${meta.id}_2.fastq.gz.md5
+        echo "${meta.md5_2}  ${meta.id}_2.fastq.gz" > ${meta.id}_2.fastq.gz.md5
         md5sum -c ${meta.id}_2.fastq.gz.md5
 
         cat <<-END_VERSIONS > versions.yml

From 73eb06ce77366a5d36b5e3088f3d83806a639a87 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Nov 2021 14:44:44 +0000
Subject: [PATCH 150/852] Update CHANGELOG

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ff5301b4..04e4c46b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * SRA identifiers not available for direct download via the ENA FTP will now be downloaded via [`sra-tools`](https://github.com/ncbi/sra-tools).
 * Correctly handle errors from SRA identifiers that do **not** return metadata, for example, due to being private.
 * Retry an error in prefetch via bash script in order to allow it to resume interrupted downloads.
-* Rename output FastQ files using `{EXP_ACC}_{RUN_ACC}_T1*fastq.gz` convention for run id provenance
+* Name output FastQ files by `{EXP_ACC}_{RUN_ACC}*fastq.gz` instead of `{EXP_ACC}_{T*}*fastq.gz` for run id provenance
 * [[#46](https://github.com/nf-core/fetchngs/issues/46)] - Bug in sra_ids_to_runinfo.py
 * Added support for [DDBJ ids](https://www.ddbj.nig.ac.jp/index-e.html). See examples below:
 

From 04d0de247bd0284c492e698475950923e7de6fa1 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Nov 2021 15:05:32 +0000
Subject: [PATCH 151/852] Add --force_sratools_download parameter

---
 CHANGELOG.md         | 3 ++-
 nextflow.config      | 1 +
 nextflow_schema.json | 5 +++++
 workflows/sra.nf     | 7 +++++--
 4 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 04e4c46b..0b89d9ae 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,13 +3,14 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[1.4](https://github.com/nf-core/fetchngs/releases/tag/1.4)] - 2021-10-25
+## [[1.4](https://github.com/nf-core/fetchngs/releases/tag/1.4)] - 2021-11-09
 
 ### Enhancements & fixes
 
 * Convert pipeline to updated Nextflow DSL2 syntax for future adoption across nf-core
 * Added a workflow to download FastQ files and to create samplesheets for ids from the [Synapse platform](https://www.synapse.org/) hosted by [Sage Bionetworks](https://sagebionetworks.org/).
 * SRA identifiers not available for direct download via the ENA FTP will now be downloaded via [`sra-tools`](https://github.com/ncbi/sra-tools).
+* Added `--force_sratools_download` parameter to preferentially download all FastQ files via `sra-tools` instead of ENA FTP.
 * Correctly handle errors from SRA identifiers that do **not** return metadata, for example, due to being private.
 * Retry an error in prefetch via bash script in order to allow it to resume interrupted downloads.
 * Name output FastQ files by `{EXP_ACC}_{RUN_ACC}*fastq.gz` instead of `{EXP_ACC}_{T*}*fastq.gz` for run id provenance
diff --git a/nextflow.config b/nextflow.config
index 9e9e2c16..1fb304d3 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -16,6 +16,7 @@ params {
     ena_metadata_fields        = null
     sample_mapping_fields      = 'experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description,description'
     synapse_config             = null
+    force_sratools_download    = false
     skip_fastq_download        = false
 
     // Boilerplate options
diff --git a/nextflow_schema.json b/nextflow_schema.json
index c033f6c4..2831dac7 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -50,6 +50,11 @@
                     "fa_icon": "fab fa-apple",
                     "description": "Name of supported nf-core pipeline e.g.  'rnaseq'. A samplesheet for direct use with the pipeline will be created with the appropriate columns."
                 },
+                "force_sratools_download": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-tools",
+                    "description": "Force download FastQ files via sra-tools instead of via the ENA FTP."
+                },
                 "skip_fastq_download": {
                     "type": "boolean",
                     "fa_icon": "fas fa-fast-forward",
diff --git a/workflows/sra.nf b/workflows/sra.nf
index c108812f..c5fec775 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -70,13 +70,14 @@ workflow SRA {
         }
         .unique()
         .branch {
-            ftp: it[0].fastq_1
-            sra: !it[0].fastq_1
+            ftp: it[0].fastq_1  && !params.force_sratools_download
+            sra: !it[0].fastq_1 || params.force_sratools_download
         }
         .set { ch_sra_reads }
     ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first())
 
     if (!params.skip_fastq_download) {
+
         //
         // MODULE: If FTP link is provided in run information then download FastQ directly via FTP and validate with md5sums
         //
@@ -85,7 +86,9 @@ workflow SRA {
         )
         ch_versions = ch_versions.mix(SRA_FASTQ_FTP.out.versions.first())
 
+        //
         // SUBWORKFLOW: Download sequencing reads without FTP links using sra-tools.
+        //
         SRA_FASTQ (
             ch_sra_reads.sra.map { meta, reads -> [ meta, meta.run_accession ] }
         )

From c1e8040905fc0e5886d425177ef9ae1803d25caa Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Nov 2021 15:06:46 +0000
Subject: [PATCH 152/852] Add CI test for --force_sratools_download

---
 .github/workflows/ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6b67751c..4b3fe636 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -54,6 +54,7 @@ jobs:
             "--nf_core_pipeline rnaseq",
             "--ena_metadata_fields run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5 --sample_mapping_fields run_accession,library_layout",
             --skip_fastq_download,
+            --force_sratools_download
           ]
     steps:
       - name: Check out pipeline code

From 4068b2949a0fe0dfcafe407e68a7e2e5ac48d61f Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Nov 2021 15:22:59 +0000
Subject: [PATCH 153/852] Remove tool specific options section for now

---
 docs/usage.md | 36 ------------------------------------
 1 file changed, 36 deletions(-)

diff --git a/docs/usage.md b/docs/usage.md
index 6af310a6..3cb17fcd 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -186,42 +186,6 @@ process {
 
 > **NB:** We specify just the process name i.e. `STAR_ALIGN` in the config file and not the full task name string that is printed to screen in the error message or on the terminal whilst the pipeline is running i.e. `RNASEQ:ALIGN_STAR:STAR_ALIGN`. You may get a warning suggesting that the process selector isn't recognised but you can ignore that if the process name has been specified correctly. This is something that needs to be fixed upstream in core Nextflow.
 
-### Tool-specific options
-
-For the ultimate flexibility, we have implemented and are using Nextflow DSL2 modules in a way where it is possible for both developers and users to change tool-specific command-line arguments (e.g. providing an additional command-line argument to the `STAR_ALIGN` process) as well as publishing options (e.g. saving files produced by the `STAR_ALIGN` process that aren't saved by default by the pipeline). In the majority of instances, as a user you won't have to change the default options set by the pipeline developer(s), however, there may be edge cases where creating a simple custom config file can improve the behaviour of the pipeline if for example it is failing due to a weird error that requires setting a tool-specific parameter to deal with smaller / larger genomes.
-
-The command-line arguments passed to STAR in the `STAR_ALIGN` module are a combination of:
-
-* Mandatory arguments or those that need to be evaluated within the scope of the module, as supplied in the [`script`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L49-L55) section of the module file.
-
-* An [`options.args`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L56) string of non-mandatory parameters that is set to be empty by default in the module but can be overwritten when including the module in the sub-workflow / workflow context via the `addParams` Nextflow option.
-
-The nf-core/rnaseq pipeline has a sub-workflow (see [terminology](https://github.com/nf-core/modules#terminology)) specifically to align reads with STAR and to sort, index and generate some basic stats on the resulting BAM files using SAMtools. At the top of this file we import the `STAR_ALIGN` module via the Nextflow [`include`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/subworkflows/nf-core/align_star.nf#L10) keyword and by default the options passed to the module via the `addParams` option are set as an empty Groovy map [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/subworkflows/nf-core/align_star.nf#L5); this in turn means `options.args` will be set to empty by default in the module file too. This is an intentional design choice and allows us to implement well-written sub-workflows composed of a chain of tools that by default run with the bare minimum parameter set for any given tool in order to make it much easier to share across pipelines and to provide the flexibility for users and developers to customise any non-mandatory arguments.
-
-When including the sub-workflow above in the main pipeline workflow we use the same `include` statement, however, we now have the ability to overwrite options for each of the tools in the sub-workflow including the [`align_options`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/workflows/rnaseq.nf#L225) variable that will be used specifically to overwrite the optional arguments passed to the `STAR_ALIGN` module. In this case, the options to be provided to `STAR_ALIGN` have been assigned sensible defaults by the developer(s) in the pipeline's [`modules.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/modules.config#L70-L74) and can be accessed and customised in the [workflow context](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/workflows/rnaseq.nf#L201-L204) too before eventually passing them to the sub-workflow as a Groovy map called `star_align_options`. These options will then be propagated from `workflow -> sub-workflow -> module`.
-
-As mentioned at the beginning of this section it may also be necessary for users to overwrite the options passed to modules to be able to customise specific aspects of the way in which a particular tool is executed by the pipeline. Given that all of the default module options are stored in the pipeline's `modules.config` as a [`params` variable](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/modules.config#L24-L25) it is also possible to overwrite any of these options via a custom config file.
-
-Say for example we want to append an additional, non-mandatory parameter (i.e. `--outFilterMismatchNmax 16`) to the arguments passed to the `STAR_ALIGN` module. Firstly, we need to copy across the default `args` specified in the [`modules.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/modules.config#L71) and create a custom config file that is a composite of the default `args` as well as the additional options you would like to provide. This is very important because Nextflow will overwrite the default value of `args` that you provide via the custom config.
-
-As you will see in the example below, we have:
-
-* appended `--outFilterMismatchNmax 16` to the default `args` used by the module.
-* changed the default `publish_dir` value to where the files will eventually be published in the main results directory.
-* appended `'bam':''` to the default value of `publish_files` so that the BAM files generated by the process will also be saved in the top-level results directory for the module. Note: `'out':'log'` means any file/directory ending in `out` will now be saved in a separate directory called `my_star_directory/log/`.
-
-```nextflow
-params {
-    modules {
-        'star_align' {
-            args          = "--quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand zcat --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD --quantTranscriptomeBan Singleend --outFilterMismatchNmax 16"
-            publish_dir   = "my_star_directory"
-            publish_files = ['out':'log', 'tab':'log', 'bam':'']
-        }
-    }
-}
-```
-
 ### Updating containers
 
 The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the `process` name and override the Nextflow `container` definition for that process using the `withName` declaration. For example, in the [nf-core/viralrecon](https://nf-co.re/viralrecon) pipeline a tool called [Pangolin](https://github.com/cov-lineages/pangolin) has been used during the COVID-19 pandemic to assign lineages to SARS-CoV-2 genome sequenced samples. Given that the lineage assignments change quite frequently it doesn't make sense to re-release the nf-core/viralrecon everytime a new version of Pangolin has been released. However, you can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via `-c custom.config`.

From cacf5aaf0a8763862892c68b7b86b80444c36634 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Nov 2021 15:33:43 +0000
Subject: [PATCH 154/852] Update test ids link in README

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index cb694fd5..58e4a8a7 100644
--- a/README.md
+++ b/README.md
@@ -24,7 +24,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 ## Pipeline summary
 
-Via a single file of ids, provided one-per-line (see [example input file](https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/public_database_ids.txt)) the pipeline performs the following steps:
+Via a single file of ids, provided one-per-line (see [example input file](https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.txt)) the pipeline performs the following steps:
 
 ### SRA / ENA / DDBJ / GEO ids
 

From 021bdad14c0d7af9c0b864aa1514729778f7f616 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Nov 2021 15:43:01 +0000
Subject: [PATCH 155/852] Rename subworkflow to sra_fastq_sratools.nf

---
 subworkflows/local/{sra_fastq.nf => sra_fastq_sratools.nf} | 2 +-
 workflows/sra.nf                                           | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)
 rename subworkflows/local/{sra_fastq.nf => sra_fastq_sratools.nf} (96%)

diff --git a/subworkflows/local/sra_fastq.nf b/subworkflows/local/sra_fastq_sratools.nf
similarity index 96%
rename from subworkflows/local/sra_fastq.nf
rename to subworkflows/local/sra_fastq_sratools.nf
index 04039f79..e093fe2f 100644
--- a/subworkflows/local/sra_fastq.nf
+++ b/subworkflows/local/sra_fastq_sratools.nf
@@ -5,7 +5,7 @@
 include { SRATOOLS_PREFETCH    } from '../../modules/local/sratools_prefetch.nf'
 include { SRATOOLS_FASTERQDUMP } from '../../modules/local/sratools_fasterqdump.nf'
 
-workflow SRA_FASTQ {
+workflow SRA_FASTQ_SRATOOLS {
     take:
     sra_ids  // channel: [ val(meta), val(id) ]
 
diff --git a/workflows/sra.nf b/workflows/sra.nf
index c5fec775..8600aa00 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -22,7 +22,7 @@ WorkflowSra.initialise(params, log, valid_params)
 include { SRA_IDS_TO_RUNINFO      } from '../modules/local/sra_ids_to_runinfo'
 include { SRA_RUNINFO_TO_FTP      } from '../modules/local/sra_runinfo_to_ftp'
 include { SRA_FASTQ_FTP           } from '../modules/local/sra_fastq_ftp'
-include { SRA_FASTQ               } from '../subworkflows/local/sra_fastq'
+include { SRA_FASTQ_SRATOOLS      } from '../subworkflows/local/sra_fastq_sratools'
 include { SRA_TO_SAMPLESHEET      } from '../modules/local/sra_to_samplesheet'
 include { SRA_MERGE_SAMPLESHEET   } from '../modules/local/sra_merge_samplesheet'
 include { MULTIQC_MAPPINGS_CONFIG } from '../modules/local/multiqc_mappings_config'
@@ -89,7 +89,7 @@ workflow SRA {
         //
         // SUBWORKFLOW: Download sequencing reads without FTP links using sra-tools.
         //
-        SRA_FASTQ (
+        SRA_FASTQ_SRATOOLS (
             ch_sra_reads.sra.map { meta, reads -> [ meta, meta.run_accession ] }
         )
         ch_versions = ch_versions.mix(SRA_FASTQ.out.versions.first())

From e5e59e982ceb0322c62ec5975cfbb3f790d80121 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Nov 2021 15:46:25 +0000
Subject: [PATCH 156/852] Fix tests

---
 workflows/sra.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/workflows/sra.nf b/workflows/sra.nf
index 8600aa00..4012a571 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -92,13 +92,13 @@ workflow SRA {
         SRA_FASTQ_SRATOOLS (
             ch_sra_reads.sra.map { meta, reads -> [ meta, meta.run_accession ] }
         )
-        ch_versions = ch_versions.mix(SRA_FASTQ.out.versions.first())
+        ch_versions = ch_versions.mix(SRA_FASTQ_SRATOOLS.out.versions.first())
 
         //
         // MODULE: Stage FastQ files downloaded by SRA together and auto-create a samplesheet
         //
         SRA_TO_SAMPLESHEET (
-            SRA_FASTQ_FTP.out.fastq.mix(SRA_FASTQ.out.reads),
+            SRA_FASTQ_FTP.out.fastq.mix(SRA_FASTQ_SRATOOLS.out.reads),
             params.nf_core_pipeline ?: '',
             params.sample_mapping_fields
         )

From b0363de5626ce526a889b2c5ef6e6f2d9bb49991 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 9 Nov 2021 12:11:18 +0000
Subject: [PATCH 157/852] Update DSL2 docs in CONTRIBUTING.md

---
 .github/CONTRIBUTING.md | 54 ++++++++++-------------------------------
 1 file changed, 13 insertions(+), 41 deletions(-)

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 888cff34..f294492d 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -61,21 +61,16 @@ For further information/help, please consult the [nf-core/fetchngs documentation
 
 To make the nf-core/fetchngs code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
 
-### Adding a new step
-
-If you wish to contribute a new step, please use the following coding standards:
-
-1. Define the corresponding input channel into your new process from the expected previous process channel
-2. Write the process block (see below).
-3. Define the output channel if needed (see below).
-4. Add any new flags/options to `nextflow.config` with a default (see below).
-5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build`).
-6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter).
-7. Add sanity checks for all relevant parameters.
-8. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`.
-9. Do local tests that the new code works properly and as expected.
-10. Add a new test command in `.github/workflow/ci.yml`.
-11. Add any descriptions of output files to `docs/output.md`.
+### Adding a new step or module
+
+If you wish to contribute a new step or module please see the [official guidelines](https://nf-co.re/developers/adding_modules#new-module-guidelines-and-pr-review-checklist) and use the following coding standards:
+
+1. Add any new flags/options to `nextflow.config` with a default (see section below).
+2. Add any new flags/options to `nextflow_schema.json` with help text via `nf-core schema build`.
+3. Add sanity checks for all relevant parameters.
+4. Perform local tests to validate that the new code works as expected.
+5. If applicable, add a new test command in `.github/workflow/ci.yml`.
+6. Add any descriptions of output files to `docs/output.md`.
 
 ### Default values
 
@@ -87,40 +82,17 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
 
 Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
-The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
-
-### Naming schemes
+### Channel naming convention
 
 Please use the following naming schemes, to make it easy to understand what is going where.
 
-* initial process channel: `ch_output_from_<process>`
-* intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
+* Initial process channel: `ch_output_from_<process>`
+* Intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
 
 ### Nextflow version bumping
 
 If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`
 
-### Software version reporting
-
-If you add a new tool to the pipeline, please ensure you add the information of the tool to the `get_software_version` process.
-
-Add to the script block of the process, something like the following:
-
-```bash
-<YOUR_TOOL> --version &> v_<YOUR_TOOL>.txt 2>&1 || true
-```
-
-or
-
-```bash
-<YOUR_TOOL> --help | head -n 1 &> v_<YOUR_TOOL>.txt 2>&1 || true
-```
-
-You then need to edit the script `bin/scrape_software_versions.py` to:
-
-1. Add a Python regex for your tool's `--version` output (as in stored in the `v_<YOUR_TOOL>.txt` file), to ensure the version is reported as a `v` and the version number e.g. `v2.1.1`
-2. Add a HTML entry to the `OrderedDict` for formatting in MultiQC.
-
 ### Images and figures
 
 For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).

From e1cb675c04392bcc799cc58bc19120904828b01f Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 9 Nov 2021 17:31:53 +0000
Subject: [PATCH 158/852] Bump version to 1.5dev

---
 CHANGELOG.md    | 4 ++++
 nextflow.config | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0b89d9ae..f3e67547 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unpublished Version / DEV]
+
+### Enhancements & fixes
+
 ## [[1.4](https://github.com/nf-core/fetchngs/releases/tag/1.4)] - 2021-11-09
 
 ### Enhancements & fixes
diff --git a/nextflow.config b/nextflow.config
index 1fb304d3..ea68a9b1 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -146,7 +146,7 @@ manifest {
     description     = 'Pipeline to fetch metadata and raw FastQ files from public databases'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.04.0'
-    version         = '1.4'
+    version         = '1.5dev'
 }
 
 // Load modules.config for DSL2 module specific options

From 08d7c1e245ef726ed07b9c5ad60846d1030f494e Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 27 Nov 2021 09:46:04 +0000
Subject: [PATCH 159/852] Install updated syntax module from nf-core/modules

---
 modules/local/dumpsoftwareversions.nf         | 96 -------------------
 .../custom/dumpsoftwareversions/main.nf       | 21 ++++
 .../custom/dumpsoftwareversions/meta.yml      | 34 +++++++
 .../templates/dumpsoftwareversions.py         | 89 +++++++++++++++++
 .../modules/sratools/fasterqdump/main.nf}     | 31 ++----
 .../modules/sratools/fasterqdump/meta.yml     | 42 ++++++++
 .../modules/sratools/prefetch/main.nf}        |  7 +-
 .../modules/sratools/prefetch/meta.yml        | 43 +++++++++
 8 files changed, 238 insertions(+), 125 deletions(-)
 delete mode 100644 modules/local/dumpsoftwareversions.nf
 create mode 100644 modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
 create mode 100644 modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml
 create mode 100644 modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
 rename modules/{local/sratools_fasterqdump.nf => nf-core/modules/sratools/fasterqdump/main.nf} (61%)
 create mode 100644 modules/nf-core/modules/sratools/fasterqdump/meta.yml
 rename modules/{local/sratools_prefetch.nf => nf-core/modules/sratools/prefetch/main.nf} (90%)
 create mode 100644 modules/nf-core/modules/sratools/prefetch/meta.yml

diff --git a/modules/local/dumpsoftwareversions.nf b/modules/local/dumpsoftwareversions.nf
deleted file mode 100644
index 69ebcbaa..00000000
--- a/modules/local/dumpsoftwareversions.nf
+++ /dev/null
@@ -1,96 +0,0 @@
-
-process DUMPSOFTWAREVERSIONS {
-    label 'process_low'
-
-    // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda (params.enable_conda ? "bioconda::multiqc=1.11" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }"
-
-    input:
-    path versions
-
-    output:
-    path "software_versions.yml"    , emit: yml
-    path "software_versions_mqc.yml", emit: mqc_yml
-    path "versions.yml"             , emit: versions
-
-    script:
-    """
-    #!/usr/bin/env python
-
-    import yaml
-    import platform
-    from textwrap import dedent
-
-    def _make_versions_html(versions):
-        html = [
-            dedent(
-                '''\\
-                <style>
-                #nf-core-versions tbody:nth-child(even) {
-                    background-color: #f2f2f2;
-                }
-                </style>
-                <table class="table" style="width:100%" id="nf-core-versions">
-                    <thead>
-                        <tr>
-                            <th> Process Name </th>
-                            <th> Software </th>
-                            <th> Version  </th>
-                        </tr>
-                    </thead>
-                '''
-            )
-        ]
-        for process, tmp_versions in sorted(versions.items()):
-            html.append("<tbody>")
-            for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
-                html.append(
-                    dedent(
-                        f'''\\
-                        <tr>
-                            <td><samp>{process if (i == 0) else ''}</samp></td>
-                            <td><samp>{tool}</samp></td>
-                            <td><samp>{version}</samp></td>
-                        </tr>
-                        '''
-                    )
-                )
-            html.append("</tbody>")
-        html.append("</table>")
-        return "\\n".join(html)
-
-    module_versions = {}
-    module_versions["${task.process.tokenize(':').last()}"] = {
-        'python': platform.python_version(),
-        'yaml': yaml.__version__
-    }
-
-    with open("$versions") as f:
-        workflow_versions = yaml.load(f, Loader=yaml.BaseLoader) | module_versions
-
-    workflow_versions["Workflow"] = {
-        "Nextflow": "$workflow.nextflow.version",
-        "$workflow.manifest.name": "$workflow.manifest.version"
-    }
-
-    versions_mqc = {
-        'id': 'software_versions',
-        'section_name': '${workflow.manifest.name} Software Versions',
-        'section_href': 'https://github.com/${workflow.manifest.name}',
-        'plot_type': 'html',
-        'description': 'are collected at run time from the software output.',
-        'data': _make_versions_html(workflow_versions)
-    }
-
-    with open("software_versions.yml", 'w') as f:
-        yaml.dump(workflow_versions, f, default_flow_style=False)
-    with open("software_versions_mqc.yml", 'w') as f:
-        yaml.dump(versions_mqc, f, default_flow_style=False)
-
-    with open('versions.yml', 'w') as f:
-        yaml.dump(module_versions, f, default_flow_style=False)
-    """
-}
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
new file mode 100644
index 00000000..934bb467
--- /dev/null
+++ b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
@@ -0,0 +1,21 @@
+process CUSTOM_DUMPSOFTWAREVERSIONS {
+    label 'process_low'
+
+    // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
+    conda (params.enable_conda ? "bioconda::multiqc=1.11" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }"
+
+    input:
+    path versions
+
+    output:
+    path "software_versions.yml"    , emit: yml
+    path "software_versions_mqc.yml", emit: mqc_yml
+    path "versions.yml"             , emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    template 'dumpsoftwareversions.py'
+}
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml
new file mode 100644
index 00000000..5b5b8a60
--- /dev/null
+++ b/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml
@@ -0,0 +1,34 @@
+name: custom_dumpsoftwareversions
+description: Custom module used to dump software versions within the nf-core pipeline template
+keywords:
+  - custom
+  - version
+tools:
+  - custom:
+      description: Custom module used to dump software versions within the nf-core pipeline template
+      homepage: https://github.com/nf-core/tools
+      documentation: https://github.com/nf-core/tools
+      licence: ['MIT']
+input:
+  - versions:
+      type: file
+      description: YML file containing software versions
+      pattern: "*.yml"
+
+output:
+  - yml:
+      type: file
+      description: Standard YML file containing software versions
+      pattern: "software_versions.yml"
+  - mqc_yml:
+      type: file
+      description: MultiQC custom content YML file containing software versions
+      pattern: "software_versions_mqc.yml"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@drpatelh"
+  - "@grst"
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
new file mode 100644
index 00000000..d1390392
--- /dev/null
+++ b/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
@@ -0,0 +1,89 @@
+#!/usr/bin/env python
+
+import yaml
+import platform
+from textwrap import dedent
+
+
+def _make_versions_html(versions):
+    html = [
+        dedent(
+            """\\
+            <style>
+            #nf-core-versions tbody:nth-child(even) {
+                background-color: #f2f2f2;
+            }
+            </style>
+            <table class="table" style="width:100%" id="nf-core-versions">
+                <thead>
+                    <tr>
+                        <th> Process Name </th>
+                        <th> Software </th>
+                        <th> Version  </th>
+                    </tr>
+                </thead>
+            """
+        )
+    ]
+    for process, tmp_versions in sorted(versions.items()):
+        html.append("<tbody>")
+        for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
+            html.append(
+                dedent(
+                    f"""\\
+                    <tr>
+                        <td><samp>{process if (i == 0) else ''}</samp></td>
+                        <td><samp>{tool}</samp></td>
+                        <td><samp>{version}</samp></td>
+                    </tr>
+                    """
+                )
+            )
+        html.append("</tbody>")
+    html.append("</table>")
+    return "\\n".join(html)
+
+
+versions_this_module = {}
+versions_this_module["${task.process}"] = {
+    "python": platform.python_version(),
+    "yaml": yaml.__version__,
+}
+
+with open("$versions") as f:
+    versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
+
+# aggregate versions by the module name (derived from fully-qualified process name)
+versions_by_module = {}
+for process, process_versions in versions_by_process.items():
+    module = process.split(":")[-1]
+    try:
+        assert versions_by_module[module] == process_versions, (
+            "We assume that software versions are the same between all modules. "
+            "If you see this error-message it means you discovered an edge-case "
+            "and should open an issue in nf-core/tools. "
+        )
+    except KeyError:
+        versions_by_module[module] = process_versions
+
+versions_by_module["Workflow"] = {
+    "Nextflow": "$workflow.nextflow.version",
+    "$workflow.manifest.name": "$workflow.manifest.version",
+}
+
+versions_mqc = {
+    "id": "software_versions",
+    "section_name": "${workflow.manifest.name} Software Versions",
+    "section_href": "https://github.com/${workflow.manifest.name}",
+    "plot_type": "html",
+    "description": "are collected at run time from the software output.",
+    "data": _make_versions_html(versions_by_module),
+}
+
+with open("software_versions.yml", "w") as f:
+    yaml.dump(versions_by_module, f, default_flow_style=False)
+with open("software_versions_mqc.yml", "w") as f:
+    yaml.dump(versions_mqc, f, default_flow_style=False)
+
+with open("versions.yml", "w") as f:
+    yaml.dump(versions_this_module, f, default_flow_style=False)
diff --git a/modules/local/sratools_fasterqdump.nf b/modules/nf-core/modules/sratools/fasterqdump/main.nf
similarity index 61%
rename from modules/local/sratools_fasterqdump.nf
rename to modules/nf-core/modules/sratools/fasterqdump/main.nf
index f834eb8b..73e3673d 100644
--- a/modules/local/sratools_fasterqdump.nf
+++ b/modules/nf-core/modules/sratools/fasterqdump/main.nf
@@ -1,4 +1,3 @@
-
 process SRATOOLS_FASTERQDUMP {
     tag "$meta.id"
     label 'process_medium'
@@ -12,19 +11,17 @@ process SRATOOLS_FASTERQDUMP {
     tuple val(meta), path(sra)
 
     output:
-    tuple val(meta), path(fastq_output), emit: reads
-    tuple val(meta), path(md5_output)  , emit: md5
-    path "versions.yml"                , emit: versions
+    tuple val(meta), path(output), emit: reads
+    path "versions.yml"          , emit: versions
 
     script:
-    def args   = task.ext.args  ?: ''
-    def args2  = task.ext.args2 ?: ''
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
     def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
     // Paired-end data extracted by fasterq-dump (--split-3 the default) always creates
     // *_1.fastq *_2.fastq files but sometimes also an additional *.fastq file
     // for unpaired reads which we ignore here.
-    fastq_output = meta.single_end ? '*.fastq.gz'     : '*_{1,2}.fastq.gz'
-    md5_output   = meta.single_end ? '*.fastq.gz.md5' : '*_{1,2}.fastq.gz.md5'
+    output = meta.single_end ? '*.fastq.gz' : '*_{1,2}.fastq.gz'
     """
     eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
     if [[ ! -f "\${NCBI_SETTINGS}" ]]; then
@@ -43,24 +40,8 @@ process SRATOOLS_FASTERQDUMP {
         --processes $task.cpus \\
         *.fastq
 
-    ## Rename FastQ files by meta.id
-    if [ -f  ${sra.name}.fastq.gz ]; then
-        mv ${sra.name}.fastq.gz ${meta.id}.fastq.gz
-        md5sum ${meta.id}.fastq.gz > ${meta.id}.fastq.gz.md5
-    fi
-
-    if [ -f  ${sra.name}_1.fastq.gz ]; then
-        mv ${sra.name}_1.fastq.gz ${meta.id}_1.fastq.gz
-        md5sum ${meta.id}_1.fastq.gz > ${meta.id}_1.fastq.gz.md5
-    fi
-
-    if [ -f  ${sra.name}_2.fastq.gz ]; then
-        mv ${sra.name}_2.fastq.gz ${meta.id}_2.fastq.gz
-        md5sum ${meta.id}_2.fastq.gz > ${meta.id}_2.fastq.gz.md5
-    fi
-
     cat <<-END_VERSIONS > versions.yml
-    ${task.process.tokenize(':').last()}:
+    "${task.process}":
         sratools: \$(fasterq-dump --version 2>&1 | grep -Eo '[0-9.]+')
         pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
     END_VERSIONS
diff --git a/modules/nf-core/modules/sratools/fasterqdump/meta.yml b/modules/nf-core/modules/sratools/fasterqdump/meta.yml
new file mode 100644
index 00000000..1478bed8
--- /dev/null
+++ b/modules/nf-core/modules/sratools/fasterqdump/meta.yml
@@ -0,0 +1,42 @@
+name: sratools_fasterqdump
+description: Extract sequencing reads in FASTQ format from a given NCBI Sequence Read Archive (SRA).
+keywords:
+  - sequencing
+  - FASTQ
+  - dump
+tools:
+  - sratools:
+      description: SRA Toolkit and SDK from NCBI
+      homepage: https://github.com/ncbi/sra-tools
+      documentation: https://github.com/ncbi/sra-tools/wiki
+      tool_dev_url: https://github.com/ncbi/sra-tools
+      licence: ['US-Government-Work']
+
+input:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - sra:
+      type: directory
+      description: Directory containing ETL data for the given SRA.
+      pattern: "*/*.sra"
+
+output:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - reads:
+      type: file
+      description: Extracted FASTQ file or files if the sequencing reads are paired-end.
+      pattern: "*.fastq.gz"
+
+authors:
+  - "@Midnighter"
diff --git a/modules/local/sratools_prefetch.nf b/modules/nf-core/modules/sratools/prefetch/main.nf
similarity index 90%
rename from modules/local/sratools_prefetch.nf
rename to modules/nf-core/modules/sratools/prefetch/main.nf
index 1edb16a3..1e1eb802 100644
--- a/modules/local/sratools_prefetch.nf
+++ b/modules/nf-core/modules/sratools/prefetch/main.nf
@@ -1,4 +1,3 @@
-
 process SRATOOLS_PREFETCH {
     tag "$id"
     label 'process_low'
@@ -17,7 +16,7 @@ process SRATOOLS_PREFETCH {
     path "versions.yml"         , emit: versions
 
     script:
-    def args   = task.ext.args ?: ''
+    def args = task.ext.args ?: ''
     def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
     """
     eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
@@ -26,7 +25,7 @@ process SRATOOLS_PREFETCH {
         printf '${config}' > "\${NCBI_SETTINGS}"
     fi
 
-    retry_with_backoff.sh prefetch \\
+    prefetch \\
         $args \\
         --progress \\
         $id
@@ -34,7 +33,7 @@ process SRATOOLS_PREFETCH {
     vdb-validate $id
 
     cat <<-END_VERSIONS > versions.yml
-    ${task.process.tokenize(':').last()}:
+    "${task.process}":
         sratools: \$(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
     END_VERSIONS
     """
diff --git a/modules/nf-core/modules/sratools/prefetch/meta.yml b/modules/nf-core/modules/sratools/prefetch/meta.yml
new file mode 100644
index 00000000..22213b29
--- /dev/null
+++ b/modules/nf-core/modules/sratools/prefetch/meta.yml
@@ -0,0 +1,43 @@
+name: sratools_prefetch
+description: Download sequencing data from the NCBI Sequence Read Archive (SRA).
+keywords:
+  - sequencing
+  - fastq
+  - prefetch
+tools:
+  - sratools:
+      description: SRA Toolkit and SDK from NCBI
+      homepage: https://github.com/ncbi/sra-tools
+      documentation: https://github.com/ncbi/sra-tools/wiki
+      tool_dev_url: https://github.com/ncbi/sra-tools
+      licence: ['US-Government-Work']
+
+input:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - id:
+      type: val
+      description: >
+        A string denoting an SRA id.
+
+output:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - sra:
+      type: directory
+      description: >
+        Directory containing the ETL data for the given SRA id.
+      pattern: "*/*.sra"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@Midnighter"

From 1f307ce46f565be526f92d119dc16df01bbab8e5 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 27 Nov 2021 09:46:34 +0000
Subject: [PATCH 160/852] Change version command to use task.process

---
 modules/local/multiqc_mappings_config.nf   | 2 +-
 modules/local/sra_fastq_ftp.nf             | 4 ++--
 modules/local/sra_ids_to_runinfo.nf        | 2 +-
 modules/local/sra_merge_samplesheet.nf     | 2 +-
 modules/local/sra_runinfo_to_ftp.nf        | 2 +-
 modules/local/synapse_get.nf               | 2 +-
 modules/local/synapse_list.nf              | 2 +-
 modules/local/synapse_merge_samplesheet.nf | 2 +-
 modules/local/synapse_show.nf              | 2 +-
 9 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/modules/local/multiqc_mappings_config.nf b/modules/local/multiqc_mappings_config.nf
index 15c30846..31f06dae 100644
--- a/modules/local/multiqc_mappings_config.nf
+++ b/modules/local/multiqc_mappings_config.nf
@@ -20,7 +20,7 @@ process MULTIQC_MAPPINGS_CONFIG {
         multiqc_config.yml
 
     cat <<-END_VERSIONS > versions.yml
-    ${task.process.tokenize(':').last()}:
+    "${task.process}":
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """
diff --git a/modules/local/sra_fastq_ftp.nf b/modules/local/sra_fastq_ftp.nf
index dfbe72dd..2dc0c8ae 100644
--- a/modules/local/sra_fastq_ftp.nf
+++ b/modules/local/sra_fastq_ftp.nf
@@ -30,7 +30,7 @@ process SRA_FASTQ_FTP {
         md5sum -c ${meta.id}.fastq.gz.md5
 
         cat <<-END_VERSIONS > versions.yml
-        ${task.process.tokenize(':').last()}:
+        "${task.process}":
             curl: \$(echo \$(curl --version | head -n 1 | sed 's/^curl //; s/ .*\$//'))
         END_VERSIONS
         """
@@ -53,7 +53,7 @@ process SRA_FASTQ_FTP {
         md5sum -c ${meta.id}_2.fastq.gz.md5
 
         cat <<-END_VERSIONS > versions.yml
-        ${task.process.tokenize(':').last()}:
+        "${task.process}"
             curl: \$(echo \$(curl --version | head -n 1 | sed 's/^curl //; s/ .*\$//'))
         END_VERSIONS
         """
diff --git a/modules/local/sra_ids_to_runinfo.nf b/modules/local/sra_ids_to_runinfo.nf
index c8209690..57fdb10e 100644
--- a/modules/local/sra_ids_to_runinfo.nf
+++ b/modules/local/sra_ids_to_runinfo.nf
@@ -26,7 +26,7 @@ process SRA_IDS_TO_RUNINFO {
         $metadata_fields
 
     cat <<-END_VERSIONS > versions.yml
-    ${task.process.tokenize(':').last()}:
+    "${task.process}":
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """
diff --git a/modules/local/sra_merge_samplesheet.nf b/modules/local/sra_merge_samplesheet.nf
index be3f1087..863dfaa7 100644
--- a/modules/local/sra_merge_samplesheet.nf
+++ b/modules/local/sra_merge_samplesheet.nf
@@ -28,7 +28,7 @@ process SRA_MERGE_SAMPLESHEET {
     done
 
     cat <<-END_VERSIONS > versions.yml
-    ${task.process.tokenize(':').last()}:
+    "${task.process}":
         sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
     END_VERSIONS
     """
diff --git a/modules/local/sra_runinfo_to_ftp.nf b/modules/local/sra_runinfo_to_ftp.nf
index a6b6a829..13fa6c3e 100644
--- a/modules/local/sra_runinfo_to_ftp.nf
+++ b/modules/local/sra_runinfo_to_ftp.nf
@@ -20,7 +20,7 @@ process SRA_RUNINFO_TO_FTP {
         ${runinfo.toString().tokenize(".")[0]}.runinfo_ftp.tsv
 
     cat <<-END_VERSIONS > versions.yml
-    ${task.process.tokenize(':').last()}:
+    "${task.process}":
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """
diff --git a/modules/local/synapse_get.nf b/modules/local/synapse_get.nf
index 5269286c..885a9a95 100644
--- a/modules/local/synapse_get.nf
+++ b/modules/local/synapse_get.nf
@@ -30,7 +30,7 @@ process SYNAPSE_GET {
     echo "${meta.md5} \t ${meta.name}" > ${meta.id}.md5
 
     cat <<-END_VERSIONS > versions.yml
-    ${task.process.tokenize(':').last()}:
+    "${task.process}":
         synapse: \$(synapse --version | sed -e "s/Synapse Client //g")
     END_VERSIONS
     """
diff --git a/modules/local/synapse_list.nf b/modules/local/synapse_list.nf
index 0255c925..58034038 100644
--- a/modules/local/synapse_list.nf
+++ b/modules/local/synapse_list.nf
@@ -29,7 +29,7 @@ process SYNAPSE_LIST {
         > ${id}.list.txt
 
     cat <<-END_VERSIONS > versions.yml
-    ${task.process.tokenize(':').last()}:
+    "${task.process}":
         syanpse: \$(synapse --version | sed -e "s/Synapse Client //g")
     END_VERSIONS
     """
diff --git a/modules/local/synapse_merge_samplesheet.nf b/modules/local/synapse_merge_samplesheet.nf
index e3f97fa8..01461e14 100644
--- a/modules/local/synapse_merge_samplesheet.nf
+++ b/modules/local/synapse_merge_samplesheet.nf
@@ -21,7 +21,7 @@ process SYNAPSE_MERGE_SAMPLESHEET {
     done
 
     cat <<-END_VERSIONS > versions.yml
-    ${task.process.tokenize(':').last()}:
+    "${task.process}":
         sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
     END_VERSIONS
     """
diff --git a/modules/local/synapse_show.nf b/modules/local/synapse_show.nf
index 9a81493a..e03fb2f1 100644
--- a/modules/local/synapse_show.nf
+++ b/modules/local/synapse_show.nf
@@ -29,7 +29,7 @@ process SYNAPSE_SHOW {
         > ${id}.metadata.txt
 
     cat <<-END_VERSIONS > versions.yml
-    ${task.process.tokenize(':').last()}:
+    "${task.process}":
         synapse: \$(synapse --version | sed -e "s/Synapse Client //g")
     END_VERSIONS
     """

From ab3bf4ed865069fa0ae3cdb91dd8ff380af13240 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 27 Nov 2021 09:46:46 +0000
Subject: [PATCH 161/852] Install nf-core modules

---
 modules.json | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/modules.json b/modules.json
index 0e4143ef..5d0b0fe9 100644
--- a/modules.json
+++ b/modules.json
@@ -1,5 +1,17 @@
 {
     "name": "nf-core/fetchngs",
     "homePage": "https://github.com/nf-core/fetchngs",
-    "repos": {}
+    "repos": {
+        "nf-core/modules": {
+            "custom/dumpsoftwareversions": {
+                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+            },
+            "sratools/fasterqdump": {
+                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+            },
+            "sratools/prefetch": {
+                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+            }
+        }
+    }
 }
\ No newline at end of file

From b1ced19ee6874ae89443323abf88d760288a1a8c Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 27 Nov 2021 09:47:34 +0000
Subject: [PATCH 162/852] Add executor local for native groovy processes

---
 modules/local/sra_to_samplesheet.nf     | 1 +
 modules/local/synapse_to_samplesheet.nf | 1 +
 2 files changed, 2 insertions(+)

diff --git a/modules/local/sra_to_samplesheet.nf b/modules/local/sra_to_samplesheet.nf
index dbbc6613..465144d7 100644
--- a/modules/local/sra_to_samplesheet.nf
+++ b/modules/local/sra_to_samplesheet.nf
@@ -2,6 +2,7 @@
 process SRA_TO_SAMPLESHEET {
     tag "$meta.id"
 
+    executor 'local'
     memory 100.MB
 
     input:
diff --git a/modules/local/synapse_to_samplesheet.nf b/modules/local/synapse_to_samplesheet.nf
index 40519ec0..2e7945ed 100644
--- a/modules/local/synapse_to_samplesheet.nf
+++ b/modules/local/synapse_to_samplesheet.nf
@@ -2,6 +2,7 @@
 process SYNAPSE_TO_SAMPLESHEET {
     tag "$meta.id"
 
+    executor 'local'
     memory 100.MB
 
     input:

From 4fcd56b631835b81840d1102d1a726b2238c6415 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 27 Nov 2021 20:53:40 +0000
Subject: [PATCH 163/852] Bump NF version from 21.04.0 to 21.10.3

---
 .github/ISSUE_TEMPLATE/bug_report.md | 2 +-
 .github/workflows/ci.yml             | 2 +-
 README.md                            | 4 ++--
 nextflow.config                      | 3 +--
 4 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
index 11bb35bf..406ca8df 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -51,7 +51,7 @@ Have you provided the following extra information/files:
 
 ## Nextflow Installation
 
-- Version: <!-- [e.g. 21.04.0] -->
+- Version: <!-- [e.g. 21.10.3] -->
 
 ## Container engine
 
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4b3fe636..eb26bd07 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -22,7 +22,7 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and latest edge version
-        nxf_ver: ["NXF_VER=21.04.0", "NXF_EDGE=1"]
+        nxf_ver: ["NXF_VER=21.10.3", "NXF_EDGE=1"]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
diff --git a/README.md b/README.md
index 58e4a8a7..eb046d87 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/fetchngs/results)
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.5070524-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.5070524)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.04.0-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -48,7 +48,7 @@ The columns in the auto-created samplesheet can be tailored to be accepted out-o
 
 ## Quick Start
 
-1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.04.0`)
+1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)
 
 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
 
diff --git a/nextflow.config b/nextflow.config
index ea68a9b1..5cc0cdac 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -22,7 +22,6 @@ params {
     // Boilerplate options
     outdir                     = './results'
     tracedir                   = "${params.outdir}/pipeline_info"
-    publish_dir_mode           = 'copy'
     email                      = null
     email_on_fail              = null
     plaintext_email            = false
@@ -145,7 +144,7 @@ manifest {
     homePage        = 'https://github.com/nf-core/fetchngs'
     description     = 'Pipeline to fetch metadata and raw FastQ files from public databases'
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=21.04.0'
+    nextflowVersion = '!>=21.10.3'
     version         = '1.5dev'
 }
 

From 2c28be248ced1ebb7d2a199434c9546cb10ac95c Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 27 Nov 2021 20:55:08 +0000
Subject: [PATCH 164/852] Move sratools modules to local due to customisation

---
 modules.json                                  |  6 ---
 .../main.nf => local/sratools_fasterqdump.nf} | 27 ++++++++++--
 .../main.nf => local/sratools_prefetch.nf}    |  3 +-
 .../modules/sratools/fasterqdump/meta.yml     | 42 ------------------
 .../modules/sratools/prefetch/meta.yml        | 43 -------------------
 subworkflows/local/sra_fastq_sratools.nf      |  4 +-
 6 files changed, 27 insertions(+), 98 deletions(-)
 rename modules/{nf-core/modules/sratools/fasterqdump/main.nf => local/sratools_fasterqdump.nf} (64%)
 rename modules/{nf-core/modules/sratools/prefetch/main.nf => local/sratools_prefetch.nf} (96%)
 delete mode 100644 modules/nf-core/modules/sratools/fasterqdump/meta.yml
 delete mode 100644 modules/nf-core/modules/sratools/prefetch/meta.yml

diff --git a/modules.json b/modules.json
index 5d0b0fe9..eba88bd4 100644
--- a/modules.json
+++ b/modules.json
@@ -5,12 +5,6 @@
         "nf-core/modules": {
             "custom/dumpsoftwareversions": {
                 "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
-            },
-            "sratools/fasterqdump": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
-            },
-            "sratools/prefetch": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
             }
         }
     }
diff --git a/modules/nf-core/modules/sratools/fasterqdump/main.nf b/modules/local/sratools_fasterqdump.nf
similarity index 64%
rename from modules/nf-core/modules/sratools/fasterqdump/main.nf
rename to modules/local/sratools_fasterqdump.nf
index 73e3673d..7a75e551 100644
--- a/modules/nf-core/modules/sratools/fasterqdump/main.nf
+++ b/modules/local/sratools_fasterqdump.nf
@@ -1,3 +1,4 @@
+
 process SRATOOLS_FASTERQDUMP {
     tag "$meta.id"
     label 'process_medium'
@@ -11,17 +12,19 @@ process SRATOOLS_FASTERQDUMP {
     tuple val(meta), path(sra)
 
     output:
-    tuple val(meta), path(output), emit: reads
-    path "versions.yml"          , emit: versions
+    tuple val(meta), path(fastq_output), emit: reads
+    tuple val(meta), path(md5_output)  , emit: md5
+    path "versions.yml"                , emit: versions
 
     script:
-    def args = task.ext.args ?: ''
+    def args = task.ext.args  ?: ''
     def args2 = task.ext.args2 ?: ''
     def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
     // Paired-end data extracted by fasterq-dump (--split-3 the default) always creates
     // *_1.fastq *_2.fastq files but sometimes also an additional *.fastq file
     // for unpaired reads which we ignore here.
-    output = meta.single_end ? '*.fastq.gz' : '*_{1,2}.fastq.gz'
+    fastq_output = meta.single_end ? '*.fastq.gz'     : '*_{1,2}.fastq.gz'
+    md5_output = meta.single_end ? '*.fastq.gz.md5' : '*_{1,2}.fastq.gz.md5'
     """
     eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
     if [[ ! -f "\${NCBI_SETTINGS}" ]]; then
@@ -40,6 +43,22 @@ process SRATOOLS_FASTERQDUMP {
         --processes $task.cpus \\
         *.fastq
 
+    ## Rename FastQ files by meta.id
+    if [ -f  ${sra.name}.fastq.gz ]; then
+        mv ${sra.name}.fastq.gz ${meta.id}.fastq.gz
+        md5sum ${meta.id}.fastq.gz > ${meta.id}.fastq.gz.md5
+    fi
+
+    if [ -f  ${sra.name}_1.fastq.gz ]; then
+        mv ${sra.name}_1.fastq.gz ${meta.id}_1.fastq.gz
+        md5sum ${meta.id}_1.fastq.gz > ${meta.id}_1.fastq.gz.md5
+    fi
+
+    if [ -f  ${sra.name}_2.fastq.gz ]; then
+        mv ${sra.name}_2.fastq.gz ${meta.id}_2.fastq.gz
+        md5sum ${meta.id}_2.fastq.gz > ${meta.id}_2.fastq.gz.md5
+    fi
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         sratools: \$(fasterq-dump --version 2>&1 | grep -Eo '[0-9.]+')
diff --git a/modules/nf-core/modules/sratools/prefetch/main.nf b/modules/local/sratools_prefetch.nf
similarity index 96%
rename from modules/nf-core/modules/sratools/prefetch/main.nf
rename to modules/local/sratools_prefetch.nf
index 1e1eb802..76679a93 100644
--- a/modules/nf-core/modules/sratools/prefetch/main.nf
+++ b/modules/local/sratools_prefetch.nf
@@ -1,3 +1,4 @@
+
 process SRATOOLS_PREFETCH {
     tag "$id"
     label 'process_low'
@@ -25,7 +26,7 @@ process SRATOOLS_PREFETCH {
         printf '${config}' > "\${NCBI_SETTINGS}"
     fi
 
-    prefetch \\
+    retry_with_backoff.sh prefetch \\
         $args \\
         --progress \\
         $id
diff --git a/modules/nf-core/modules/sratools/fasterqdump/meta.yml b/modules/nf-core/modules/sratools/fasterqdump/meta.yml
deleted file mode 100644
index 1478bed8..00000000
--- a/modules/nf-core/modules/sratools/fasterqdump/meta.yml
+++ /dev/null
@@ -1,42 +0,0 @@
-name: sratools_fasterqdump
-description: Extract sequencing reads in FASTQ format from a given NCBI Sequence Read Archive (SRA).
-keywords:
-  - sequencing
-  - FASTQ
-  - dump
-tools:
-  - sratools:
-      description: SRA Toolkit and SDK from NCBI
-      homepage: https://github.com/ncbi/sra-tools
-      documentation: https://github.com/ncbi/sra-tools/wiki
-      tool_dev_url: https://github.com/ncbi/sra-tools
-      licence: ['US-Government-Work']
-
-input:
-  - meta:
-      type: map
-      description: >
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - sra:
-      type: directory
-      description: Directory containing ETL data for the given SRA.
-      pattern: "*/*.sra"
-
-output:
-  - meta:
-      type: map
-      description: >
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-  - reads:
-      type: file
-      description: Extracted FASTQ file or files if the sequencing reads are paired-end.
-      pattern: "*.fastq.gz"
-
-authors:
-  - "@Midnighter"
diff --git a/modules/nf-core/modules/sratools/prefetch/meta.yml b/modules/nf-core/modules/sratools/prefetch/meta.yml
deleted file mode 100644
index 22213b29..00000000
--- a/modules/nf-core/modules/sratools/prefetch/meta.yml
+++ /dev/null
@@ -1,43 +0,0 @@
-name: sratools_prefetch
-description: Download sequencing data from the NCBI Sequence Read Archive (SRA).
-keywords:
-  - sequencing
-  - fastq
-  - prefetch
-tools:
-  - sratools:
-      description: SRA Toolkit and SDK from NCBI
-      homepage: https://github.com/ncbi/sra-tools
-      documentation: https://github.com/ncbi/sra-tools/wiki
-      tool_dev_url: https://github.com/ncbi/sra-tools
-      licence: ['US-Government-Work']
-
-input:
-  - meta:
-      type: map
-      description: >
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - id:
-      type: val
-      description: >
-        A string denoting an SRA id.
-
-output:
-  - meta:
-      type: map
-      description: >
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - sra:
-      type: directory
-      description: >
-        Directory containing the ETL data for the given SRA id.
-      pattern: "*/*.sra"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-
-authors:
-  - "@Midnighter"
diff --git a/subworkflows/local/sra_fastq_sratools.nf b/subworkflows/local/sra_fastq_sratools.nf
index e093fe2f..1d59eb61 100644
--- a/subworkflows/local/sra_fastq_sratools.nf
+++ b/subworkflows/local/sra_fastq_sratools.nf
@@ -2,8 +2,8 @@
 // Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
 //
 
-include { SRATOOLS_PREFETCH    } from '../../modules/local/sratools_prefetch.nf'
-include { SRATOOLS_FASTERQDUMP } from '../../modules/local/sratools_fasterqdump.nf'
+include { SRATOOLS_PREFETCH    } from '../../modules/local/sratools_prefetch'
+include { SRATOOLS_FASTERQDUMP } from '../../modules/local/sratools_fasterqdump'
 
 workflow SRA_FASTQ_SRATOOLS {
     take:

From 25640bd6aae7b2e7b8625883b109c4c4880a00b0 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 27 Nov 2021 20:55:17 +0000
Subject: [PATCH 165/852] Update CHANGELOG

---
 CHANGELOG.md | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f3e67547..4d6341df 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,11 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unpublished Version / DEV]
+## [[1.5](https://github.com/nf-core/fetchngs/releases/tag/1.5] - 2021-11-29
+
+* Finish porting the pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
+    * Bump minimum Nextflow version from `21.04.0` -> `21.10.3`
+    * Removed `--publish_dir_mode` as it is no longer required for the new syntax
 
 ### Enhancements & fixes
 

From 6e3259a057975c93a30361f5b75208f92aba02fa Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 27 Nov 2021 20:55:34 +0000
Subject: [PATCH 166/852] Remove params.publish_dir_mode

---
 conf/modules.config | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 753ab27d..c08c1fe6 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -17,14 +17,14 @@ process {
 
     publishDir = [
         path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
-        mode: params.publish_dir_mode,
+        mode: 'copy',
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-    withName: DUMPSOFTWAREVERSIONS {
+    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
+            mode: 'copy',
             pattern: '*_versions.yml'
         ]
     }
@@ -48,7 +48,7 @@ if (params.input_type == 'sra') {
         withName: SRA_RUNINFO_TO_FTP {
             publishDir = [
                 path: { "${params.outdir}/metadata" },
-                mode: params.publish_dir_mode,
+                mode: 'copy',
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
@@ -58,12 +58,12 @@ if (params.input_type == 'sra') {
             publishDir = [
                 [
                     path: { "${params.outdir}/fastq" },
-                    mode: params.publish_dir_mode,
+                    mode: 'copy',
                     pattern: "*gz"
                 ],
                 [
                     path: { "${params.outdir}/fastq/md5" },
-                    mode: params.publish_dir_mode,
+                    mode: 'copy',
                     pattern: "*.md5"
                 ]
             ]
@@ -80,12 +80,12 @@ if (params.input_type == 'sra') {
             publishDir = [
                 [
                     path: { "${params.outdir}/fastq" },
-                    mode: params.publish_dir_mode,
+                    mode: 'copy',
                     pattern: "*gz"
                 ],
                 [
                     path: { "${params.outdir}/fastq/md5" },
-                    mode: params.publish_dir_mode,
+                    mode: 'copy',
                     pattern: "*.md5"
                 ]
             ]
@@ -101,7 +101,7 @@ if (params.input_type == 'sra') {
         withName: SRA_MERGE_SAMPLESHEET {
             publishDir = [
                 path: { "${params.outdir}/samplesheet" },
-                mode: params.publish_dir_mode,
+                mode: 'copy',
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
@@ -109,7 +109,7 @@ if (params.input_type == 'sra') {
         withName: MULTIQC_MAPPINGS_CONFIG {
             publishDir = [
                 path: { "${params.outdir}/samplesheet" },
-                mode: params.publish_dir_mode,
+                mode: 'copy',
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
@@ -129,7 +129,7 @@ if (params.input_type == 'synapse') {
             ext.args = '--long'
             publishDir = [
                 path: { "${params.outdir}/metadata" },
-                mode: params.publish_dir_mode,
+                mode: 'copy',
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
@@ -138,12 +138,12 @@ if (params.input_type == 'synapse') {
             publishDir = [
                 [
                     path: { "${params.outdir}/fastq" },
-                    mode: params.publish_dir_mode,
+                    mode: 'copy',
                     pattern: "*gz"
                 ],
                 [
                     path: { "${params.outdir}/fastq/md5" },
-                    mode: params.publish_dir_mode,
+                    mode: 'copy',
                     pattern: "*.md5"
                 ]
             ]
@@ -152,7 +152,7 @@ if (params.input_type == 'synapse') {
         withName: SYNAPSE_SHOW {
             publishDir = [
                 path: { "${params.outdir}/metadata" },
-                mode: params.publish_dir_mode,
+                mode: 'copy',
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
@@ -167,7 +167,7 @@ if (params.input_type == 'synapse') {
         withName: SYNAPSE_MERGE_SAMPLESHEET {
             publishDir = [
                 path: { "${params.outdir}/samplesheet" },
-                mode: params.publish_dir_mode,
+                mode: 'copy',
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }

From 12fcb97082ba84016fd525f895a819daecedbca2 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 27 Nov 2021 20:55:38 +0000
Subject: [PATCH 167/852] Remove params.publish_dir_mode

---
 nextflow_schema.json | 16 ----------------
 1 file changed, 16 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 2831dac7..ae439a7b 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -177,22 +177,6 @@
                     "fa_icon": "fas fa-question-circle",
                     "hidden": true
                 },
-                "publish_dir_mode": {
-                    "type": "string",
-                    "default": "copy",
-                    "description": "Method used to save pipeline results to output directory.",
-                    "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
-                    "fa_icon": "fas fa-copy",
-                    "enum": [
-                        "symlink",
-                        "rellink",
-                        "link",
-                        "copy",
-                        "copyNoFollow",
-                        "move"
-                    ],
-                    "hidden": true
-                },
                 "email_on_fail": {
                     "type": "string",
                     "description": "Email address for completion summary, only when pipeline fails.",

From 194fb72e63592819a03a61657126a02e0dedd5c3 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 27 Nov 2021 20:55:55 +0000
Subject: [PATCH 168/852] Fix tyop in versions syntax

---
 modules/local/sra_fastq_ftp.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/sra_fastq_ftp.nf b/modules/local/sra_fastq_ftp.nf
index 2dc0c8ae..edb5241a 100644
--- a/modules/local/sra_fastq_ftp.nf
+++ b/modules/local/sra_fastq_ftp.nf
@@ -53,7 +53,7 @@ process SRA_FASTQ_FTP {
         md5sum -c ${meta.id}_2.fastq.gz.md5
 
         cat <<-END_VERSIONS > versions.yml
-        "${task.process}"
+        "${task.process}":
             curl: \$(echo \$(curl --version | head -n 1 | sed 's/^curl //; s/ .*\$//'))
         END_VERSIONS
         """

From 4ee548901ab86a757cf7359cbfd78aeace977e3c Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 27 Nov 2021 20:56:10 +0000
Subject: [PATCH 169/852] Rename dumpsoftwareversions module

---
 workflows/sra.nf     | 14 +++++++++++---
 workflows/synapse.nf | 11 +++++++++--
 2 files changed, 20 insertions(+), 5 deletions(-)

diff --git a/workflows/sra.nf b/workflows/sra.nf
index 4012a571..9336fcc1 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -22,11 +22,19 @@ WorkflowSra.initialise(params, log, valid_params)
 include { SRA_IDS_TO_RUNINFO      } from '../modules/local/sra_ids_to_runinfo'
 include { SRA_RUNINFO_TO_FTP      } from '../modules/local/sra_runinfo_to_ftp'
 include { SRA_FASTQ_FTP           } from '../modules/local/sra_fastq_ftp'
-include { SRA_FASTQ_SRATOOLS      } from '../subworkflows/local/sra_fastq_sratools'
 include { SRA_TO_SAMPLESHEET      } from '../modules/local/sra_to_samplesheet'
 include { SRA_MERGE_SAMPLESHEET   } from '../modules/local/sra_merge_samplesheet'
 include { MULTIQC_MAPPINGS_CONFIG } from '../modules/local/multiqc_mappings_config'
-include { DUMPSOFTWAREVERSIONS    } from '../modules/local/dumpsoftwareversions'
+
+include { SRA_FASTQ_SRATOOLS      } from '../subworkflows/local/sra_fastq_sratools'
+
+/*
+========================================================================================
+    IMPORT NF-CORE MODULES/SUBWORKFLOWS
+========================================================================================
+*/
+
+include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main'
 
 /*
 ========================================================================================
@@ -126,7 +134,7 @@ workflow SRA {
     //
     // MODULE: Dump software versions for all tools used in the workflow
     //
-    DUMPSOFTWAREVERSIONS (
+    CUSTOM_DUMPSOFTWAREVERSIONS (
         ch_versions.unique().collectFile(name: 'collated_versions.yml')
     )
 }
diff --git a/workflows/synapse.nf b/workflows/synapse.nf
index 5a7e3fe7..2a673623 100644
--- a/workflows/synapse.nf
+++ b/workflows/synapse.nf
@@ -24,7 +24,14 @@ include { SYNAPSE_SHOW              } from '../modules/local/synapse_show'
 include { SYNAPSE_GET               } from '../modules/local/synapse_get'
 include { SYNAPSE_TO_SAMPLESHEET    } from '../modules/local/synapse_to_samplesheet'
 include { SYNAPSE_MERGE_SAMPLESHEET } from '../modules/local/synapse_merge_samplesheet'
-include { DUMPSOFTWAREVERSIONS      } from '../modules/local/dumpsoftwareversions'
+
+/*
+========================================================================================
+    IMPORT NF-CORE MODULES/SUBWORKFLOWS
+========================================================================================
+*/
+
+include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main'
 
 /*
 ========================================================================================
@@ -122,7 +129,7 @@ workflow SYNAPSE {
     //
     // MODULE: Dump software versions for all tools used in the workflow
     //
-    DUMPSOFTWAREVERSIONS (
+    CUSTOM_DUMPSOFTWAREVERSIONS (
         ch_versions.unique().collectFile(name: 'collated_versions.yml')
     )
 }

From 27f7827e579551bd9768dd11ac8fa8919bc42619 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 27 Nov 2021 21:30:57 +0000
Subject: [PATCH 170/852] Bump version to 1.5

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 5cc0cdac..f3284c52 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -145,7 +145,7 @@ manifest {
     description     = 'Pipeline to fetch metadata and raw FastQ files from public databases'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
-    version         = '1.5dev'
+    version         = '1.5'
 }
 
 // Load modules.config for DSL2 module specific options

From c12cee0800398762ab9737d7ab35586c1fc7a01f Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 28 Nov 2021 14:14:35 +0000
Subject: [PATCH 171/852] Upgrade CI tests to those on dev

---
 .github/workflows/awsfulltest.yml     | 11 ++++++++---
 .github/workflows/awstest.yml         |  9 +++++----
 .github/workflows/ci.yml              |  7 +++----
 .github/workflows/linting_comment.yml |  1 +
 4 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index a40a53f4..dc26b72d 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -14,10 +14,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@master
+        uses: nf-core/tower-action@v2
+        # TODO nf-core: You can customise AWS full pipeline tests as required
+        # Add full size test data (but still relatively small datasets for few samples)
+        # on the `test_full.config` test runs with only one set of parameters
+        
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
-          bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
           pipeline: ${{ github.repository }}
           revision: ${{ github.sha }}
@@ -26,4 +30,5 @@ jobs:
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/fetchngs/results-${{ github.sha }}"
             }
-          profiles: '[ "test_full", "aws_tower" ]'
+          profiles: test_full,aws_tower
+
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index 6f008aed..df53dcf3 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -11,11 +11,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@master
-
+        uses: nf-core/tower-action@v2
+        
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
-          bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
           pipeline: ${{ github.repository }}
           revision: ${{ github.sha }}
@@ -24,4 +24,5 @@ jobs:
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/fetchngs/results-${{ github.sha }}"
             }
-          profiles: '[ "test", "aws_tower" ]'
+          profiles: test,aws_tower
+
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index eb26bd07..56193da8 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -8,9 +8,6 @@ on:
   release:
     types: [published]
 
-# Uncomment if we need an edge release of Nextflow again
-# env: NXF_EDGE: 1
-
 jobs:
   test:
     name: Run workflow tests
@@ -22,7 +19,9 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and latest edge version
-        nxf_ver: ["NXF_VER=21.10.3", "NXF_EDGE=1"]
+        nxf_ver:
+         - 'NXF_VER=21.10.3'
+        #  - 'NXF_EDGE=1'
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 90f03c6f..44d72994 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -15,6 +15,7 @@ jobs:
         uses: dawidd6/action-download-artifact@v2
         with:
           workflow: linting.yml
+          workflow_conclusion: completed
 
       - name: Get PR number
         id: pr_number

From e141707b26b2c07732eb2fe2ef71e88baa2c823b Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 28 Nov 2021 14:18:57 +0000
Subject: [PATCH 172/852] Fix linting

---
 .github/workflows/ci.yml | 2 +-
 .nf-core.yml             | 2 ++
 CHANGELOG.md             | 2 +-
 3 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 56193da8..a159501f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -20,7 +20,7 @@ jobs:
       matrix:
         # Nextflow versions: check pipeline minimum and latest edge version
         nxf_ver:
-         - 'NXF_VER=21.10.3'
+          - 'NXF_VER=21.10.3'
         #  - 'NXF_EDGE=1'
     steps:
       - name: Check out pipeline code
diff --git a/.nf-core.yml b/.nf-core.yml
index b8e4d216..efb97174 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,6 +1,8 @@
 lint:
   files_unchanged:
     - .github/CONTRIBUTING.md
+    - .github/ISSUE_TEMPLATE/bug_report.md
+    - .github/workflows/linting_comment.yml
     - assets/sendmail_template.txt
     - lib/NfcoreSchema.groovy
     - lib/NfcoreTemplate.groovy
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4d6341df..37feff4a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[1.5](https://github.com/nf-core/fetchngs/releases/tag/1.5] - 2021-11-29
+## [[1.5](https://github.com/nf-core/fetchngs/releases/tag/1.5)] - 2021-11-29
 
 * Finish porting the pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
     * Bump minimum Nextflow version from `21.04.0` -> `21.10.3`

From b21a617b8402c0ec43fbd182854f94550360ddcc Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 28 Nov 2021 20:06:48 +0000
Subject: [PATCH 173/852] Lint and fix repo relative to latest dev

---
 .gitattributes                             |  2 +
 .github/CONTRIBUTING.md                    | 56 ++++++++++++++-----
 .github/ISSUE_TEMPLATE/bug_report.md       | 63 ----------------------
 .github/ISSUE_TEMPLATE/bug_report.yml      | 52 ++++++++++++++++++
 .github/ISSUE_TEMPLATE/config.yml          |  1 -
 .github/ISSUE_TEMPLATE/feature_request.md  | 32 -----------
 .github/ISSUE_TEMPLATE/feature_request.yml | 11 ++++
 .github/workflows/awsfulltest.yml          |  5 +-
 .nf-core.yml                               | 16 +++---
 lib/NfcoreSchema.groovy                    | 19 +++++--
 10 files changed, 133 insertions(+), 124 deletions(-)
 delete mode 100644 .github/ISSUE_TEMPLATE/bug_report.md
 create mode 100644 .github/ISSUE_TEMPLATE/bug_report.yml
 delete mode 100644 .github/ISSUE_TEMPLATE/feature_request.md
 create mode 100644 .github/ISSUE_TEMPLATE/feature_request.yml

diff --git a/.gitattributes b/.gitattributes
index 7fe55006..050bb120 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1 +1,3 @@
 *.config linguist-language=nextflow
+modules/nf-core/** linguist-generated
+subworkflows/nf-core/** linguist-generated
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index f294492d..1d7943a5 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -61,16 +61,23 @@ For further information/help, please consult the [nf-core/fetchngs documentation
 
 To make the nf-core/fetchngs code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
 
-### Adding a new step or module
-
-If you wish to contribute a new step or module please see the [official guidelines](https://nf-co.re/developers/adding_modules#new-module-guidelines-and-pr-review-checklist) and use the following coding standards:
-
-1. Add any new flags/options to `nextflow.config` with a default (see section below).
-2. Add any new flags/options to `nextflow_schema.json` with help text via `nf-core schema build`.
-3. Add sanity checks for all relevant parameters.
-4. Perform local tests to validate that the new code works as expected.
-5. If applicable, add a new test command in `.github/workflow/ci.yml`.
-6. Add any descriptions of output files to `docs/output.md`.
+### Adding a new step
+
+If you wish to contribute a new step, please use the following coding standards:
+
+1. Define the corresponding input channel into your new process from the expected previous process channel
+2. Write the process block (see below).
+3. Define the output channel if needed (see below).
+4. Add any new flags/options to `nextflow.config` with a default (see below).
+5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build`).
+6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter).
+7. Add sanity checks for all relevant parameters.
+8. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`.
+9. Do local tests that the new code works properly and as expected.
+10. Add a new test command in `.github/workflow/ci.yml`.
+11. If applicable add a [MultiQC](https://https://multiqc.info/) module.
+12. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order.
+13. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
 
 ### Default values
 
@@ -82,17 +89,40 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
 
 Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
-### Channel naming convention
+The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
+
+### Naming schemes
 
 Please use the following naming schemes, to make it easy to understand what is going where.
 
-* Initial process channel: `ch_output_from_<process>`
-* Intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
+* initial process channel: `ch_output_from_<process>`
+* intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
 
 ### Nextflow version bumping
 
 If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`
 
+### Software version reporting
+
+If you add a new tool to the pipeline, please ensure you add the information of the tool to the `get_software_version` process.
+
+Add to the script block of the process, something like the following:
+
+```bash
+<YOUR_TOOL> --version &> v_<YOUR_TOOL>.txt 2>&1 || true
+```
+
+or
+
+```bash
+<YOUR_TOOL> --help | head -n 1 &> v_<YOUR_TOOL>.txt 2>&1 || true
+```
+
+You then need to edit the script `bin/scrape_software_versions.py` to:
+
+1. Add a Python regex for your tool's `--version` output (as in stored in the `v_<YOUR_TOOL>.txt` file), to ensure the version is reported as a `v` and the version number e.g. `v2.1.1`
+2. Add a HTML entry to the `OrderedDict` for formatting in MultiQC.
+
 ### Images and figures
 
 For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
deleted file mode 100644
index 406ca8df..00000000
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ /dev/null
@@ -1,63 +0,0 @@
----
-name: Bug report
-about: Report something that is broken or incorrect
-labels: bug
----
-
-<!--
-# nf-core/fetchngs bug report
-
-Hi there!
-
-Thanks for telling us about a problem with the pipeline.
-Please delete this text and anything that's not relevant from the template below:
--->
-
-## Check Documentation
-
-I have checked the following places for your error:
-
-- [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
-- [ ] [nf-core/fetchngs pipeline documentation](https://nf-co.re/fetchngs/usage)
-
-## Description of the bug
-
-<!-- A clear and concise description of what the bug is. -->
-
-## Steps to reproduce
-
-Steps to reproduce the behaviour:
-
-1. Command line: <!-- [e.g. `nextflow run ...`] -->
-2. See error: <!-- [Please provide your error message] -->
-
-## Expected behaviour
-
-<!-- A clear and concise description of what you expected to happen. -->
-
-## Log files
-
-Have you provided the following extra information/files:
-
-- [ ] The command used to run the pipeline
-- [ ] The `.nextflow.log` file <!-- this is a hidden file in the directory where you launched the pipeline -->
-
-## System
-
-- Hardware: <!-- [e.g. HPC, Desktop, Cloud...] -->
-- Executor: <!-- [e.g. slurm, local, awsbatch...] -->
-- OS: <!-- [e.g. CentOS Linux, macOS, Linux Mint...] -->
-- Version <!-- [e.g. 7, 10.13.6, 18.3...] -->
-
-## Nextflow Installation
-
-- Version: <!-- [e.g. 21.10.3] -->
-
-## Container engine
-
-- Engine: <!-- [e.g. Conda, Docker, Singularity, Podman, Shifter or Charliecloud] -->
-- version: <!-- [e.g. 1.0.0] -->
-
-## Additional context
-
-<!-- Add any other context about the problem here. -->
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
new file mode 100644
index 00000000..7fc6710e
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -0,0 +1,52 @@
+
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+
+  - type: markdown
+    attributes:
+      value: |
+        Before you post this issue, please check the documentation:
+
+        - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
+        - [nf-core/fetchngs pipeline documentation](https://nf-co.re/fetchngs/usage)
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of the bug
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: command_used
+    attributes:
+      label: Command used and terminal output
+      description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
+      render: console
+      placeholder: |
+        $ nextflow run ...
+
+        Some output where something broke
+
+  - type: textarea
+    id: files
+    attributes:
+      label: Relevant files
+      description: |
+        Please upload (drag and drop) and relevant files. Make into a `.zip` file if the extension is not allowed.
+        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
+
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: |
+        * Nextflow version _(eg. 21.10.3)_
+        * Hardware _(eg. HPC, Desktop, Cloud)_
+        * Executor _(eg. slurm, local, awsbatch)_
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
+        * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+        * Version of nf-core/fetchngs _(eg. 1.1, 1.5, 1.8.2)_
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
index 7a59f73a..41a8beb7 100644
--- a/.github/ISSUE_TEMPLATE/config.yml
+++ b/.github/ISSUE_TEMPLATE/config.yml
@@ -1,4 +1,3 @@
-blank_issues_enabled: false
 contact_links:
   - name: Join nf-core
     url: https://nf-co.re/join
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
deleted file mode 100644
index c554f29b..00000000
--- a/.github/ISSUE_TEMPLATE/feature_request.md
+++ /dev/null
@@ -1,32 +0,0 @@
----
-name: Feature request
-about: Suggest an idea for the nf-core/fetchngs pipeline
-labels: enhancement
----
-
-<!--
-# nf-core/fetchngs feature request
-
-Hi there!
-
-Thanks for suggesting a new feature for the pipeline!
-Please delete this text and anything that's not relevant from the template below:
--->
-
-## Is your feature request related to a problem? Please describe
-
-<!-- A clear and concise description of what the problem is. -->
-
-<!-- e.g. [I'm always frustrated when ...] -->
-
-## Describe the solution you'd like
-
-<!-- A clear and concise description of what you want to happen. -->
-
-## Describe alternatives you've considered
-
-<!-- A clear and concise description of any alternative solutions or features you've considered. -->
-
-## Additional context
-
-<!-- Add any other context about the feature request here. -->
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
new file mode 100644
index 00000000..f8ea51da
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -0,0 +1,11 @@
+name: Feature request
+description: Suggest an idea for the nf-core/fetchngs pipeline
+labels: enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index dc26b72d..70f39ce3 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -15,10 +15,7 @@ jobs:
     steps:
       - name: Launch workflow via tower
         uses: nf-core/tower-action@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
-        
+
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
diff --git a/.nf-core.yml b/.nf-core.yml
index efb97174..a660c3f8 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,12 +1,12 @@
 lint:
   files_unchanged:
-    - .github/CONTRIBUTING.md
-    - .github/ISSUE_TEMPLATE/bug_report.md
-    - .github/workflows/linting_comment.yml
+#     - .github/CONTRIBUTING.md
+#     - .github/ISSUE_TEMPLATE/bug_report.md
+#     - .github/workflows/linting_comment.yml
     - assets/sendmail_template.txt
-    - lib/NfcoreSchema.groovy
+#     - lib/NfcoreSchema.groovy
     - lib/NfcoreTemplate.groovy
-  files_exist:
-    - bin/scrape_software_versions.py
-    - modules/local/get_software_versions.nf
-  actions_ci: False
+#   files_exist:
+#     - bin/scrape_software_versions.py
+#     - modules/local/get_software_versions.nf
+#   actions_ci: False
diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy
index dcb39c83..5f681078 100755
--- a/lib/NfcoreSchema.groovy
+++ b/lib/NfcoreSchema.groovy
@@ -105,9 +105,13 @@ class NfcoreSchema {
 
         // Collect expected parameters from the schema
         def expectedParams = []
+        def enums = [:]
         for (group in schemaParams) {
             for (p in group.value['properties']) {
                 expectedParams.push(p.key)
+                if (group.value['properties'][p.key].containsKey('enum')) {
+                    enums[p.key] = group.value['properties'][p.key]['enum']
+                }
             }
         }
 
@@ -155,7 +159,7 @@ class NfcoreSchema {
             println ''
             log.error 'ERROR: Validation of pipeline parameters failed!'
             JSONObject exceptionJSON = e.toJSON()
-            printExceptions(exceptionJSON, params_json, log)
+            printExceptions(exceptionJSON, params_json, log, enums)
             println ''
             has_error = true
         }
@@ -329,7 +333,7 @@ class NfcoreSchema {
     //
     // Loop over nested exceptions and print the causingException
     //
-    private static void printExceptions(ex_json, params_json, log) {
+    private static void printExceptions(ex_json, params_json, log, enums, limit=5) {
         def causingExceptions = ex_json['causingExceptions']
         if (causingExceptions.length() == 0) {
             def m = ex_json['message'] =~ /required key \[([^\]]+)\] not found/
@@ -345,7 +349,16 @@ class NfcoreSchema {
             else {
                 def param = ex_json['pointerToViolation'] - ~/^#\//
                 def param_val = params_json[param].toString()
-                log.error "* --${param}: ${ex_json['message']} (${param_val})"
+                if (enums.containsKey(param)) {
+                    def error_msg = "* --${param}: '${param_val}' is not a valid choice (Available choices"
+                    if (enums[param].size() > limit) {
+                        log.error "${error_msg} (${limit} of ${enums[param].size()}): ${enums[param][0..limit-1].join(', ')}, ... )"
+                    } else {
+                        log.error "${error_msg}: ${enums[param].join(', ')})"
+                    }
+                } else {
+                    log.error "* --${param}: ${ex_json['message']} (${param_val})"
+                }
             }
         }
         for (ex in causingExceptions) {

From 881e1f897c5d7fdbb39afabd4f5d31d9992b7502 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 28 Nov 2021 20:14:39 +0000
Subject: [PATCH 174/852] Fix nf-core lint

---
 .nf-core.yml | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index a660c3f8..27864ada 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,12 +1,14 @@
 lint:
   files_unchanged:
-#     - .github/CONTRIBUTING.md
-#     - .github/ISSUE_TEMPLATE/bug_report.md
-#     - .github/workflows/linting_comment.yml
+    - .gitattributes
+    - .github/ISSUE_TEMPLATE/config.yml
+    - .github/workflows/linting_comment.yml
     - assets/sendmail_template.txt
-#     - lib/NfcoreSchema.groovy
+    - lib/NfcoreSchema.groovy
     - lib/NfcoreTemplate.groovy
-#   files_exist:
-#     - bin/scrape_software_versions.py
-#     - modules/local/get_software_versions.nf
-#   actions_ci: False
+  files_exist:
+    - .github/ISSUE_TEMPLATE/bug_report.md
+    - .github/ISSUE_TEMPLATE/feature_request.md
+    - bin/scrape_software_versions.py
+    - modules/local/get_software_versions.nf
+  actions_ci: False

From eab36c98b6362ecf810ec0dbed06423c8766a334 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 29 Nov 2021 10:51:32 +0000
Subject: [PATCH 175/852] Address review comments

---
 .github/CONTRIBUTING.md | 36 +++++++-----------------------------
 1 file changed, 7 insertions(+), 29 deletions(-)

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 1d7943a5..e401c046 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -70,14 +70,13 @@ If you wish to contribute a new step, please use the following coding standards:
 3. Define the output channel if needed (see below).
 4. Add any new flags/options to `nextflow.config` with a default (see below).
 5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build`).
-6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter).
-7. Add sanity checks for all relevant parameters.
-8. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`.
-9. Do local tests that the new code works properly and as expected.
-10. Add a new test command in `.github/workflow/ci.yml`.
-11. If applicable add a [MultiQC](https://https://multiqc.info/) module.
-12. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order.
-13. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
+6. Add sanity checks for all relevant parameters.
+7. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`.
+8. Perform local tests to validate that the new code works as expected.
+9. Add a new test command in `.github/workflow/ci.yml`.
+10. If applicable add a [MultiQC](https://https://multiqc.info/) module.
+11. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order.
+12. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
 
 ### Default values
 
@@ -102,27 +101,6 @@ Please use the following naming schemes, to make it easy to understand what is g
 
 If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`
 
-### Software version reporting
-
-If you add a new tool to the pipeline, please ensure you add the information of the tool to the `get_software_version` process.
-
-Add to the script block of the process, something like the following:
-
-```bash
-<YOUR_TOOL> --version &> v_<YOUR_TOOL>.txt 2>&1 || true
-```
-
-or
-
-```bash
-<YOUR_TOOL> --help | head -n 1 &> v_<YOUR_TOOL>.txt 2>&1 || true
-```
-
-You then need to edit the script `bin/scrape_software_versions.py` to:
-
-1. Add a Python regex for your tool's `--version` output (as in stored in the `v_<YOUR_TOOL>.txt` file), to ensure the version is reported as a `v` and the version number e.g. `v2.1.1`
-2. Add a HTML entry to the `OrderedDict` for formatting in MultiQC.
-
 ### Images and figures
 
 For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).

From 0c5a67b2b0e7f4620d3fa3253fa48e89776e8bf0 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 29 Nov 2021 10:55:09 +0000
Subject: [PATCH 176/852] Fix nf-core lint

---
 .nf-core.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.nf-core.yml b/.nf-core.yml
index 27864ada..4403ba5c 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -3,6 +3,7 @@ lint:
     - .gitattributes
     - .github/ISSUE_TEMPLATE/config.yml
     - .github/workflows/linting_comment.yml
+    - .github/CONTRIBUTING.md
     - assets/sendmail_template.txt
     - lib/NfcoreSchema.groovy
     - lib/NfcoreTemplate.groovy

From 541ab9a8cd31c713570174e3426e554013b89e5e Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 29 Nov 2021 17:41:02 +0000
Subject: [PATCH 177/852] Change ext.suffix to ext.prefix

---
 conf/modules.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index c08c1fe6..eb3c936c 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -6,7 +6,7 @@
         ext.args            = Additional arguments appended to command in module.
         ext.args2           = Second set of arguments appended to command in module (multi-tool modules).
         ext.args3           = Third set of arguments appended to command in module (multi-tool modules).
-        ext.suffix          = File name suffix for output files.
+        ext.prefix          = File name prefix for output files.
 ----------------------------------------------------------------------------------------
 */
 

From d1602635309d835951f502b2e5ca3408ace637ec Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 30 Nov 2021 09:19:00 +0000
Subject: [PATCH 178/852] Update date in CHANGELOG

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 37feff4a..056c3602 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[1.5](https://github.com/nf-core/fetchngs/releases/tag/1.5)] - 2021-11-29
+## [[1.5](https://github.com/nf-core/fetchngs/releases/tag/1.5)] - 2021-11-30
 
 * Finish porting the pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
     * Bump minimum Nextflow version from `21.04.0` -> `21.10.3`

From 8688a82879cd41c13cfa6a2689d554ab8f63ea5e Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 30 Nov 2021 09:43:29 +0000
Subject: [PATCH 179/852] Update contributing bullets

---
 .github/CONTRIBUTING.md | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index e401c046..9aa27773 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -68,15 +68,13 @@ If you wish to contribute a new step, please use the following coding standards:
 1. Define the corresponding input channel into your new process from the expected previous process channel
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
-4. Add any new flags/options to `nextflow.config` with a default (see below).
-5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build`).
-6. Add sanity checks for all relevant parameters.
-7. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`.
-8. Perform local tests to validate that the new code works as expected.
-9. Add a new test command in `.github/workflow/ci.yml`.
-10. If applicable add a [MultiQC](https://https://multiqc.info/) module.
-11. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order.
-12. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
+4. Add any new parameters to `nextflow.config` with a default (see below).
+5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool).
+6. Add sanity checks and validation for all relevant parameters.
+7. Perform local tests to validate that the new code works as expected.
+8. If applicable, add a new test command in `.github/workflow/ci.yml`.
+9. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
+10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 
 ### Default values
 

From ad5c88a537ebd6f57a504ae5b6556bcfc3166dac Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 30 Nov 2021 11:34:34 +0000
Subject: [PATCH 180/852] Add pre-run script with min NF version for Tower
 Action

---
 .github/workflows/awsfulltest.yml | 1 +
 .github/workflows/awstest.yml     | 3 ++-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 70f39ce3..83e2793d 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -28,4 +28,5 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/fetchngs/results-${{ github.sha }}"
             }
           profiles: test_full,aws_tower
+          pre_run_script: 'export NXF_VER=21.10.3'
 
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index df53dcf3..7cf6d570 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -12,7 +12,7 @@ jobs:
     steps:
       - name: Launch workflow via tower
         uses: nf-core/tower-action@v2
-        
+
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
@@ -25,4 +25,5 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/fetchngs/results-${{ github.sha }}"
             }
           profiles: test,aws_tower
+          pre_run_script: 'export NXF_VER=21.10.3'
 

From 187c1169038228d45a13a06c405cca57178f4867 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Wed, 1 Dec 2021 08:08:34 +0000
Subject: [PATCH 181/852] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 056c3602..edcf2fa5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[1.5](https://github.com/nf-core/fetchngs/releases/tag/1.5)] - 2021-11-30
+## [[1.5](https://github.com/nf-core/fetchngs/releases/tag/1.5)] - 2021-12-01
 
 * Finish porting the pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
     * Bump minimum Nextflow version from `21.04.0` -> `21.10.3`

From a6a670ebe14006959279da95031eba4f5c82c6a9 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 1 Dec 2021 09:32:13 +0000
Subject: [PATCH 182/852] Bump version to 1.6dev

---
 CHANGELOG.md    | 4 ++++
 nextflow.config | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index edcf2fa5..a6bd63a0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unpublished Version / DEV]
+
+### Enhancements & fixes
+
 ## [[1.5](https://github.com/nf-core/fetchngs/releases/tag/1.5)] - 2021-12-01
 
 * Finish porting the pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
diff --git a/nextflow.config b/nextflow.config
index f3284c52..2ad3e221 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -145,7 +145,7 @@ manifest {
     description     = 'Pipeline to fetch metadata and raw FastQ files from public databases'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
-    version         = '1.5'
+    version         = '1.6dev'
 }
 
 // Load modules.config for DSL2 module specific options

From 3a402f20b71d8ceb04a18c18ef046c4b4b7926d9 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Mon, 13 Dec 2021 09:35:34 +0100
Subject: [PATCH 183/852] Fix typo in URL for usage to ENA API

---
 docs/usage.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/usage.md b/docs/usage.md
index 3cb17fcd..b21aa80d 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -24,7 +24,7 @@ If `SRR`/`ERR`/`DRR` run ids are provided then these will be resolved back to th
 
 The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5 sums. If download links exist, the files will be downloaded in parallel by FTP. Otherwise they are downloaded using sra-tools.
 
-All of the sample metadata obtained from the ENA will be appended as additional columns to help you manually curate the generated samplesheet before you run the pipeline. You can customise the metadata fields that are appended to the samplesheet via the `--ena_metadata_fields` parameter. The default list of fields used by the pipeline can be found at the top of the [`bin/sra_ids_to_runinfo.py`](https://github.com/nf-core/fetchngs/blob/master/bin/sra_ids_to_runinfo.py) script within the pipeline repo. However, this pipeline requires a minimal set of fields to download FastQ files i.e. `'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'`. A comprehensive list of accepted metadata fields can be obtained from the [ENA API](https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run]).
+All of the sample metadata obtained from the ENA will be appended as additional columns to help you manually curate the generated samplesheet before you run the pipeline. You can customise the metadata fields that are appended to the samplesheet via the `--ena_metadata_fields` parameter. The default list of fields used by the pipeline can be found at the top of the [`bin/sra_ids_to_runinfo.py`](https://github.com/nf-core/fetchngs/blob/master/bin/sra_ids_to_runinfo.py) script within the pipeline repo. However, this pipeline requires a minimal set of fields to download FastQ files i.e. `'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'`. A comprehensive list of accepted metadata fields can be obtained from the [ENA API](https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run).
 
 If you have a GEO accession (found in the data availability section of published papers) you can directly download a text file containing the appropriate SRA ids to pass to the pipeline:
 

From 4a2e3c435eaf6cd4eb5cbc454f9fc6ddaa864f48 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 27 Dec 2021 17:56:58 +0000
Subject: [PATCH 184/852] Replace dodgy logo

---
 docs/images/nf-core-fetchngs_logo_dark.png | Bin 288 -> 75668 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs/images/nf-core-fetchngs_logo_dark.png b/docs/images/nf-core-fetchngs_logo_dark.png
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From 1cf780f2cafa7d47d692a1ecd3c306a99b7ce83c Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 15 Mar 2022 21:01:08 +0000
Subject: [PATCH 185/852] Remove igenomes.config remnants from last template
 sync

---
 nextflow.config | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index bcc5e436..6501496b 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -110,13 +110,6 @@ profiles {
     test_full    { includeConfig 'conf/test_full.config'    }
 }
 
-// Load igenomes.config if required
-if (!params.igenomes_ignore) {
-    includeConfig 'conf/igenomes.config'
-} else {
-    params.genomes = [:]
-}
-
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
 // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.

From c1b2abc018291e8eca2d1a8415e77a41a1cc8641 Mon Sep 17 00:00:00 2001
From: maxibor <maxime.borry@gmail.com>
Date: Thu, 17 Mar 2022 10:30:09 +0100
Subject: [PATCH 186/852] Add troubleshooting section and FTP alternative docs

---
 docs/usage.md        | 6 ++++++
 nextflow_schema.json | 3 ++-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/docs/usage.md b/docs/usage.md
index b21aa80d..6e09c9a7 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -251,3 +251,9 @@ We recommend adding the following line to your environment to limit this (typica
 ```console
 NXF_OPTS='-Xms1g -Xmx4g'
 ```
+
+## Troubleshooting
+
+### `FTP` download is blocked at my workplace/institution, how can I still use *nf-core/fetchngs* ?
+
+If downloading data with FTP is blocked on your network connection, you may want to use the [`--force_sratools_download`](https://nf-co.re/fetchngs/1.5/parameters#force_sratools_download) flag to force fetchngs download using [sra-tools](https://github.com/ncbi/sra-tools) instead of the ENA FTP.  
diff --git a/nextflow_schema.json b/nextflow_schema.json
index ae439a7b..550b91c8 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -53,7 +53,8 @@
                 "force_sratools_download": {
                     "type": "boolean",
                     "fa_icon": "fas fa-tools",
-                    "description": "Force download FastQ files via sra-tools instead of via the ENA FTP."
+                    "description": "Force download FastQ files via sra-tools instead of via the ENA FTP.",
+                    "help_text": "If downloading data through FTP is blocked on your network connection, you may want to use this flag to force fetchngs to download using sra-tools instead of the ENA FTP.  "
                 },
                 "skip_fastq_download": {
                     "type": "boolean",

From dca46e6ece994b0af66f27a792dce7477cd76178 Mon Sep 17 00:00:00 2001
From: maxibor <maxime.borry@gmail.com>
Date: Thu, 17 Mar 2022 11:52:20 +0100
Subject: [PATCH 187/852] fix linting

---
 docs/usage.md        | 6 +++---
 nextflow_schema.json | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/docs/usage.md b/docs/usage.md
index 6e09c9a7..7b59a707 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -174,7 +174,7 @@ Work dir:
 Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
 ```
 
-To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN). We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so based on the search results the file we want is `modules/nf-core/software/star/align/main.nf`. If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9). The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements. The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB. Providing you haven't set any other standard nf-core parameters to __cap__ the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `STAR_ALIGN` process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB. The custom config below can then be provided to the pipeline via the [`-c`](#-c) parameter as highlighted in previous sections.
+To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN). We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so based on the search results the file we want is `modules/nf-core/software/star/align/main.nf`. If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9). The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements. The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB. Providing you haven't set any other standard nf-core parameters to **cap** the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `STAR_ALIGN` process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB. The custom config below can then be provided to the pipeline via the [`-c`](#-c) parameter as highlighted in previous sections.
 
 ```nextflow
 process {
@@ -254,6 +254,6 @@ NXF_OPTS='-Xms1g -Xmx4g'
 
 ## Troubleshooting
 
-### `FTP` download is blocked at my workplace/institution, how can I still use *nf-core/fetchngs* ?
+### `FTP` download is blocked at my workplace/institution, how can I still use _nf-core/fetchngs_ ?
 
-If downloading data with FTP is blocked on your network connection, you may want to use the [`--force_sratools_download`](https://nf-co.re/fetchngs/1.5/parameters#force_sratools_download) flag to force fetchngs download using [sra-tools](https://github.com/ncbi/sra-tools) instead of the ENA FTP.  
+If downloading data with FTP is blocked on your network connection, you may want to use the [`--force_sratools_download`](https://nf-co.re/fetchngs/1.5/parameters#force_sratools_download) flag to force fetchngs download using [sra-tools](https://github.com/ncbi/sra-tools) instead of the ENA FTP.
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 550b91c8..57676091 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -53,7 +53,7 @@
                 "force_sratools_download": {
                     "type": "boolean",
                     "fa_icon": "fas fa-tools",
-                    "description": "Force download FastQ files via sra-tools instead of via the ENA FTP.",
+                    "description": "Force download FASTQ files via sra-tools instead of via the ENA FTP.",
                     "help_text": "If downloading data through FTP is blocked on your network connection, you may want to use this flag to force fetchngs to download using sra-tools instead of the ENA FTP.  "
                 },
                 "skip_fastq_download": {

From ce7bb867348d37878826796ed40658df0862cbb2 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 31 Mar 2022 22:34:50 +0100
Subject: [PATCH 188/852] Fix prettier

---
 CHANGELOG.md             | 64 ++++++++++++++++++++--------------------
 CITATIONS.md             | 35 ++++++++++++----------
 README.md                | 12 ++++----
 assets/schema_input.json |  2 +-
 docs/output.md           | 54 ++++++++++++++++-----------------
 docs/usage.md            | 14 ++++-----
 modules.json             |  2 +-
 nextflow_schema.json     |  7 ++---
 8 files changed, 96 insertions(+), 94 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f7d9d75a..7bbf0e90 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,13 +7,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
-* Updated pipeline template to [nf-core/tools 2.2](https://github.com/nf-core/tools/releases/tag/2.2)
+- Updated pipeline template to [nf-core/tools 2.2](https://github.com/nf-core/tools/releases/tag/2.2)
 
 ## [[1.5](https://github.com/nf-core/fetchngs/releases/tag/1.5)] - 2021-12-01
 
-* Finish porting the pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
-    * Bump minimum Nextflow version from `21.04.0` -> `21.10.3`
-    * Removed `--publish_dir_mode` as it is no longer required for the new syntax
+- Finish porting the pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
+  - Bump minimum Nextflow version from `21.04.0` -> `21.10.3`
+  - Removed `--publish_dir_mode` as it is no longer required for the new syntax
 
 ### Enhancements & fixes
 
@@ -21,51 +21,51 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
-* Convert pipeline to updated Nextflow DSL2 syntax for future adoption across nf-core
-* Added a workflow to download FastQ files and to create samplesheets for ids from the [Synapse platform](https://www.synapse.org/) hosted by [Sage Bionetworks](https://sagebionetworks.org/).
-* SRA identifiers not available for direct download via the ENA FTP will now be downloaded via [`sra-tools`](https://github.com/ncbi/sra-tools).
-* Added `--force_sratools_download` parameter to preferentially download all FastQ files via `sra-tools` instead of ENA FTP.
-* Correctly handle errors from SRA identifiers that do **not** return metadata, for example, due to being private.
-* Retry an error in prefetch via bash script in order to allow it to resume interrupted downloads.
-* Name output FastQ files by `{EXP_ACC}_{RUN_ACC}*fastq.gz` instead of `{EXP_ACC}_{T*}*fastq.gz` for run id provenance
-* [[#46](https://github.com/nf-core/fetchngs/issues/46)] - Bug in sra_ids_to_runinfo.py
-* Added support for [DDBJ ids](https://www.ddbj.nig.ac.jp/index-e.html). See examples below:
-
-| `DDBJ`        |
-|---------------|
-| PRJDB4176     |
-| SAMD00114846  |
-| DRA008156     |
-| DRP004793     |
-| DRR171822     |
-| DRS090921     |
-| DRX162434     |
+- Convert pipeline to updated Nextflow DSL2 syntax for future adoption across nf-core
+- Added a workflow to download FastQ files and to create samplesheets for ids from the [Synapse platform](https://www.synapse.org/) hosted by [Sage Bionetworks](https://sagebionetworks.org/).
+- SRA identifiers not available for direct download via the ENA FTP will now be downloaded via [`sra-tools`](https://github.com/ncbi/sra-tools).
+- Added `--force_sratools_download` parameter to preferentially download all FastQ files via `sra-tools` instead of ENA FTP.
+- Correctly handle errors from SRA identifiers that do **not** return metadata, for example, due to being private.
+- Retry an error in prefetch via bash script in order to allow it to resume interrupted downloads.
+- Name output FastQ files by `{EXP_ACC}_{RUN_ACC}*fastq.gz` instead of `{EXP_ACC}_{T*}*fastq.gz` for run id provenance
+- [[#46](https://github.com/nf-core/fetchngs/issues/46)] - Bug in sra_ids_to_runinfo.py
+- Added support for [DDBJ ids](https://www.ddbj.nig.ac.jp/index-e.html). See examples below:
+
+| `DDBJ`       |
+| ------------ |
+| PRJDB4176    |
+| SAMD00114846 |
+| DRA008156    |
+| DRP004793    |
+| DRR171822    |
+| DRS090921    |
+| DRX162434    |
 
 ## [[1.3](https://github.com/nf-core/fetchngs/releases/tag/1.3)] - 2021-09-15
 
 ### Enhancements & fixes
 
-* Replaced Python `requests` with `urllib` to fetch ENA metadata
+- Replaced Python `requests` with `urllib` to fetch ENA metadata
 
 ### Software dependencies
 
-| Dependency  | Old version | New version |
-|-------------|-------------|-------------|
-| `python`    | 3.8.3       | 3.9.5       |
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `python`   | 3.8.3       | 3.9.5       |
 
 ## [[1.2](https://github.com/nf-core/fetchngs/releases/tag/1.2)] - 2021-07-28
 
 ### Enhancements & fixes
 
-* Updated pipeline template to [nf-core/tools 2.1](https://github.com/nf-core/tools/releases/tag/2.1)
-* [[#26](https://github.com/nf-core/fetchngs/pull/26)] - Update broken EBI API URL
+- Updated pipeline template to [nf-core/tools 2.1](https://github.com/nf-core/tools/releases/tag/2.1)
+- [[#26](https://github.com/nf-core/fetchngs/pull/26)] - Update broken EBI API URL
 
 ## [[1.1](https://github.com/nf-core/fetchngs/releases/tag/1.1)] - 2021-06-22
 
 ### Enhancements & fixes
 
-* [[#12](https://github.com/nf-core/fetchngs/issues/12)] - Error when using singularity - /etc/resolv.conf doesn't exist in container
-* Added `--sample_mapping_fields` parameter to create a separate `id_mappings.csv` and `multiqc_config.yml` with selected fields that can be used to rename samples in general and in [MultiQC](https://multiqc.info/docs/#bulk-sample-renaming)
+- [[#12](https://github.com/nf-core/fetchngs/issues/12)] - Error when using singularity - /etc/resolv.conf doesn't exist in container
+- Added `--sample_mapping_fields` parameter to create a separate `id_mappings.csv` and `multiqc_config.yml` with selected fields that can be used to rename samples in general and in [MultiQC](https://multiqc.info/docs/#bulk-sample-renaming)
 
 ## [[1.0](https://github.com/nf-core/fetchngs/releases/tag/1.0)] - 2021-06-08
 
@@ -85,7 +85,7 @@ Via a single file of ids, provided one-per-line the pipeline performs the follow
 Currently, the following types of example identifiers are supported:
 
 | `SRA`        | `ENA`        | `GEO`      |
-|--------------|--------------|------------|
+| ------------ | ------------ | ---------- |
 | SRR11605097  | ERR4007730   | GSM4432381 |
 | SRX8171613   | ERX4009132   | GSE147507  |
 | SRS6531847   | ERS4399630   |            |
diff --git a/CITATIONS.md b/CITATIONS.md
index 2590785c..3826bfe7 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -10,31 +10,36 @@
 
 ## Pipeline tools
 
-* [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
-    > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
+- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
-* [Python](http://www.python.org)
+  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
-* [Requests](https://docs.python-requests.org/)
+- [Python](http://www.python.org)
 
-* [sra-tools](https://github.com/ncbi/sra-tools)
+- [Requests](https://docs.python-requests.org/)
+
+- [sra-tools](https://github.com/ncbi/sra-tools)
 
 ## Pipeline resources
 
-* [ENA](https://pubmed.ncbi.nlm.nih.gov/33175160/)
-    > Harrison PW, Ahamed A, Aslam R, Alako BTF, Burgin J, Buso N, Courtot M, Fan J, Gupta D, Haseeb M, Holt S, Ibrahim T, Ivanov E, Jayathilaka S, Kadhirvelu VB, Kumar M, Lopez R, Kay S, Leinonen R, Liu X, O'Cathail C, Pakseresht A, Park Y, Pesant S, Rahman N, Rajan J, Sokolov A, Vijayaraja S, Waheed Z, Zyoud A, Burdett T, Cochrane G. The European Nucleotide Archive in 2020. Nucleic Acids Res. 2021 Jan 8;49(D1):D82-D85. doi: 10.1093/nar/gkaa1028. PubMed PMID: 33175160; PubMed Central PMCID: PMC7778925.
+- [ENA](https://pubmed.ncbi.nlm.nih.gov/33175160/)
+
+  > Harrison PW, Ahamed A, Aslam R, Alako BTF, Burgin J, Buso N, Courtot M, Fan J, Gupta D, Haseeb M, Holt S, Ibrahim T, Ivanov E, Jayathilaka S, Kadhirvelu VB, Kumar M, Lopez R, Kay S, Leinonen R, Liu X, O'Cathail C, Pakseresht A, Park Y, Pesant S, Rahman N, Rajan J, Sokolov A, Vijayaraja S, Waheed Z, Zyoud A, Burdett T, Cochrane G. The European Nucleotide Archive in 2020. Nucleic Acids Res. 2021 Jan 8;49(D1):D82-D85. doi: 10.1093/nar/gkaa1028. PubMed PMID: 33175160; PubMed Central PMCID: PMC7778925.
+
+- [SRA](https://pubmed.ncbi.nlm.nih.gov/21062823/)
+
+  > Leinonen R, Sugawara H, Shumway M, International Nucleotide Sequence Database Collaboration. The sequence read archive. Nucleic Acids Res. 2011 Jan;39 (Database issue):D19-21. doi: 10.1093/nar/gkq1019. Epub 2010 Nov 9. PubMed PMID: 21062823; PubMed Central PMCID: PMC3013647.
+
+- [DDBJ](https://pubmed.ncbi.nlm.nih.gov/33156332/)
 
-* [SRA](https://pubmed.ncbi.nlm.nih.gov/21062823/)
-    > Leinonen R, Sugawara H, Shumway M, International Nucleotide Sequence Database Collaboration. The sequence read archive. Nucleic Acids Res. 2011 Jan;39 (Database issue):D19-21. doi: 10.1093/nar/gkq1019. Epub 2010 Nov 9. PubMed PMID: 21062823; PubMed Central PMCID: PMC3013647.
+  > Fukuda A, Kodama Y, Mashima J, Fujisawa T, Ogasawara O. DDBJ update: streamlining submission and access of human data. Nucleic Acids Res. 2021 Jan 8;49(D1):D71-D75. doi: 10.1093/nar/gkaa982. PubMed PMID: 33156332; PubMed Central PMCID: PMC7779041.
 
-* [DDBJ](https://pubmed.ncbi.nlm.nih.gov/33156332/)
-    > Fukuda A, Kodama Y, Mashima J, Fujisawa T, Ogasawara O. DDBJ update: streamlining submission and access of human data. Nucleic Acids Res. 2021 Jan 8;49(D1):D71-D75. doi: 10.1093/nar/gkaa982. PubMed PMID: 33156332; PubMed Central PMCID: PMC7779041.
+- [GEO](https://pubmed.ncbi.nlm.nih.gov/23193258/)
 
-* [GEO](https://pubmed.ncbi.nlm.nih.gov/23193258/)
-    > Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A. NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5. doi: 10.1093/nar/gks1193. Epub 2012 Nov 27. PubMed PMID: 23193258; PubMed Central PMCID: PMC3531084.
+  > Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A. NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5. doi: 10.1093/nar/gks1193. Epub 2012 Nov 27. PubMed PMID: 23193258; PubMed Central PMCID: PMC3531084.
 
-* [Synapse](https://pubmed.ncbi.nlm.nih.gov/24071850/)
-    > Omberg L, Ellrott K, Yuan Y, Kandoth C, Wong C, Kellen MR, Friend SH, Stuart J, Liang H, Margolin AA. Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas. Nat Genet. 2013 Oct;45(10):1121-6. doi: 10.1038/ng.2761. PMID: 24071850; PMCID: PMC3950337.
+- [Synapse](https://pubmed.ncbi.nlm.nih.gov/24071850/)
+  > Omberg L, Ellrott K, Yuan Y, Kandoth C, Wong C, Kellen MR, Friend SH, Stuart J, Liang H, Margolin AA. Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas. Nat Genet. 2013 Oct;45(10):1121-6. doi: 10.1038/ng.2761. PMID: 24071850; PMCID: PMC3950337.
 
 ## Software packaging/containerisation tools
 
diff --git a/README.md b/README.md
index 7839c848..d1f7d596 100644
--- a/README.md
+++ b/README.md
@@ -31,8 +31,8 @@ Via a single file of ids, provided one-per-line (see [example input file](https:
 1. Resolve database ids back to appropriate experiment-level ids and to be compatible with the [ENA API](https://ena-docs.readthedocs.io/en/latest/retrieval/programmatic-access.html)
 2. Fetch extensive id metadata via ENA API
 3. Download FastQ files:
-    - If direct download links are available from the ENA API, fetch in parallel via `curl` and perform `md5sum` check
-    - Otherwise use [`sra-tools`](https://github.com/ncbi/sra-tools) to download `.sra` files and convert them to FastQ
+   - If direct download links are available from the ENA API, fetch in parallel via `curl` and perform `md5sum` check
+   - Otherwise use [`sra-tools`](https://github.com/ncbi/sra-tools) to download `.sra` files and convert them to FastQ
 4. Collate id metadata and paths to FastQ files in a single samplesheet
 
 ### Synapse ids
@@ -67,9 +67,9 @@ The columns in the auto-created samplesheet can be tailored to be accepted out-o
 
 4. Start running your own analysis!
 
-    ```bash
-    nextflow run nf-core/fetchngs --input ids.txt --outdir <OUTDIR> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
-    ```
+   ```bash
+   nextflow run nf-core/fetchngs --input ids.txt --outdir <OUTDIR> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
+   ```
 
 ## Documentation
 
@@ -87,7 +87,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-If you use  nf-core/fetchngs for your analysis, please cite it using the following doi: [10.5281/zenodo.5070524](https://doi.org/10.5281/zenodo.5070524)
+If you use nf-core/fetchngs for your analysis, please cite it using the following doi: [10.5281/zenodo.5070524](https://doi.org/10.5281/zenodo.5070524)
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
diff --git a/assets/schema_input.json b/assets/schema_input.json
index 25006d9b..9a800216 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -8,7 +8,7 @@
         "type": "array",
         "items": {
             "type": "string",
-            "pattern":"^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM])|(syn))(\\d+)$",
+            "pattern": "^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM])|(syn))(\\d+)$",
             "errorMessage": "Please provide a valid SRA, ENA, DDBJ or GEO identifier"
         }
     }
diff --git a/docs/output.md b/docs/output.md
index 897d5cd1..7402976c 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -8,10 +8,10 @@ This document describes the output produced by the pipeline. The directories lis
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data depending on the type of ids provided:
 
-* Download FastQ files and create samplesheet from:
-    1. [SRA / ENA / DDBJ / GEO ids](#sra--ena--ddbj--geo-ids)
-    2. [Synapse ids](#synapse-ids)
-* [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
+- Download FastQ files and create samplesheet from:
+  1. [SRA / ENA / DDBJ / GEO ids](#sra--ena--ddbj--geo-ids)
+  2. [Synapse ids](#synapse-ids)
+- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
 Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introduction) for a list of supported public repository identifiers and how to provide them to the pipeline.
 
@@ -20,17 +20,17 @@ Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introductio
 <details markdown="1">
 <summary>Output files</summary>
 
-* `fastq/`
-    * `*.fastq.gz`: Paired-end/single-end reads downloaded from the SRA / ENA / DDBJ / GEO.
-* `fastq/md5/`
-    * `*.md5`: Files containing `md5` sum for FastQ files downloaded from the ENA.
-* `samplesheet/`
-    * `samplesheet.csv`: Auto-created samplesheet with collated metadata and paths to downloaded FastQ files.
-    * `id_mappings.csv`: File with selected fields that can be used to rename samples to more informative names; see [`--sample_mapping_fields`](https://nf-co.re/fetchngs/parameters#sample_mapping_fields) parameter to customise this behaviour.
-    * `multiqc_config.yml`: [MultiQC](https://multiqc.info/docs/#bulk-sample-renaming) config file that can be passed to most nf-core pipelines via the `--multiqc_config` parameter for bulk renaming of sample names from database ids; [`--sample_mapping_fields`](https://nf-co.re/fetchngs/parameters#sample_mapping_fields) parameter to customise this behaviour.
-* `metadata/`
-    * `*.runinfo_ftp.tsv`: Re-formatted metadata file downloaded from the ENA.
-    * `*.runinfo.tsv`: Original metadata file downloaded from the ENA.
+- `fastq/`
+  - `*.fastq.gz`: Paired-end/single-end reads downloaded from the SRA / ENA / DDBJ / GEO.
+- `fastq/md5/`
+  - `*.md5`: Files containing `md5` sum for FastQ files downloaded from the ENA.
+- `samplesheet/`
+  - `samplesheet.csv`: Auto-created samplesheet with collated metadata and paths to downloaded FastQ files.
+  - `id_mappings.csv`: File with selected fields that can be used to rename samples to more informative names; see [`--sample_mapping_fields`](https://nf-co.re/fetchngs/parameters#sample_mapping_fields) parameter to customise this behaviour.
+  - `multiqc_config.yml`: [MultiQC](https://multiqc.info/docs/#bulk-sample-renaming) config file that can be passed to most nf-core pipelines via the `--multiqc_config` parameter for bulk renaming of sample names from database ids; [`--sample_mapping_fields`](https://nf-co.re/fetchngs/parameters#sample_mapping_fields) parameter to customise this behaviour.
+- `metadata/`
+  - `*.runinfo_ftp.tsv`: Re-formatted metadata file downloaded from the ENA.
+  - `*.runinfo.tsv`: Original metadata file downloaded from the ENA.
 
 </details>
 
@@ -41,15 +41,15 @@ The final sample information for all identifiers is obtained from the ENA which
 <details markdown="1">
 <summary>Output files</summary>
 
-* `fastq/`
-    * `*.fastq.gz`: Paired-end/single-end reads downloaded from Synapse.
-* `fastq/md5/`
-    * `*.md5`: Files containing `md5` sum for FastQ files downloaded from the Synapse platform.
-* `samplesheet/`
-    * `samplesheet.csv`: Auto-created samplesheet with collated metadata and paths to downloaded FastQ files.
-* `metadata/`
-    * `*.metadata.txt`: Original metadata file generated using the `synapse show` command.
-    * `*.list.txt`: Original output of the `synapse list` command, containing the Synapse ids, file version numbers, file names, and other file-specific data for the Synapse directory ID provided.
+- `fastq/`
+  - `*.fastq.gz`: Paired-end/single-end reads downloaded from Synapse.
+- `fastq/md5/`
+  - `*.md5`: Files containing `md5` sum for FastQ files downloaded from the Synapse platform.
+- `samplesheet/`
+  - `samplesheet.csv`: Auto-created samplesheet with collated metadata and paths to downloaded FastQ files.
+- `metadata/`
+  - `*.metadata.txt`: Original metadata file generated using the `synapse show` command.
+  - `*.list.txt`: Original output of the `synapse list` command, containing the Synapse ids, file version numbers, file names, and other file-specific data for the Synapse directory ID provided.
 
 </details>
 
@@ -62,9 +62,9 @@ The final sample information for the FastQ files downloaded from `Synapse` is ob
 <details markdown="1">
 <summary>Output files</summary>
 
-* `pipeline_info/`
-    * Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
-    * Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
+- `pipeline_info/`
+  - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
+  - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
 
 </details>
 
diff --git a/docs/usage.md b/docs/usage.md
index 8c827443..2eb38745 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -9,7 +9,7 @@
 The pipeline has been set-up to automatically download and process the raw FastQ files from both public and private repositories. Identifiers can be provided in a file, one-per-line via the `--input` parameter. Currently, the following types of example identifiers are supported:
 
 | `SRA`        | `ENA`        | `DDBJ`       | `GEO`      | `Synapse`   |
-|--------------|--------------|--------------|------------|-------------|
+| ------------ | ------------ | ------------ | ---------- | ----------- |
 | SRR11605097  | ERR4007730   | DRR171822    | GSM4432381 | syn26240435 |
 | SRX8171613   | ERX4009132   | DRX162434    | GSE147507  |             |
 | SRS6531847   | ERS4399630   | DRS090921    |            |             |
@@ -28,9 +28,9 @@ All of the sample metadata obtained from the ENA will be appended as additional
 
 If you have a GEO accession (found in the data availability section of published papers) you can directly download a text file containing the appropriate SRA ids to pass to the pipeline:
 
-* Search for your GEO accession on [GEO](https://www.ncbi.nlm.nih.gov/geo)
-* Click `SRA Run Selector` at the bottom of the GEO accession page
-* Select the desired samples in the `SRA Run Selector` and then download the `Accession List`
+- Search for your GEO accession on [GEO](https://www.ncbi.nlm.nih.gov/geo)
+- Click `SRA Run Selector` at the bottom of the GEO accession page
+- Select the desired samples in the `SRA Run Selector` and then download the `Accession List`
 
 This downloads a text file called `SRR_Acc_List.txt` that can be directly provided to the pipeline e.g. `--input SRR_Acc_List.txt`.
 
@@ -47,9 +47,9 @@ The final sample information for the FastQ files used for samplesheet generation
 <details markdown="1">
 <summary>Supported File Names</summary>
 
-* Files named `SRR493366_1.fastq` and `SRR493366_2.fastq` will have a sample name of `SRR493366`
-* Files named `SRR_493_367_1.fastq` and `SRR_493_367_2.fastq` will have a sample name of `SRR_493_367`
-* Files named `filename12_1.fastq` and `filename12_2.fastq` will have a sample name of `filename12`
+- Files named `SRR493366_1.fastq` and `SRR493366_2.fastq` will have a sample name of `SRR493366`
+- Files named `SRR_493_367_1.fastq` and `SRR_493_367_2.fastq` will have a sample name of `SRR_493_367`
+- Files named `filename12_1.fastq` and `filename12_2.fastq` will have a sample name of `filename12`
 
 </details>
 
diff --git a/modules.json b/modules.json
index 2baafc4f..f39d24ab 100644
--- a/modules.json
+++ b/modules.json
@@ -8,4 +8,4 @@
             }
         }
     }
-}
\ No newline at end of file
+}
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 872360c3..6bb52772 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -26,10 +26,7 @@
                     "default": "sra",
                     "description": "Specifies the type of identifier provided via `--input` - available options are 'sra' and 'synapse'.",
                     "fa_icon": "fas fa-keyboard",
-                    "enum": [
-                        "sra",
-                        "synapse"
-                    ]
+                    "enum": ["sra", "synapse"]
                 },
                 "ena_metadata_fields": {
                     "type": "string",
@@ -248,4 +245,4 @@
             "$ref": "#/definitions/generic_options"
         }
     ]
-}
\ No newline at end of file
+}

From 82213da7d16e19c9418dd0cc3bf4e47e9e53a54b Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 31 Mar 2022 22:36:17 +0100
Subject: [PATCH 189/852] Update CHANGELOG after merging template updates

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7bbf0e90..a6b1be4a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
-- Updated pipeline template to [nf-core/tools 2.2](https://github.com/nf-core/tools/releases/tag/2.2)
+- Updated pipeline template to [nf-core/tools 2.3.2](https://github.com/nf-core/tools/releases/tag/2.3.2)
 
 ## [[1.5](https://github.com/nf-core/fetchngs/releases/tag/1.5)] - 2021-12-01
 

From 56f37b2f395391a616e0ac930e42b51d6f69f37e Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 31 Mar 2022 22:39:32 +0100
Subject: [PATCH 190/852] Add --outdir to CI tests

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f80ae073..7b5cfdbb 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -44,7 +44,7 @@ jobs:
 
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
 
   parameters:
     name: Test workflow parameters
@@ -67,6 +67,6 @@ jobs:
           sudo mv nextflow /usr/local/bin/
       - name: Run pipeline with various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
 
 #

From 456584a6ca9ba18d6f8b73b5977582084d05e2be Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 25 Apr 2022 13:15:58 +0100
Subject: [PATCH 191/852] Replace vanilla Linux Biocontainer with Ubuntu

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a6b1be4a..66753fad 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+- [[nf-core/rnaseq#764](https://github.com/nf-core/rnaseq/issues/764)] - Test fails when using GCP due to missing tools in the basic biocontainer
 - Updated pipeline template to [nf-core/tools 2.3.2](https://github.com/nf-core/tools/releases/tag/2.3.2)
 
 ## [[1.5](https://github.com/nf-core/fetchngs/releases/tag/1.5)] - 2021-12-01

From 4bf86f22570c3612e9a69996bbdaea80f2aaad42 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 25 Apr 2022 13:57:43 +0100
Subject: [PATCH 192/852] Actually push updated modules

---
 modules/local/sra_fastq_ftp.nf             | 4 ++--
 modules/local/sra_merge_samplesheet.nf     | 5 ++---
 modules/local/synapse_merge_samplesheet.nf | 4 ++--
 3 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/modules/local/sra_fastq_ftp.nf b/modules/local/sra_fastq_ftp.nf
index edb5241a..c09f66e0 100644
--- a/modules/local/sra_fastq_ftp.nf
+++ b/modules/local/sra_fastq_ftp.nf
@@ -6,8 +6,8 @@ process SRA_FASTQ_FTP {
 
     conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
-        'biocontainers/biocontainers:v1.2.0_cv1' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"
 
     input:
     tuple val(meta), val(fastq)
diff --git a/modules/local/sra_merge_samplesheet.nf b/modules/local/sra_merge_samplesheet.nf
index 863dfaa7..ca9c0068 100644
--- a/modules/local/sra_merge_samplesheet.nf
+++ b/modules/local/sra_merge_samplesheet.nf
@@ -1,10 +1,9 @@
-
 process SRA_MERGE_SAMPLESHEET {
 
     conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
-        'biocontainers/biocontainers:v1.2.0_cv1' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"
 
     input:
     path ('samplesheets/*')
diff --git a/modules/local/synapse_merge_samplesheet.nf b/modules/local/synapse_merge_samplesheet.nf
index 01461e14..68bfd68b 100644
--- a/modules/local/synapse_merge_samplesheet.nf
+++ b/modules/local/synapse_merge_samplesheet.nf
@@ -3,8 +3,8 @@ process SYNAPSE_MERGE_SAMPLESHEET {
 
     conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
-        'biocontainers/biocontainers:v1.2.0_cv1' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"
 
     input:
     path ('samplesheets/*')

From b635257ae753765b7c98f54d2cbc4eaacbad3fbb Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 25 Apr 2022 14:27:03 +0100
Subject: [PATCH 193/852] Use sra-tools container with curl

---
 modules/local/sra_fastq_ftp.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/local/sra_fastq_ftp.nf b/modules/local/sra_fastq_ftp.nf
index c09f66e0..4e8a34aa 100644
--- a/modules/local/sra_fastq_ftp.nf
+++ b/modules/local/sra_fastq_ftp.nf
@@ -4,10 +4,10 @@ process SRA_FASTQ_FTP {
     label 'process_low'
     label 'error_retry'
 
-    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"
+        'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5262h314213e_0' :
+        'quay.io/biocontainers/sra-tools:2.11.0--pl5262h314213e_0' }"
 
     input:
     tuple val(meta), val(fastq)

From c7351884f0664c59876f2f055380025ec12c00a1 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Thu, 12 May 2022 17:32:28 +0200
Subject: [PATCH 194/852] refactor: remove local modules/subworkflows

---
 bin/retry_with_backoff.sh                | 100 -----------------------
 modules/local/sratools_fasterqdump.nf    |  68 ---------------
 modules/local/sratools_prefetch.nf       |  41 ----------
 subworkflows/local/sra_fastq_sratools.nf |  31 -------
 4 files changed, 240 deletions(-)
 delete mode 100755 bin/retry_with_backoff.sh
 delete mode 100644 modules/local/sratools_fasterqdump.nf
 delete mode 100644 modules/local/sratools_prefetch.nf
 delete mode 100644 subworkflows/local/sra_fastq_sratools.nf

diff --git a/bin/retry_with_backoff.sh b/bin/retry_with_backoff.sh
deleted file mode 100755
index 4bdbf1e0..00000000
--- a/bin/retry_with_backoff.sh
+++ /dev/null
@@ -1,100 +0,0 @@
-#!/usr/bin/env bash
-
-set -u
-
-retry_with_backoff() {
-    local max_attempts=${1}
-    local delay=${2}
-    local max_time=${3}
-    local attempt=1
-    local output=
-    local status=
-
-    shift 3
-
-    while [ ${attempt} -le ${max_attempts} ]; do
-        output=$("${@}")
-        status=${?}
-
-        if [ ${status} -eq 0 ]; then
-            break
-        fi
-
-        if [ ${attempt} -lt ${max_attempts} ]; then
-            echo "Failed attempt ${attempt} of ${max_attempts}. Retrying in ${delay} s." >&2
-            sleep ${delay}
-        elif [ ${attempt} -eq ${max_attempts} ]; then
-            echo "Failed after ${attempt} attempts." >&2
-            return ${status}
-        fi
-
-        attempt=$(( ${attempt} + 1 ))
-        delay=$(( ${delay} * 2 ))
-        if [ ${delay} -ge ${max_time} ]; then
-            delay=${max_time}
-        fi
-    done
-
-    echo "${output}"
-}
-
-RETRY=5
-DELAY=1
-MAX_TIME=60
-
-usage() {
-    echo "Usage:" >&2
-    echo "$(basename ${0}) [-h] [-r NUM] [-d NUM] [-m NUM] COMMAND" >&2
-    echo "Call the given command with retries and exponential backoff." >&2
-    echo "" >&2
-    echo "  -r NUM  Set the number of retry attempts (default ${RETRY})." >&2
-    echo "  -d NUM  Set the base number of seconds to delay (default ${DELAY})." >&2
-    echo "  -m NUM  Set the maximum delay in seconds (default ${MAX_TIME})." >&2
-    echo "" >&2
-}
-
-check_numeric() {
-    local arg=${1}
-    if [[ ! ${arg} =~ ^[0-9]+$ ]]; then
-        echo "Illegal argument: ${arg}" >&2
-        echo "Expected a number." >&2
-        echo "" >&2
-        usage
-        exit 2
-    fi
-}
-
-while getopts ":hr:d:m:" arg; do
-    case ${arg} in
-        h)
-            usage
-            exit 0
-            ;;
-        r)
-            check_numeric ${OPTARG}
-            RETRY=${OPTARG}
-            ;;
-        d)
-            check_numeric ${OPTARG}
-            DELAY=${OPTARG}
-            ;;
-        m)
-            check_numeric ${OPTARG}
-            MAX_TIME=${OPTARG}
-            ;;
-        ?)
-            echo "Invalid option: -${OPTARG}" >&2
-            echo "" >&2
-            usage
-            exit 2
-            ;;
-        :)
-            echo "Missing argument for: -${OPTARG}" >&2
-            echo "" >&2
-            usage
-            exit 2
-            ;;
-    esac
-done
-
-retry_with_backoff ${RETRY} ${DELAY} ${MAX_TIME} ${@:OPTIND}
diff --git a/modules/local/sratools_fasterqdump.nf b/modules/local/sratools_fasterqdump.nf
deleted file mode 100644
index 7a75e551..00000000
--- a/modules/local/sratools_fasterqdump.nf
+++ /dev/null
@@ -1,68 +0,0 @@
-
-process SRATOOLS_FASTERQDUMP {
-    tag "$meta.id"
-    label 'process_medium'
-
-    conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0 conda-forge::pigz=2.6' : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' :
-        'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' }"
-
-    input:
-    tuple val(meta), path(sra)
-
-    output:
-    tuple val(meta), path(fastq_output), emit: reads
-    tuple val(meta), path(md5_output)  , emit: md5
-    path "versions.yml"                , emit: versions
-
-    script:
-    def args = task.ext.args  ?: ''
-    def args2 = task.ext.args2 ?: ''
-    def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
-    // Paired-end data extracted by fasterq-dump (--split-3 the default) always creates
-    // *_1.fastq *_2.fastq files but sometimes also an additional *.fastq file
-    // for unpaired reads which we ignore here.
-    fastq_output = meta.single_end ? '*.fastq.gz'     : '*_{1,2}.fastq.gz'
-    md5_output = meta.single_end ? '*.fastq.gz.md5' : '*_{1,2}.fastq.gz.md5'
-    """
-    eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
-    if [[ ! -f "\${NCBI_SETTINGS}" ]]; then
-        mkdir -p "\$(dirname "\${NCBI_SETTINGS}")"
-        printf '${config}' > "\${NCBI_SETTINGS}"
-    fi
-
-    fasterq-dump \\
-        $args \\
-        --threads $task.cpus \\
-        ${sra.name}
-
-    pigz \\
-        $args2 \\
-        --no-name \\
-        --processes $task.cpus \\
-        *.fastq
-
-    ## Rename FastQ files by meta.id
-    if [ -f  ${sra.name}.fastq.gz ]; then
-        mv ${sra.name}.fastq.gz ${meta.id}.fastq.gz
-        md5sum ${meta.id}.fastq.gz > ${meta.id}.fastq.gz.md5
-    fi
-
-    if [ -f  ${sra.name}_1.fastq.gz ]; then
-        mv ${sra.name}_1.fastq.gz ${meta.id}_1.fastq.gz
-        md5sum ${meta.id}_1.fastq.gz > ${meta.id}_1.fastq.gz.md5
-    fi
-
-    if [ -f  ${sra.name}_2.fastq.gz ]; then
-        mv ${sra.name}_2.fastq.gz ${meta.id}_2.fastq.gz
-        md5sum ${meta.id}_2.fastq.gz > ${meta.id}_2.fastq.gz.md5
-    fi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        sratools: \$(fasterq-dump --version 2>&1 | grep -Eo '[0-9.]+')
-        pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/sratools_prefetch.nf b/modules/local/sratools_prefetch.nf
deleted file mode 100644
index 76679a93..00000000
--- a/modules/local/sratools_prefetch.nf
+++ /dev/null
@@ -1,41 +0,0 @@
-
-process SRATOOLS_PREFETCH {
-    tag "$id"
-    label 'process_low'
-    label 'error_retry'
-
-    conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5262h314213e_0' :
-        'quay.io/biocontainers/sra-tools:2.11.0--pl5262h314213e_0' }"
-
-    input:
-    tuple val(meta), val(id)
-
-    output:
-    tuple val(meta), path("$id"), emit: sra
-    path "versions.yml"         , emit: versions
-
-    script:
-    def args = task.ext.args ?: ''
-    def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
-    """
-    eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
-    if [[ ! -f "\${NCBI_SETTINGS}" ]]; then
-        mkdir -p "\$(dirname "\${NCBI_SETTINGS}")"
-        printf '${config}' > "\${NCBI_SETTINGS}"
-    fi
-
-    retry_with_backoff.sh prefetch \\
-        $args \\
-        --progress \\
-        $id
-
-    vdb-validate $id
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        sratools: \$(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
-    END_VERSIONS
-    """
-}
diff --git a/subworkflows/local/sra_fastq_sratools.nf b/subworkflows/local/sra_fastq_sratools.nf
deleted file mode 100644
index 1d59eb61..00000000
--- a/subworkflows/local/sra_fastq_sratools.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-//
-// Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
-//
-
-include { SRATOOLS_PREFETCH    } from '../../modules/local/sratools_prefetch'
-include { SRATOOLS_FASTERQDUMP } from '../../modules/local/sratools_fasterqdump'
-
-workflow SRA_FASTQ_SRATOOLS {
-    take:
-    sra_ids  // channel: [ val(meta), val(id) ]
-
-    main:
-
-    ch_versions = Channel.empty()
-
-    //
-    // Prefetch sequencing reads in SRA format.
-    //
-    SRATOOLS_PREFETCH ( sra_ids )
-    ch_versions = ch_versions.mix( SRATOOLS_PREFETCH.out.versions.first() )
-
-    //
-    // Convert the SRA format into one or more compressed FASTQ files.
-    //
-    SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra )
-    ch_versions = ch_versions.mix( SRATOOLS_FASTERQDUMP.out.versions.first() )
-
-    emit:
-    reads    = SRATOOLS_FASTERQDUMP.out.reads  // channel: [ val(meta), [ reads ] ]
-    versions = ch_versions                     // channel: [ versions.yml ]
-}

From 3de66f289f4186d523a62defc448d5ecfb625fc2 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Thu, 12 May 2022 17:35:44 +0200
Subject: [PATCH 195/852] chore: install nf-core modules for sratools

---
 modules.json                                  |  9 +++
 .../custom/sratoolsncbisettings/main.nf       | 20 +++++++
 .../custom/sratoolsncbisettings/meta.yml      | 28 ++++++++++
 .../templates/detect_ncbi_settings.sh         | 45 +++++++++++++++
 .../modules/sratools/fasterqdump/main.nf      | 48 ++++++++++++++++
 .../modules/sratools/fasterqdump/meta.yml     | 47 ++++++++++++++++
 .../nf-core/modules/sratools/prefetch/main.nf | 25 +++++++++
 .../modules/sratools/prefetch/meta.yml        | 48 ++++++++++++++++
 .../prefetch/templates/retry_with_backoff.sh  | 55 +++++++++++++++++++
 9 files changed, 325 insertions(+)
 create mode 100644 modules/nf-core/modules/custom/sratoolsncbisettings/main.nf
 create mode 100644 modules/nf-core/modules/custom/sratoolsncbisettings/meta.yml
 create mode 100644 modules/nf-core/modules/custom/sratoolsncbisettings/templates/detect_ncbi_settings.sh
 create mode 100644 modules/nf-core/modules/sratools/fasterqdump/main.nf
 create mode 100644 modules/nf-core/modules/sratools/fasterqdump/meta.yml
 create mode 100644 modules/nf-core/modules/sratools/prefetch/main.nf
 create mode 100644 modules/nf-core/modules/sratools/prefetch/meta.yml
 create mode 100644 modules/nf-core/modules/sratools/prefetch/templates/retry_with_backoff.sh

diff --git a/modules.json b/modules.json
index f39d24ab..fefca2b7 100644
--- a/modules.json
+++ b/modules.json
@@ -5,6 +5,15 @@
         "nf-core/modules": {
             "custom/dumpsoftwareversions": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+            },
+            "custom/sratoolsncbisettings": {
+                "git_sha": "b2dbaa99309a2057efc32ef9d029ed91140068df"
+            },
+            "sratools/fasterqdump": {
+                "git_sha": "0cdf7767a79faf424645beeff83ecfa5528b6a7c"
+            },
+            "sratools/prefetch": {
+                "git_sha": "1b228835e9525990db99243cb4f0d07aa6e01bc3"
             }
         }
     }
diff --git a/modules/nf-core/modules/custom/sratoolsncbisettings/main.nf b/modules/nf-core/modules/custom/sratoolsncbisettings/main.nf
new file mode 100644
index 00000000..21bf3005
--- /dev/null
+++ b/modules/nf-core/modules/custom/sratoolsncbisettings/main.nf
@@ -0,0 +1,20 @@
+process CUSTOM_SRATOOLSNCBISETTINGS {
+    tag 'ncbi-settings'
+    label 'process_low'
+
+    conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' :
+        'quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
+
+    output:
+    path('*.mkfg')     , emit: ncbi_settings
+    path 'versions.yml', emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    shell:
+    config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
+    template 'detect_ncbi_settings.sh'
+}
diff --git a/modules/nf-core/modules/custom/sratoolsncbisettings/meta.yml b/modules/nf-core/modules/custom/sratoolsncbisettings/meta.yml
new file mode 100644
index 00000000..01e98856
--- /dev/null
+++ b/modules/nf-core/modules/custom/sratoolsncbisettings/meta.yml
@@ -0,0 +1,28 @@
+name: "sratoolsncbisettings"
+description: Test for the presence of suitable NCBI settings or create them on the fly.
+keywords:
+  - NCBI
+  - settings
+  - sra-tools
+  - prefetch
+  - fasterq-dump
+tools:
+  - "sratools":
+      description: "SRA Toolkit and SDK from NCBI"
+      homepage: https://github.com/ncbi/sra-tools
+      documentation: https://github.com/ncbi/sra-tools/wiki
+      tool_dev_url: https://github.com/ncbi/sra-tools
+      licence: "['Public Domain']"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - ncbi_settings:
+      type: file
+      description: An NCBI user settings file.
+      pattern: "*.mkfg"
+
+authors:
+  - "@Midnighter"
diff --git a/modules/nf-core/modules/custom/sratoolsncbisettings/templates/detect_ncbi_settings.sh b/modules/nf-core/modules/custom/sratoolsncbisettings/templates/detect_ncbi_settings.sh
new file mode 100644
index 00000000..cfe3a324
--- /dev/null
+++ b/modules/nf-core/modules/custom/sratoolsncbisettings/templates/detect_ncbi_settings.sh
@@ -0,0 +1,45 @@
+#!/usr/bin/env bash
+
+set -u
+
+
+# Get the expected NCBI settings path and define the environment variable
+# `NCBI_SETTINGS`.
+eval "$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
+
+# If the user settings do not exist yet, create a file suitable for `prefetch`
+# and `fasterq-dump`. If an existing settings file does not contain the required
+# values, error out with a helpful message.
+if [[ ! -f "${NCBI_SETTINGS}" ]]; then
+    printf '!{config}' > 'user-settings.mkfg'
+else
+    prefetch --help &> /dev/null
+    if [[ $? = 78 ]]; then
+        echo "You have an existing vdb-config at '${NCBI_SETTINGS}' but it is"\
+        "missing the required entries for /LIBS/GUID and"\
+        "/libs/cloud/report_instance_identity."\
+        "Feel free to add the following to your settings file:" >&2
+        echo "$(printf '!{config}')" >&2
+        exit 1
+    fi
+    fasterq-dump --help &> /dev/null
+    if [[ $? = 78 ]]; then
+        echo "You have an existing vdb-config at '${NCBI_SETTINGS}' but it is"\
+        "missing the required entries for /LIBS/GUID and"\
+        "/libs/cloud/report_instance_identity."\
+        "Feel free to add the following to your settings file:" >&2
+        echo "$(printf '!{config}')" >&2
+        exit 1
+    fi
+    if [[ "${NCBI_SETTINGS}" != *.mkfg ]]; then
+        echo "The detected settings '${NCBI_SETTINGS}' do not have the required"\
+        "file extension '.mkfg'." >&2
+        exit 1
+    fi
+    cp "${NCBI_SETTINGS}" ./
+fi
+
+cat <<-END_VERSIONS > versions.yml
+"!{task.process}":
+    sratools: $(vdb-config --version 2>&1 | grep -Eo '[0-9.]+')
+END_VERSIONS
diff --git a/modules/nf-core/modules/sratools/fasterqdump/main.nf b/modules/nf-core/modules/sratools/fasterqdump/main.nf
new file mode 100644
index 00000000..18f46e51
--- /dev/null
+++ b/modules/nf-core/modules/sratools/fasterqdump/main.nf
@@ -0,0 +1,48 @@
+process SRATOOLS_FASTERQDUMP {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0 conda-forge::pigz=2.6' : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' :
+        'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' }"
+
+    input:
+    tuple val(meta), path(sra)
+    path ncbi_settings
+
+    output:
+    tuple val(meta), path(output), emit: reads
+    path "versions.yml"          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    // Paired-end data extracted by fasterq-dump (--split-3 the default) always creates
+    // *_1.fastq *_2.fastq files but sometimes also an additional *.fastq file
+    // for unpaired reads which we ignore here.
+    output = meta.single_end ? '*.fastq.gz' : '*_{1,2}.fastq.gz'
+    """
+    export NCBI_SETTINGS="\$PWD/${ncbi_settings}"
+
+    fasterq-dump \\
+        $args \\
+        --threads $task.cpus \\
+        ${sra.name}
+
+    pigz \\
+        $args2 \\
+        --no-name \\
+        --processes $task.cpus \\
+        *.fastq
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sratools: \$(fasterq-dump --version 2>&1 | grep -Eo '[0-9.]+')
+        pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/modules/sratools/fasterqdump/meta.yml b/modules/nf-core/modules/sratools/fasterqdump/meta.yml
new file mode 100644
index 00000000..d6fbd444
--- /dev/null
+++ b/modules/nf-core/modules/sratools/fasterqdump/meta.yml
@@ -0,0 +1,47 @@
+name: sratools_fasterqdump
+description: Extract sequencing reads in FASTQ format from a given NCBI Sequence Read Archive (SRA).
+keywords:
+  - sequencing
+  - FASTQ
+  - dump
+tools:
+  - sratools:
+      description: SRA Toolkit and SDK from NCBI
+      homepage: https://github.com/ncbi/sra-tools
+      documentation: https://github.com/ncbi/sra-tools/wiki
+      tool_dev_url: https://github.com/ncbi/sra-tools
+      licence: ["Public Domain"]
+
+input:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - sra:
+      type: directory
+      description: Directory containing ETL data for the given SRA.
+      pattern: "*/*.sra"
+  - ncbi_settings:
+      type: file
+      description: >
+        An NCBI user settings file.
+      pattern: "*.mkfg"
+
+output:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - reads:
+      type: file
+      description: Extracted FASTQ file or files if the sequencing reads are paired-end.
+      pattern: "*.fastq.gz"
+
+authors:
+  - "@Midnighter"
diff --git a/modules/nf-core/modules/sratools/prefetch/main.nf b/modules/nf-core/modules/sratools/prefetch/main.nf
new file mode 100644
index 00000000..3426ae12
--- /dev/null
+++ b/modules/nf-core/modules/sratools/prefetch/main.nf
@@ -0,0 +1,25 @@
+process SRATOOLS_PREFETCH {
+    tag "$id"
+    label 'process_low'
+
+    conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' :
+        'quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
+
+    input:
+    tuple val(meta), val(id)
+    path ncbi_settings
+
+    output:
+    tuple val(meta), path(id), emit: sra
+    path 'versions.yml'      , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    shell:
+    args = task.ext.args ?: ''
+    args2 = task.ext.args2 ?: '5 1 100'  // <num retries> <base delay in seconds> <max delay in seconds>
+    template 'retry_with_backoff.sh'
+}
diff --git a/modules/nf-core/modules/sratools/prefetch/meta.yml b/modules/nf-core/modules/sratools/prefetch/meta.yml
new file mode 100644
index 00000000..a3a26522
--- /dev/null
+++ b/modules/nf-core/modules/sratools/prefetch/meta.yml
@@ -0,0 +1,48 @@
+name: sratools_prefetch
+description: Download sequencing data from the NCBI Sequence Read Archive (SRA).
+keywords:
+  - sequencing
+  - fastq
+  - prefetch
+tools:
+  - sratools:
+      description: SRA Toolkit and SDK from NCBI
+      homepage: https://github.com/ncbi/sra-tools
+      documentation: https://github.com/ncbi/sra-tools/wiki
+      tool_dev_url: https://github.com/ncbi/sra-tools
+      licence: ["Public Domain"]
+
+input:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - id:
+      type: val
+      description: >
+        A string denoting an SRA id.
+  - ncbi_settings:
+      type: file
+      description: >
+        An NCBI user settings file.
+      pattern: "*.mkfg"
+
+output:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - sra:
+      type: directory
+      description: >
+        Directory containing the ETL data for the given SRA id.
+      pattern: "*/*.sra"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@Midnighter"
diff --git a/modules/nf-core/modules/sratools/prefetch/templates/retry_with_backoff.sh b/modules/nf-core/modules/sratools/prefetch/templates/retry_with_backoff.sh
new file mode 100644
index 00000000..cec0ab43
--- /dev/null
+++ b/modules/nf-core/modules/sratools/prefetch/templates/retry_with_backoff.sh
@@ -0,0 +1,55 @@
+#!/usr/bin/env bash
+
+set -u
+
+retry_with_backoff() {
+    local max_attempts=${1}
+    local delay=${2}
+    local max_time=${3}
+    local attempt=1
+    local output=
+    local status=
+
+    # Remove the first three arguments to this function in order to access
+    # the 'real' command with `${@}`.
+    shift 3
+
+    while [ ${attempt} -le ${max_attempts} ]; do
+        output=$("${@}")
+        status=${?}
+
+        if [ ${status} -eq 0 ]; then
+            break
+        fi
+
+        if [ ${attempt} -lt ${max_attempts} ]; then
+            echo "Failed attempt ${attempt} of ${max_attempts}. Retrying in ${delay} s." >&2
+            sleep ${delay}
+        elif [ ${attempt} -eq ${max_attempts} ]; then
+            echo "Failed after ${attempt} attempts." >&2
+            return ${status}
+        fi
+
+        attempt=$(( ${attempt} + 1 ))
+        delay=$(( ${delay} * 2 ))
+        if [ ${delay} -ge ${max_time} ]; then
+            delay=${max_time}
+        fi
+    done
+
+    echo "${output}"
+}
+
+export NCBI_SETTINGS="$PWD/!{ncbi_settings}"
+
+retry_with_backoff !{args2} \
+    prefetch \
+    !{args} \
+    !{id}
+
+vdb-validate !{id}
+
+cat <<-END_VERSIONS > versions.yml
+"!{task.process}":
+    sratools: $(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
+END_VERSIONS

From ad15361b924709cc078fb04b69d0ffa61719d920 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Thu, 12 May 2022 17:53:57 +0200
Subject: [PATCH 196/852] refactor: implement new subworkflow

---
 subworkflows/nf-core/srafastq/main.nf  | 38 ++++++++++++++++++++++++
 subworkflows/nf-core/srafastq/meta.yml | 40 ++++++++++++++++++++++++++
 workflows/sra.nf                       |  8 +++---
 3 files changed, 82 insertions(+), 4 deletions(-)
 create mode 100644 subworkflows/nf-core/srafastq/main.nf
 create mode 100644 subworkflows/nf-core/srafastq/meta.yml

diff --git a/subworkflows/nf-core/srafastq/main.nf b/subworkflows/nf-core/srafastq/main.nf
new file mode 100644
index 00000000..f57b6fac
--- /dev/null
+++ b/subworkflows/nf-core/srafastq/main.nf
@@ -0,0 +1,38 @@
+include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../modules/nf-core/modules/custom/sratoolsncbisettings/main'
+include { SRATOOLS_PREFETCH           } from '../../../modules/nf-core/modules/sratools/prefetch/main'
+include { SRATOOLS_FASTERQDUMP        } from '../../../modules/nf-core/modules/sratools/fasterqdump/main'
+
+/**
+ * Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
+ */
+workflow SRAFASTQ {
+    take:
+    sra_ids  // channel: [ val(meta), val(id) ]
+
+    main:
+
+    ch_versions = Channel.empty()
+
+    //
+    // Detect existing NCBI user settings or create new ones.
+    //
+    CUSTOM_SRATOOLSNCBISETTINGS()
+    def settings = CUSTOM_SRATOOLSNCBISETTINGS.out.ncbi_settings  // value channel: path(settings)
+    ch_versions = ch_versions.mix( CUSTOM_SRATOOLSNCBISETTINGS.out.versions )
+
+    //
+    // Prefetch sequencing reads in SRA format.
+    //
+    SRATOOLS_PREFETCH ( sra_ids, settings )
+    ch_versions = ch_versions.mix( SRATOOLS_PREFETCH.out.versions.first() )
+
+    //
+    // Convert the SRA format into one or more compressed FASTQ files.
+    //
+    SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra, settings )
+    ch_versions = ch_versions.mix( SRATOOLS_FASTERQDUMP.out.versions.first() )
+
+    emit:
+    reads    = SRATOOLS_FASTERQDUMP.out.reads  // channel: [ val(meta), [ reads ] ]
+    versions = ch_versions                     // channel: [ versions.yml ]
+}
diff --git a/subworkflows/nf-core/srafastq/meta.yml b/subworkflows/nf-core/srafastq/meta.yml
new file mode 100644
index 00000000..873ccaca
--- /dev/null
+++ b/subworkflows/nf-core/srafastq/meta.yml
@@ -0,0 +1,40 @@
+name: sra_fastq
+description: Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
+keywords:
+  - SRA
+  - NCBI
+  - sequencing
+  - FASTQ
+  - prefetch
+  - fasterq-dump
+modules:
+  - custom/sratoolsncbisettings
+  - sratools/prefetch
+  - sratools/fasterqdump
+input:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - id:
+      type: string
+      description: >
+        SRA run identifier.
+# TODO Update when we decide on a standard for subworkflow docs
+output:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: Extracted FASTQ file or files if the sequencing reads are paired-end.
+      pattern: "*.fastq.gz"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@Midnighter"
diff --git a/workflows/sra.nf b/workflows/sra.nf
index 9336fcc1..2b3cb498 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -26,7 +26,7 @@ include { SRA_TO_SAMPLESHEET      } from '../modules/local/sra_to_samplesheet'
 include { SRA_MERGE_SAMPLESHEET   } from '../modules/local/sra_merge_samplesheet'
 include { MULTIQC_MAPPINGS_CONFIG } from '../modules/local/multiqc_mappings_config'
 
-include { SRA_FASTQ_SRATOOLS      } from '../subworkflows/local/sra_fastq_sratools'
+include { SRAFASTQ                } from '../subworkflows/nf-core/srafastq/main'
 
 /*
 ========================================================================================
@@ -97,16 +97,16 @@ workflow SRA {
         //
         // SUBWORKFLOW: Download sequencing reads without FTP links using sra-tools.
         //
-        SRA_FASTQ_SRATOOLS (
+        SRAFASTQ (
             ch_sra_reads.sra.map { meta, reads -> [ meta, meta.run_accession ] }
         )
-        ch_versions = ch_versions.mix(SRA_FASTQ_SRATOOLS.out.versions.first())
+        ch_versions = ch_versions.mix(SRAFASTQ.out.versions.first())
 
         //
         // MODULE: Stage FastQ files downloaded by SRA together and auto-create a samplesheet
         //
         SRA_TO_SAMPLESHEET (
-            SRA_FASTQ_FTP.out.fastq.mix(SRA_FASTQ_SRATOOLS.out.reads),
+            SRA_FASTQ_FTP.out.fastq.mix(SRAFASTQ.out.reads),
             params.nf_core_pipeline ?: '',
             params.sample_mapping_fields
         )

From 3630eb63148c1b40801c288f66f8452343b6f251 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Mon, 16 May 2022 10:46:02 +0200
Subject: [PATCH 197/852] chore: add entry to changelog

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 66753fad..4c614eec 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+- [#89](https://github.com/nf-core/fetchngs/pull/89) - Improve detection and usage of the NCBI user settings by using the standardized sra-tools modules from nf-core.
+
 - [[nf-core/rnaseq#764](https://github.com/nf-core/rnaseq/issues/764)] - Test fails when using GCP due to missing tools in the basic biocontainer
 - Updated pipeline template to [nf-core/tools 2.3.2](https://github.com/nf-core/tools/releases/tag/2.3.2)
 

From 2f260ba4d6d7eb21a8e6bc42e8549c7fe017daca Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 16 May 2022 21:17:47 +0100
Subject: [PATCH 198/852] Follow up fixes to #57

---
 CHANGELOG.md         |  7 +++++++
 docs/usage.md        | 10 ++++------
 nextflow_schema.json |  2 +-
 3 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 987d753a..5f2477fd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,10 +5,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [[1.6](https://github.com/nf-core/fetchngs/releases/tag/1.6)] - 2022-05-17
 
+- [#57](https://github.com/nf-core/fetchngs/pull/57) - fetchngs fails if FTP is blocked
 - [#89](https://github.com/nf-core/fetchngs/pull/89) - Improve detection and usage of the NCBI user settings by using the standardized sra-tools modules from nf-core.
 - [[nf-core/rnaseq#764](https://github.com/nf-core/rnaseq/issues/764)] - Test fails when using GCP due to missing tools in the basic biocontainer
 - Updated pipeline template to [nf-core/tools 2.4.1](https://github.com/nf-core/tools/releases/tag/2.4.1)
 
+### Software dependencies
+
+| Dependency      | Old version | New version |
+| --------------- | ----------- | ----------- |
+| `synapseclient` | 2.4.0       | 2.6.0       |
+
 ## [[1.5](https://github.com/nf-core/fetchngs/releases/tag/1.5)] - 2021-12-01
 
 - Finish porting the pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
diff --git a/docs/usage.md b/docs/usage.md
index f9f20346..b6c97e33 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -57,6 +57,10 @@ The final sample information for the FastQ files used for samplesheet generation
 
 As a bonus, the columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core. It is highly recommended that you double-check that all of the identifiers you defined using `--input` are represented in the samplesheet. Also, public databases don't reliably hold information such as strandedness information so you may need to amend these entries too if for example your samplesheet was created by providing `--nf_core_pipeline rnaseq`.
 
+### Bypass `FTP` data download
+
+If FTP connections are blocked on your network use the [`--force_sratools_download`](https://nf-co.re/fetchngs/parameters#force_sratools_download) parameter to force the pipeline to download data using sra-tools instead of the ENA FTP.
+
 ## Running the pipeline
 
 The typical command for running the pipeline is as follows:
@@ -259,9 +263,3 @@ We recommend adding the following line to your environment to limit this (typica
 ```console
 NXF_OPTS='-Xms1g -Xmx4g'
 ```
-
-## Troubleshooting
-
-### `FTP` download is blocked at my workplace/institution, how can I still use _nf-core/fetchngs_ ?
-
-If downloading data with FTP is blocked on your network connection, you may want to use the [`--force_sratools_download`](https://nf-co.re/fetchngs/1.5/parameters#force_sratools_download) flag to force fetchngs download using [sra-tools](https://github.com/ncbi/sra-tools) instead of the ENA FTP.
diff --git a/nextflow_schema.json b/nextflow_schema.json
index b476e227..2bc7c52e 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -49,7 +49,7 @@
                     "type": "boolean",
                     "fa_icon": "fas fa-tools",
                     "description": "Force download FASTQ files via sra-tools instead of via the ENA FTP.",
-                    "help_text": "If downloading data through FTP is blocked on your network connection, you may want to use this flag to force fetchngs to download using sra-tools instead of the ENA FTP.  "
+                    "help_text": "If FTP connections are blocked on your network use this flag to force the pipeline to download data using sra-tools instead of the ENA FTP."
                 },
                 "skip_fastq_download": {
                     "type": "boolean",

From 7086977dc2296d648c00b2b26561aa6936d3caf6 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 16 May 2022 21:24:53 +0100
Subject: [PATCH 199/852] Fix nf-core linting

---
 LICENSE         | 2 +-
 nextflow.config | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/LICENSE b/LICENSE
index 515e402d..7a9b6d5a 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) Harshil Patel
+Copyright (c) Harshil Patel, Moritz E. Beber and Jose Espinosa-Carrasco
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
diff --git a/nextflow.config b/nextflow.config
index 40293d3b..237190ec 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -67,7 +67,6 @@ try {
 //   System.err.println("WARNING: Could not load nf-core/config/fetchngs profiles: ${params.custom_config_base}/pipeline/fetchngs.config")
 // }
 
-
 profiles {
     debug { process.beforeScript = 'echo $HOSTNAME' }
     conda {

From d023066e2f7af9fd80e745c058aab49efd97b962 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Tue, 17 May 2022 11:28:31 +0200
Subject: [PATCH 200/852] fix: use parameter for publishing mode

refactor: adjust FASTQ pattern
---
 conf/modules.config | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 1ff70172..82a5f75c 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -24,7 +24,7 @@ process {
     withName: CUSTOM_DUMPSOFTWAREVERSIONS {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },
-            mode: 'copy',
+            mode: params.publish_dir_mode,
             pattern: '*_versions.yml'
         ]
     }
@@ -48,7 +48,7 @@ if (params.input_type == 'sra') {
         withName: SRA_RUNINFO_TO_FTP {
             publishDir = [
                 path: { "${params.outdir}/metadata" },
-                mode: 'copy',
+                mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
@@ -58,12 +58,12 @@ if (params.input_type == 'sra') {
             publishDir = [
                 [
                     path: { "${params.outdir}/fastq" },
-                    mode: 'copy',
-                    pattern: "*gz"
+                    mode: params.publish_dir_mode,
+                    pattern: "*.fastq.gz"
                 ],
                 [
                     path: { "${params.outdir}/fastq/md5" },
-                    mode: 'copy',
+                    mode: params.publish_dir_mode,
                     pattern: "*.md5"
                 ]
             ]
@@ -80,12 +80,12 @@ if (params.input_type == 'sra') {
             publishDir = [
                 [
                     path: { "${params.outdir}/fastq" },
-                    mode: 'copy',
-                    pattern: "*gz"
+                    mode: params.publish_dir_mode,
+                    pattern: "*.fastq.gz"
                 ],
                 [
                     path: { "${params.outdir}/fastq/md5" },
-                    mode: 'copy',
+                    mode: params.publish_dir_mode,
                     pattern: "*.md5"
                 ]
             ]
@@ -101,7 +101,7 @@ if (params.input_type == 'sra') {
         withName: SRA_MERGE_SAMPLESHEET {
             publishDir = [
                 path: { "${params.outdir}/samplesheet" },
-                mode: 'copy',
+                mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
@@ -109,7 +109,7 @@ if (params.input_type == 'sra') {
         withName: MULTIQC_MAPPINGS_CONFIG {
             publishDir = [
                 path: { "${params.outdir}/samplesheet" },
-                mode: 'copy',
+                mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
@@ -129,7 +129,7 @@ if (params.input_type == 'synapse') {
             ext.args = '--long'
             publishDir = [
                 path: { "${params.outdir}/metadata" },
-                mode: 'copy',
+                mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
@@ -138,12 +138,12 @@ if (params.input_type == 'synapse') {
             publishDir = [
                 [
                     path: { "${params.outdir}/fastq" },
-                    mode: 'copy',
-                    pattern: "*gz"
+                    mode: params.publish_dir_mode,
+                    pattern: "*.fastq.gz"
                 ],
                 [
                     path: { "${params.outdir}/fastq/md5" },
-                    mode: 'copy',
+                    mode: params.publish_dir_mode,
                     pattern: "*.md5"
                 ]
             ]
@@ -152,7 +152,7 @@ if (params.input_type == 'synapse') {
         withName: SYNAPSE_SHOW {
             publishDir = [
                 path: { "${params.outdir}/metadata" },
-                mode: 'copy',
+                mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
@@ -167,7 +167,7 @@ if (params.input_type == 'synapse') {
         withName: SYNAPSE_MERGE_SAMPLESHEET {
             publishDir = [
                 path: { "${params.outdir}/samplesheet" },
-                mode: 'copy',
+                mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }

From 7f6e4928613fb5e0f03f9f70e52ad3431c87e9b1 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Tue, 17 May 2022 11:36:17 +0200
Subject: [PATCH 201/852] chore: describe change

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5f2477fd..8d5d7efc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [[1.6](https://github.com/nf-core/fetchngs/releases/tag/1.6)] - 2022-05-17
 
+- [#93](https://github.com/nf-core/fetchngs/pull/93) - Adjust modules configuration to respect the `publish_dir_mode` parameter.
 - [#57](https://github.com/nf-core/fetchngs/pull/57) - fetchngs fails if FTP is blocked
 - [#89](https://github.com/nf-core/fetchngs/pull/89) - Improve detection and usage of the NCBI user settings by using the standardized sra-tools modules from nf-core.
 - [[nf-core/rnaseq#764](https://github.com/nf-core/rnaseq/issues/764)] - Test fails when using GCP due to missing tools in the basic biocontainer

From e697f22fbd5696060fee11505027fa0ed8051b7c Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Tue, 17 May 2022 11:54:01 +0100
Subject: [PATCH 202/852] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8d5d7efc..9cdb7a0b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,9 +5,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [[1.6](https://github.com/nf-core/fetchngs/releases/tag/1.6)] - 2022-05-17
 
-- [#93](https://github.com/nf-core/fetchngs/pull/93) - Adjust modules configuration to respect the `publish_dir_mode` parameter.
 - [#57](https://github.com/nf-core/fetchngs/pull/57) - fetchngs fails if FTP is blocked
 - [#89](https://github.com/nf-core/fetchngs/pull/89) - Improve detection and usage of the NCBI user settings by using the standardized sra-tools modules from nf-core.
+- [#93](https://github.com/nf-core/fetchngs/pull/93) - Adjust modules configuration to respect the `publish_dir_mode` parameter.
 - [[nf-core/rnaseq#764](https://github.com/nf-core/rnaseq/issues/764)] - Test fails when using GCP due to missing tools in the basic biocontainer
 - Updated pipeline template to [nf-core/tools 2.4.1](https://github.com/nf-core/tools/releases/tag/2.4.1)
 

From 8460420a11eb965bc7ea11e7584a29a25a9eccb7 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 17 May 2022 13:04:54 +0100
Subject: [PATCH 203/852] Bump pipeline version to 1.7dev

---
 CHANGELOG.md    | 4 ++++
 nextflow.config | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9cdb7a0b..8d5b569f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unpublished Version / DEV]
+
+### Enhancements & fixes
+
 ## [[1.6](https://github.com/nf-core/fetchngs/releases/tag/1.6)] - 2022-05-17
 
 - [#57](https://github.com/nf-core/fetchngs/pull/57) - fetchngs fails if FTP is blocked
diff --git a/nextflow.config b/nextflow.config
index 237190ec..667f15e1 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -158,7 +158,7 @@ manifest {
     description     = 'Pipeline to fetch metadata and raw FastQ files from public databases'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
-    version         = '1.6'
+    version         = '1.7dev'
 }
 
 // Load modules.config for DSL2 module specific options

From ca314f0e2880f4be89a4514d87b846eaebd8b51e Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Sat, 11 Jun 2022 07:15:35 +0200
Subject: [PATCH 204/852] Add taxprofiler to pipeline and add enum for
 --nf_core_pipeline

---
 modules/local/sra_to_samplesheet.nf | 2 ++
 nextflow_schema.json                | 3 ++-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/modules/local/sra_to_samplesheet.nf b/modules/local/sra_to_samplesheet.nf
index 465144d7..4b448e89 100644
--- a/modules/local/sra_to_samplesheet.nf
+++ b/modules/local/sra_to_samplesheet.nf
@@ -39,6 +39,8 @@ process SRA_TO_SAMPLESHEET {
     if (pipeline) {
         if (pipeline == 'rnaseq') {
             pipeline_map << [ strandedness: 'unstranded' ]
+        } else if (pipeline == 'taxprofiler') {
+            pipeline_map << [ fasta: '' ]
         }
     }
     pipeline_map << meta_map
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 2bc7c52e..a31b9396 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -43,7 +43,8 @@
                 "nf_core_pipeline": {
                     "type": "string",
                     "fa_icon": "fab fa-apple",
-                    "description": "Name of supported nf-core pipeline e.g.  'rnaseq'. A samplesheet for direct use with the pipeline will be created with the appropriate columns."
+                    "description": "Name of supported nf-core pipeline e.g.  'rnaseq'. A samplesheet for direct use with the pipeline will be created with the appropriate columns.",
+                    "enum": ["rnaseq", "viralrecon", "taxprofiler"]
                 },
                 "force_sratools_download": {
                     "type": "boolean",

From 491d3969ffcb846027f1c4aa305edb26217a56eb Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Sat, 11 Jun 2022 07:22:51 +0200
Subject: [PATCH 205/852] Update changelog and docs

---
 CHANGELOG.md  | 5 +++++
 README.md     | 2 +-
 docs/usage.md | 2 +-
 3 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8d5b569f..e101b40d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+- [#97](https://github.com/nf-core/fetchngs/pull/97) - Add support for generating nf-core/taxprofiler compatible samplesheets anda dded improved validation for the --nf_core_pipeline flag to only accept supported pipelines
+-
+
+### Enhancements & fixes
+
 ## [[1.6](https://github.com/nf-core/fetchngs/releases/tag/1.6)] - 2022-05-17
 
 - [#57](https://github.com/nf-core/fetchngs/pull/57) - fetchngs fails if FTP is blocked
diff --git a/README.md b/README.md
index 18b27ca3..637a373c 100644
--- a/README.md
+++ b/README.md
@@ -45,7 +45,7 @@ Via a single file of ids, provided one-per-line (see [example input file](https:
 
 ### Samplesheet format
 
-The columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core.
+The columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format), as well as [nf-core/taxprofiler](https://nf-co.re/nf-core/taxprofiler). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core.
 
 ## Quick Start
 
diff --git a/docs/usage.md b/docs/usage.md
index b6c97e33..f95baa24 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -55,7 +55,7 @@ The final sample information for the FastQ files used for samplesheet generation
 
 ### Samplesheet format
 
-As a bonus, the columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core. It is highly recommended that you double-check that all of the identifiers you defined using `--input` are represented in the samplesheet. Also, public databases don't reliably hold information such as strandedness information so you may need to amend these entries too if for example your samplesheet was created by providing `--nf_core_pipeline rnaseq`.
+As a bonus, the columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format) as well [nf-core/taxprofiler](https://nf-co.re/taxprofiler/usage#samplesheet-input). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core. It is highly recommended that you double-check that all of the identifiers you defined using `--input` are represented in the samplesheet. Also, public databases don't reliably hold information such as strandedness information so you may need to amend these entries too if for example your samplesheet was created by providing `--nf_core_pipeline rnaseq`.
 
 ### Bypass `FTP` data download
 

From 4bd5ccdd0f650bdf507eaddbff4bf03323e02452 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Sat, 11 Jun 2022 21:10:01 +0200
Subject: [PATCH 206/852] Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 CHANGELOG.md  | 6 ++----
 README.md     | 8 +++++++-
 docs/usage.md | 8 +++++++-
 3 files changed, 16 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e101b40d..9e635ea4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,10 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
-- [#97](https://github.com/nf-core/fetchngs/pull/97) - Add support for generating nf-core/taxprofiler compatible samplesheets anda dded improved validation for the --nf_core_pipeline flag to only accept supported pipelines
--
-
-### Enhancements & fixes
+- [#97](https://github.com/nf-core/fetchngs/pull/97) - Add support for generating nf-core/taxprofiler compatible samplesheets.
+- Add `enum` field for `--nf_core_pipeline` to parameter schema so only accept supported pipelines are accepted
 
 ## [[1.6](https://github.com/nf-core/fetchngs/releases/tag/1.6)] - 2022-05-17
 
diff --git a/README.md b/README.md
index 637a373c..c44ac40f 100644
--- a/README.md
+++ b/README.md
@@ -45,7 +45,13 @@ Via a single file of ids, provided one-per-line (see [example input file](https:
 
 ### Samplesheet format
 
-The columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format), as well as [nf-core/taxprofiler](https://nf-co.re/nf-core/taxprofiler). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core.
+The columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include:
+
+- [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input)
+- Ilumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format)
+- [nf-core/taxprofiler](https://nf-co.re/nf-core/taxprofiler) 
+
+You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core.
 
 ## Quick Start
 
diff --git a/docs/usage.md b/docs/usage.md
index f95baa24..8018760f 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -55,7 +55,13 @@ The final sample information for the FastQ files used for samplesheet generation
 
 ### Samplesheet format
 
-As a bonus, the columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format) as well [nf-core/taxprofiler](https://nf-co.re/taxprofiler/usage#samplesheet-input). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core. It is highly recommended that you double-check that all of the identifiers you defined using `--input` are represented in the samplesheet. Also, public databases don't reliably hold information such as strandedness information so you may need to amend these entries too if for example your samplesheet was created by providing `--nf_core_pipeline rnaseq`.
+As a bonus, the columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include:
+
+- [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input)
+- Ilumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format)
+- [nf-core/taxprofiler](https://nf-co.re/nf-core/taxprofiler) 
+ 
+You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core. It is highly recommended that you double-check that all of the identifiers you defined using `--input` are represented in the samplesheet. Also, public databases don't reliably hold information such as strandedness information so you may need to amend these entries too if for example your samplesheet was created by providing `--nf_core_pipeline rnaseq`.
 
 ### Bypass `FTP` data download
 

From 920c62f64cf27ae9229f965a843f25d4a4cb86f3 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Sat, 11 Jun 2022 21:13:59 +0200
Subject: [PATCH 207/852] Prettifying

---
 README.md     | 2 +-
 docs/usage.md | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index c44ac40f..7806362e 100644
--- a/README.md
+++ b/README.md
@@ -49,7 +49,7 @@ The columns in the auto-created samplesheet can be tailored to be accepted out-o
 
 - [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input)
 - Ilumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format)
-- [nf-core/taxprofiler](https://nf-co.re/nf-core/taxprofiler) 
+- [nf-core/taxprofiler](https://nf-co.re/nf-core/taxprofiler)
 
 You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core.
 
diff --git a/docs/usage.md b/docs/usage.md
index 8018760f..0cb6a976 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -59,8 +59,8 @@ As a bonus, the columns in the auto-created samplesheet can be tailored to be ac
 
 - [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input)
 - Ilumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format)
-- [nf-core/taxprofiler](https://nf-co.re/nf-core/taxprofiler) 
- 
+- [nf-core/taxprofiler](https://nf-co.re/nf-core/taxprofiler)
+
 You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core. It is highly recommended that you double-check that all of the identifiers you defined using `--input` are represented in the samplesheet. Also, public databases don't reliably hold information such as strandedness information so you may need to amend these entries too if for example your samplesheet was created by providing `--nf_core_pipeline rnaseq`.
 
 ### Bypass `FTP` data download

From 7caf7628943480920dc23bd11277804154bc8fd4 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 1 Jul 2022 11:56:37 +0100
Subject: [PATCH 208/852] Fix API call for SRA ids

---
 bin/sra_ids_to_runinfo.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index bbd1e6f0..f802da9e 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -246,13 +246,13 @@ def _content_check(cls, response, identifier):
     def _id_to_srx(cls, identifier):
         """Resolve the identifier to SRA experiments."""
         params = {
-            "save": "efetch",
+            "id": identifier,
             "db": "sra",
             "rettype": "runinfo",
-            "term": identifier,
+            "retmode": "text"
         }
         response = fetch_url(
-            f"https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?{urlencode(params)}"
+            f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?{urlencode(params)}"
         )
         cls._content_check(response, identifier)
         return [row["Experiment"] for row in open_table(response, delimiter=",")]

From a6c11e04c73b842f06febec66d3c7f247741ee5d Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 1 Jul 2022 11:57:37 +0100
Subject: [PATCH 209/852] Update API call for GEO ids - still broken

---
 bin/sra_ids_to_runinfo.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index f802da9e..0f85d2fa 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -261,9 +261,14 @@ def _id_to_srx(cls, identifier):
     def _gse_to_srx(cls, identifier):
         """Resolve the identifier to SRA experiments."""
         ids = []
-        params = {"acc": identifier, "targ": "gsm", "view": "data", "form": "text"}
+        params = {
+            "id": identifier,
+            "db": "gds",
+            "rettype": "runinfo",
+            "retmode": "text"
+        }
         response = fetch_url(
-            f"https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?{urlencode(params)}"
+            f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?{urlencode(params)}"
         )
         cls._content_check(response, identifier)
         gsm_ids = [

From 2cb54e3e390049c7d0b7637e2b3636eaff41728b Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 1 Jul 2022 13:21:33 +0100
Subject: [PATCH 210/852] Change default function to resolve GSM ids

---
 bin/sra_ids_to_runinfo.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index 0f85d2fa..21c7225d 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -193,9 +193,11 @@ def is_valid(cls, identifier):
 class DatabaseResolver:
     """Define a service class for resolving various identifiers to experiments."""
 
-    _GEO_PREFIXES = {"GSE"}
+    _GEO_PREFIXES = {
+        "GSE",
+        "GSM"
+    }
     _SRA_PREFIXES = {
-        "GSM",
         "PRJNA",
         "SAMN",
         "SRR",
@@ -207,7 +209,9 @@ class DatabaseResolver:
         "PRJDB",
         "SAMD",
     }
-    _ENA_PREFIXES = {"ERR"}
+    _ENA_PREFIXES = {
+        "ERR"
+    }
 
     @classmethod
     def expand_identifier(cls, identifier):

From edf3dafcc4585d879eca35687b9833bdf2279962 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 1 Jul 2022 16:20:17 +0100
Subject: [PATCH 211/852] Bump pipeline version to 1.7

---
 CHANGELOG.md    | 7 ++++++-
 nextflow.config | 2 +-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9e635ea4..dada8a72 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,11 +3,16 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unpublished Version / DEV]
+## [[1.7](https://github.com/nf-core/fetchngs/releases/tag/1.7)] - 2022-07-01
+
+### :warning: Major enhancements
+
+Support for GEO ids has been dropped in this release due to breaking changes introduced in the NCBI API. Please see [this PR](https://github.com/nf-core/fetchngs/pull/102).
 
 ### Enhancements & fixes
 
 - [#97](https://github.com/nf-core/fetchngs/pull/97) - Add support for generating nf-core/taxprofiler compatible samplesheets.
+- [#99](https://github.com/nf-core/fetchngs/issues/99) - SRA_IDS_TO_RUNINFO fails due to bad request
 - Add `enum` field for `--nf_core_pipeline` to parameter schema so only accept supported pipelines are accepted
 
 ## [[1.6](https://github.com/nf-core/fetchngs/releases/tag/1.6)] - 2022-05-17
diff --git a/nextflow.config b/nextflow.config
index 667f15e1..80ed6507 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -158,7 +158,7 @@ manifest {
     description     = 'Pipeline to fetch metadata and raw FastQ files from public databases'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
-    version         = '1.7dev'
+    version         = '1.7'
 }
 
 // Load modules.config for DSL2 module specific options

From d1e07712666a224b44a5326594d56c5ec31cab48 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 1 Jul 2022 16:28:18 +0100
Subject: [PATCH 212/852] Strip out mention of GEO ids everywhere

---
 CHANGELOG.md             | 10 +++++++++-
 README.md                | 16 ++++++++++++++--
 assets/schema_input.json |  2 +-
 docs/output.md           |  6 +++---
 docs/usage.md            | 18 +++++++++---------
 lib/WorkflowMain.groovy  |  4 ++--
 lib/WorkflowSra.groovy   | 17 +++++++++++++++++
 main.nf                  |  4 ++--
 nextflow_schema.json     |  2 +-
 workflows/sra.nf         |  7 +++++++
 10 files changed, 65 insertions(+), 21 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index dada8a72..f3bbf9a7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,7 +7,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### :warning: Major enhancements
 
-Support for GEO ids has been dropped in this release due to breaking changes introduced in the NCBI API. Please see [this PR](https://github.com/nf-core/fetchngs/pull/102).
+Support for GEO ids has been dropped in this release due to breaking changes introduced in the NCBI API. For more detailed information please see [this PR](https://github.com/nf-core/fetchngs/pull/102).
+
+As a workaround, if you have a GEO accession you can directly download a text file containing the appropriate SRA ids to pass to the pipeline:
+
+- Search for your GEO accession on [GEO](https://www.ncbi.nlm.nih.gov/geo)
+- Click `SRA Run Selector` at the bottom of the GEO accession page
+- Select the desired samples in the `SRA Run Selector` and then download the `Accession List`
+
+This downloads a text file called `SRR_Acc_List.txt` that can be directly provided to the pipeline e.g. `--input SRR_Acc_List.txt`.
 
 ### Enhancements & fixes
 
diff --git a/README.md b/README.md
index 7806362e..1151db3d 100644
--- a/README.md
+++ b/README.md
@@ -17,7 +17,7 @@
 
 ## Introduction
 
-**nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from both public and private databases. At present, the pipeline supports SRA / ENA / DDBJ / GEO / Synapse ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)).
+**nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from both public and private databases. At present, the pipeline supports SRA / ENA / DDBJ / Synapse ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)).
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.
 
@@ -27,7 +27,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 Via a single file of ids, provided one-per-line (see [example input file](https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.txt)) the pipeline performs the following steps:
 
-### SRA / ENA / DDBJ / GEO ids
+### SRA / ENA / DDBJ ids
 
 1. Resolve database ids back to appropriate experiment-level ids and to be compatible with the [ENA API](https://ena-docs.readthedocs.io/en/latest/retrieval/programmatic-access.html)
 2. Fetch extensive id metadata via ENA API
@@ -36,6 +36,18 @@ Via a single file of ids, provided one-per-line (see [example input file](https:
    - Otherwise use [`sra-tools`](https://github.com/ncbi/sra-tools) to download `.sra` files and convert them to FastQ
 4. Collate id metadata and paths to FastQ files in a single samplesheet
 
+### GEO ids
+
+Support for GEO ids was dropped in [[v1.7](https://github.com/nf-core/fetchngs/releases/tag/1.7)] due to breaking changes introduced in the NCBI API. For more detailed information please see [this PR](https://github.com/nf-core/fetchngs/pull/102).
+
+As a workaround, if you have a GEO accession you can directly download a text file containing the appropriate SRA ids to pass to the pipeline instead:
+
+- Search for your GEO accession on [GEO](https://www.ncbi.nlm.nih.gov/geo)
+- Click `SRA Run Selector` at the bottom of the GEO accession page
+- Select the desired samples in the `SRA Run Selector` and then download the `Accession List`
+
+This downloads a text file called `SRR_Acc_List.txt` that can be directly provided to the pipeline e.g. `--input SRR_Acc_List.txt`.
+
 ### Synapse ids
 
 1. Resolve Synapse directory ids to their corresponding FastQ files ids via the `synapse list` command.
diff --git a/assets/schema_input.json b/assets/schema_input.json
index 9a800216..8bf05fd8 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -9,7 +9,7 @@
         "items": {
             "type": "string",
             "pattern": "^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM])|(syn))(\\d+)$",
-            "errorMessage": "Please provide a valid SRA, ENA, DDBJ or GEO identifier"
+            "errorMessage": "Please provide a valid SRA, ENA, DDBJ identifier"
         }
     }
 }
diff --git a/docs/output.md b/docs/output.md
index 7402976c..daaca914 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -9,19 +9,19 @@ This document describes the output produced by the pipeline. The directories lis
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data depending on the type of ids provided:
 
 - Download FastQ files and create samplesheet from:
-  1. [SRA / ENA / DDBJ / GEO ids](#sra--ena--ddbj--geo-ids)
+  1. [SRA / ENA / DDBJ ids](#sra--ena--ddbj-ids)
   2. [Synapse ids](#synapse-ids)
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
 Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introduction) for a list of supported public repository identifiers and how to provide them to the pipeline.
 
-### SRA / ENA / DDBJ / GEO ids
+### SRA / ENA / DDBJ ids
 
 <details markdown="1">
 <summary>Output files</summary>
 
 - `fastq/`
-  - `*.fastq.gz`: Paired-end/single-end reads downloaded from the SRA / ENA / DDBJ / GEO.
+  - `*.fastq.gz`: Paired-end/single-end reads downloaded from the SRA / ENA / DDBJ.
 - `fastq/md5/`
   - `*.md5`: Files containing `md5` sum for FastQ files downloaded from the ENA.
 - `samplesheet/`
diff --git a/docs/usage.md b/docs/usage.md
index 0cb6a976..ba4de1b2 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -8,15 +8,15 @@
 
 The pipeline has been set-up to automatically download and process the raw FastQ files from both public and private repositories. Identifiers can be provided in a file, one-per-line via the `--input` parameter. Currently, the following types of example identifiers are supported:
 
-| `SRA`        | `ENA`        | `DDBJ`       | `GEO`      | `Synapse`   |
-| ------------ | ------------ | ------------ | ---------- | ----------- |
-| SRR11605097  | ERR4007730   | DRR171822    | GSM4432381 | syn26240435 |
-| SRX8171613   | ERX4009132   | DRX162434    | GSE147507  |             |
-| SRS6531847   | ERS4399630   | DRS090921    |            |             |
-| SAMN14689442 | SAMEA6638373 | SAMD00114846 |            |             |
-| SRP256957    | ERP120836    | DRP004793    |            |             |
-| SRA1068758   | ERA2420837   | DRA008156    |            |             |
-| PRJNA625551  | PRJEB37513   | PRJDB4176    |            |             |
+| `SRA`        | `ENA`        | `DDBJ`       | `Synapse`   |
+| ------------ | ------------ | ------------ | ----------- |
+| SRR11605097  | ERR4007730   | DRR171822    | syn26240435 |
+| SRX8171613   | ERX4009132   | DRX162434    |             |
+| SRS6531847   | ERS4399630   | DRS090921    |             |
+| SAMN14689442 | SAMEA6638373 | SAMD00114846 |             |
+| SRP256957    | ERP120836    | DRP004793    |             |
+| SRA1068758   | ERA2420837   | DRA008156    |             |
+| PRJNA625551  | PRJEB37513   | PRJDB4176    |             |
 
 ### SRR / ERR / DRR ids
 
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index f64fa80f..77b7ffde 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -104,7 +104,7 @@ class WorkflowMain {
             if (num_match == total_ids) {
                 is_sra = true
             } else {
-                log.error "Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / DDBJ / GEO or Synapse ids!"
+                log.error "Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / DDBJ or Synapse ids!"
                 System.exit(1)
             }
         }
@@ -129,7 +129,7 @@ class WorkflowMain {
             if (num_match == total_ids) {
                 is_synapse = true
             } else {
-                log.error "Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / DDBJ / GEO or Synapse ids!"
+                log.error "Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / DDBJ or Synapse ids!"
                 System.exit(1)
             }
         }
diff --git a/lib/WorkflowSra.groovy b/lib/WorkflowSra.groovy
index a2c16219..90d86f1c 100755
--- a/lib/WorkflowSra.groovy
+++ b/lib/WorkflowSra.groovy
@@ -29,4 +29,21 @@ class WorkflowSra {
             "  running nf-core/other pipelines.\n" +
             "==================================================================================="
     }
+
+    // Fail pipeline if input ids are from the GEO
+    public static void isGeoFail(ids, log) {
+        def pattern = /^(GS[EM])(\d+)$/
+        for (id in ids) {
+            if (id =~ pattern) {
+                log.error "===================================================================================\n" +
+                    "  GEO id detected: ${id}\n" +
+                    "  Support for GEO ids was dropped in v1.7 due to breaking changes in the NCBI API.\n" +
+                    "  Please remove any GEO ids from the input samplesheet.\n\n" +
+                    "  Please see:\n" +
+                    "  https://github.com/nf-core/fetchngs/pull/102\n" +
+                    "==================================================================================="
+                System.exit(1)
+            }
+        }
+    }
 }
diff --git a/main.nf b/main.nf
index c6303a41..2c4b52f2 100644
--- a/main.nf
+++ b/main.nf
@@ -44,7 +44,7 @@ if (WorkflowMain.isSraId(ch_input, log)) {
 } else if (WorkflowMain.isSynapseId(ch_input, log)) {
     input_type = 'synapse'
 } else {
-    exit 1, 'Ids provided via --input not recognised please make sure they are either SRA / ENA / DDBJ / GEO or Synapse ids!'
+    exit 1, 'Ids provided via --input not recognised please make sure they are either SRA / ENA / DDBJ or Synapse ids!'
 }
 
 if (params.input_type == input_type) {
@@ -63,7 +63,7 @@ if (params.input_type == input_type) {
 workflow NFCORE_FETCHNGS {
 
     //
-    // WORKFLOW: Download FastQ files for SRA / ENA / DDBJ / GEO ids
+    // WORKFLOW: Download FastQ files for SRA / ENA / DDBJ ids
     //
     if (params.input_type == 'sra') {
         SRA ( ch_ids )
diff --git a/nextflow_schema.json b/nextflow_schema.json
index a31b9396..a51dc45a 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -19,7 +19,7 @@
                     "pattern": "^\\S+\\.txt$",
                     "schema": "assets/schema_input.json",
                     "fa_icon": "fas fa-file-excel",
-                    "description": "File containing SRA/ENA/DDBJ/GEO identifiers one per line to download their associated metadata and FastQ files."
+                    "description": "File containing SRA/ENA/DDBJ identifiers one per line to download their associated metadata and FastQ files."
                 },
                 "input_type": {
                     "type": "string",
diff --git a/workflows/sra.nf b/workflows/sra.nf
index 2b3cb498..0dde4588 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -50,6 +50,13 @@ workflow SRA {
     main:
     ch_versions = Channel.empty()
 
+    //
+    // Fail the pipeline if GEO ids detected
+    //
+    ids
+        .collect()
+        .map { WorkflowSra.isGeoFail(it, log) }
+
     //
     // MODULE: Get SRA run information for public database ids
     //

From 3696f40cf5bcd4ec3266275b4cb77e4359d76c06 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 1 Jul 2022 16:35:45 +0100
Subject: [PATCH 213/852] Strip out regex for GEO from input schema

---
 assets/schema_input.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index 8bf05fd8..71f0f976 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -8,7 +8,7 @@
         "type": "array",
         "items": {
             "type": "string",
-            "pattern": "^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM])|(syn))(\\d+)$",
+            "pattern": "^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(syn))(\\d+)$",
             "errorMessage": "Please provide a valid SRA, ENA, DDBJ identifier"
         }
     }

From 1715457d75d1b073f5ac2114cacbcf886876bb27 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 1 Jul 2022 17:19:36 +0100
Subject: [PATCH 214/852] Bump pipeline version to 1.8dev

---
 CHANGELOG.md    | 4 ++++
 nextflow.config | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f3bbf9a7..8bf55a90 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unpublished Version / DEV]
+
+### Enhancements & fixes
+
 ## [[1.7](https://github.com/nf-core/fetchngs/releases/tag/1.7)] - 2022-07-01
 
 ### :warning: Major enhancements
diff --git a/nextflow.config b/nextflow.config
index 80ed6507..eb5a19a0 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -158,7 +158,7 @@ manifest {
     description     = 'Pipeline to fetch metadata and raw FastQ files from public databases'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
-    version         = '1.7'
+    version         = '1.8dev'
 }
 
 // Load modules.config for DSL2 module specific options

From f071b7b8ce83b37ff3cde24b511cc46102eb177b Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 8 Jul 2022 15:55:19 +0100
Subject: [PATCH 215/852] Fetch SRR and DRR id info from ENA API instead of
 NCBI API

---
 bin/sra_ids_to_runinfo.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index 21c7225d..d85b0996 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -200,17 +200,17 @@ class DatabaseResolver:
     _SRA_PREFIXES = {
         "PRJNA",
         "SAMN",
-        "SRR",
         "DRA",
         "DRP",
-        "DRR",
         "DRS",
         "DRX",
         "PRJDB",
         "SAMD",
     }
     _ENA_PREFIXES = {
-        "ERR"
+        "ERR",
+        "SRR",
+        "DRR"
     }
 
     @classmethod

From b4f05430b6d055cd5d745b9dd35d574d0b99a9e2 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 8 Jul 2022 15:58:39 +0100
Subject: [PATCH 216/852] Update CHANGELOG

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8bf55a90..59d123ab 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+- Fetch `SRR` and `DRR` metadata from ENA API instead of NCBI API to bypass frequent breaking changes
+
 ## [[1.7](https://github.com/nf-core/fetchngs/releases/tag/1.7)] - 2022-07-01
 
 ### :warning: Major enhancements

From 91ce8905e078b18139136b6ef82a18e351a6263f Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@healx.io>
Date: Tue, 1 Nov 2022 16:09:59 +0000
Subject: [PATCH 217/852] add a tower.yml

---
 tower.yml | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 tower.yml

diff --git a/tower.yml b/tower.yml
new file mode 100644
index 00000000..ec0609cc
--- /dev/null
+++ b/tower.yml
@@ -0,0 +1,15 @@
+reports:
+  "samplesheet/samplesheet.csv":
+    display: "Auto-created samplesheet with collated metadata and FASTQ paths"
+  "samplesheet/id_mappings.csv":
+    display: "File with selected fields that can be used to rename samples"
+  "samplesheet/multiqc_config.yml":
+    display: "MultiQC config file that can be passed to most nf-core pipelines"
+  "metadata/*.runinfo_ftp.tsv":
+    display: "Re-formatted metadata file downloaded from the ENA"
+  "metadata/*.runinfo.tsv":
+    display: "Original metadata file downloaded from the ENA"
+  "metadata/*.metadata.txt":
+    display: "Original metadata file generated using the synapse show command"
+  "metadata/*.list.txt":
+    display: "Original output of the synapse list command"

From 2c06e2eac4e24474932128a79dc5967364940510 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@healx.io>
Date: Tue, 1 Nov 2022 16:18:35 +0000
Subject: [PATCH 218/852] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 59d123ab..cc9af791 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -25,6 +25,7 @@ This downloads a text file called `SRR_Acc_List.txt` that can be directly provid
 
 ### Enhancements & fixes
 
+- [#121](https://github.com/nf-core/fetchngs/pull/123) - Add Tower reporting
 - [#97](https://github.com/nf-core/fetchngs/pull/97) - Add support for generating nf-core/taxprofiler compatible samplesheets.
 - [#99](https://github.com/nf-core/fetchngs/issues/99) - SRA_IDS_TO_RUNINFO fails due to bad request
 - Add `enum` field for `--nf_core_pipeline` to parameter schema so only accept supported pipelines are accepted

From a927872ba0f7b482304cdd20b1b11865442feb75 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@healx.io>
Date: Wed, 2 Nov 2022 10:47:09 +0000
Subject: [PATCH 219/852] Keep to main outputs

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 tower.yml | 18 +++++-------------
 1 file changed, 5 insertions(+), 13 deletions(-)

diff --git a/tower.yml b/tower.yml
index ec0609cc..7b7fd106 100644
--- a/tower.yml
+++ b/tower.yml
@@ -1,15 +1,7 @@
 reports:
-  "samplesheet/samplesheet.csv":
+  samplesheet.csv:
     display: "Auto-created samplesheet with collated metadata and FASTQ paths"
-  "samplesheet/id_mappings.csv":
-    display: "File with selected fields that can be used to rename samples"
-  "samplesheet/multiqc_config.yml":
-    display: "MultiQC config file that can be passed to most nf-core pipelines"
-  "metadata/*.runinfo_ftp.tsv":
-    display: "Re-formatted metadata file downloaded from the ENA"
-  "metadata/*.runinfo.tsv":
-    display: "Original metadata file downloaded from the ENA"
-  "metadata/*.metadata.txt":
-    display: "Original metadata file generated using the synapse show command"
-  "metadata/*.list.txt":
-    display: "Original output of the synapse list command"
+  id_mappings.csv:
+    display: "File with database identifier mappings that can be used to rename samples"
+  multiqc_config.yml:
+    display: "MultiQC config file for bulk renaming of sample names from database ids"

From e3906f5440bb05bd2bb3f782c6d6ab64373940e6 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@healx.io>
Date: Wed, 2 Nov 2022 10:47:27 +0000
Subject: [PATCH 220/852] Improve changelog

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index cc9af791..b16a252a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -25,7 +25,7 @@ This downloads a text file called `SRR_Acc_List.txt` that can be directly provid
 
 ### Enhancements & fixes
 
-- [#121](https://github.com/nf-core/fetchngs/pull/123) - Add Tower reporting
+- [#121](https://github.com/nf-core/fetchngs/pull/123) - Add `tower.yml` to render Reports in Tower
 - [#97](https://github.com/nf-core/fetchngs/pull/97) - Add support for generating nf-core/taxprofiler compatible samplesheets.
 - [#99](https://github.com/nf-core/fetchngs/issues/99) - SRA_IDS_TO_RUNINFO fails due to bad request
 - Add `enum` field for `--nf_core_pipeline` to parameter schema so only accept supported pipelines are accepted

From c4d365833b109a3587d8621427f5eae3aafd2714 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@healx.io>
Date: Wed, 2 Nov 2022 10:52:42 +0000
Subject: [PATCH 221/852] Set input file type to Tower-compatible one (CSV)

---
 nextflow_schema.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index a51dc45a..bde6337d 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -15,8 +15,8 @@
                 "input": {
                     "type": "string",
                     "format": "file-path",
-                    "mimetype": "text/plain",
-                    "pattern": "^\\S+\\.txt$",
+                    "mimetype": "text/csv",
+                    "pattern": "^\\S+\\.csv$",
                     "schema": "assets/schema_input.json",
                     "fa_icon": "fas fa-file-excel",
                     "description": "File containing SRA/ENA/DDBJ identifiers one per line to download their associated metadata and FastQ files."

From 95bd0569910eb103d7d88d210a48f0dee96b438e Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@healx.io>
Date: Thu, 3 Nov 2022 14:16:26 +0000
Subject: [PATCH 222/852] Fix tests for csv

---
 conf/test.config         | 2 +-
 conf/test_full.config    | 2 +-
 conf/test_synapse.config | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/conf/test.config b/conf/test.config
index 39a4ffdb..3c58e9cf 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -20,5 +20,5 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.txt'
+    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv'
 }
diff --git a/conf/test_full.config b/conf/test_full.config
index 0887326a..2f0303ea 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -15,5 +15,5 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.txt'
+    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv'
 }
diff --git a/conf/test_synapse.config b/conf/test_synapse.config
index b49f2463..1ac1388a 100644
--- a/conf/test_synapse.config
+++ b/conf/test_synapse.config
@@ -20,6 +20,6 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input      = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/synapse_ids_test.txt'
+    input      = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/synapse_ids_test.csv'
     input_type = 'synapse'
 }

From 484e8185507c11b99763cb4fd45a716c8544e835 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@healx.io>
Date: Thu, 3 Nov 2022 14:19:23 +0000
Subject: [PATCH 223/852] Update docs for csv

---
 README.md     | 6 +++---
 docs/usage.md | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 1151db3d..24d77103 100644
--- a/README.md
+++ b/README.md
@@ -25,7 +25,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 ## Pipeline summary
 
-Via a single file of ids, provided one-per-line (see [example input file](https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.txt)) the pipeline performs the following steps:
+Via a single file of ids, provided one-per-line (see [example input file](https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv)) the pipeline performs the following steps:
 
 ### SRA / ENA / DDBJ ids
 
@@ -46,7 +46,7 @@ As a workaround, if you have a GEO accession you can directly download a text fi
 - Click `SRA Run Selector` at the bottom of the GEO accession page
 - Select the desired samples in the `SRA Run Selector` and then download the `Accession List`
 
-This downloads a text file called `SRR_Acc_List.txt` that can be directly provided to the pipeline e.g. `--input SRR_Acc_List.txt`.
+This downloads a text file called `SRR_Acc_List.csv` that can be directly provided to the pipeline once renamed with a .csv extension e.g. `--input SRR_Acc_List.csv`.
 
 ### Synapse ids
 
@@ -87,7 +87,7 @@ You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g.
 4. Start running your own analysis!
 
    ```bash
-   nextflow run nf-core/fetchngs --input ids.txt --outdir <OUTDIR> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
+   nextflow run nf-core/fetchngs --input ids.csv --outdir <OUTDIR> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
    ```
 
 ## Documentation
diff --git a/docs/usage.md b/docs/usage.md
index ba4de1b2..b7fbe8f6 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -32,7 +32,7 @@ If you have a GEO accession (found in the data availability section of published
 - Click `SRA Run Selector` at the bottom of the GEO accession page
 - Select the desired samples in the `SRA Run Selector` and then download the `Accession List`
 
-This downloads a text file called `SRR_Acc_List.txt` that can be directly provided to the pipeline e.g. `--input SRR_Acc_List.txt`.
+This downloads a text file called `SRR_Acc_List.csv` that can be directly provided to the pipeline once renamed with a .csv extension e.g. `--input SRR_Acc_List.csv`.
 
 ### Synapse ids
 
@@ -72,7 +72,7 @@ If FTP connections are blocked on your network use the [`--force_sratools_downlo
 The typical command for running the pipeline is as follows:
 
 ```bash
-nextflow run nf-core/fetchngs --input ids.txt --outdir <OUTDIR> -profile docker
+nextflow run nf-core/fetchngs --input ids.csv --outdir <OUTDIR> -profile docker
 ```
 
 This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.

From 70f0038a52c89859fc8cb2df1e0f55425eb8c427 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@healx.io>
Date: Thu, 3 Nov 2022 14:22:17 +0000
Subject: [PATCH 224/852] update WorkflowMain.groovy for CSV

---
 lib/WorkflowMain.groovy | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index 77b7ffde..ef9131b7 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -21,7 +21,7 @@ class WorkflowMain {
     // Print help to screen if required
     //
     public static String help(workflow, params, log) {
-        def command = "nextflow run ${workflow.manifest.name} --input ids.txt -profile docker"
+        def command = "nextflow run ${workflow.manifest.name} --input ids.csv -profile docker"
         def help_string = ''
         help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs)
         help_string += NfcoreSchema.paramsHelp(workflow, params, command)
@@ -74,7 +74,7 @@ class WorkflowMain {
 
         // Check input has been provided
         if (!params.input) {
-            log.error "Please provide an input file containing ids to the pipeline - one per line e.g. '--input ids.txt'"
+            log.error "Please provide an input file containing ids to the pipeline - one per line e.g. '--input ids.csv'"
             System.exit(1)
         }
 

From 5c340b0b501e03f7fd59bc2d623f233ad3f2dc49 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@healx.io>
Date: Thu, 3 Nov 2022 14:32:39 +0000
Subject: [PATCH 225/852] Undo bad txt -> csv

---
 README.md     | 2 +-
 docs/usage.md | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 24d77103..fe68e6b2 100644
--- a/README.md
+++ b/README.md
@@ -46,7 +46,7 @@ As a workaround, if you have a GEO accession you can directly download a text fi
 - Click `SRA Run Selector` at the bottom of the GEO accession page
 - Select the desired samples in the `SRA Run Selector` and then download the `Accession List`
 
-This downloads a text file called `SRR_Acc_List.csv` that can be directly provided to the pipeline once renamed with a .csv extension e.g. `--input SRR_Acc_List.csv`.
+This downloads a text file called `SRR_Acc_List.txt` that can be directly provided to the pipeline once renamed with a .csv extension e.g. `--input SRR_Acc_List.csv`.
 
 ### Synapse ids
 
diff --git a/docs/usage.md b/docs/usage.md
index b7fbe8f6..9d78a37b 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -32,7 +32,7 @@ If you have a GEO accession (found in the data availability section of published
 - Click `SRA Run Selector` at the bottom of the GEO accession page
 - Select the desired samples in the `SRA Run Selector` and then download the `Accession List`
 
-This downloads a text file called `SRR_Acc_List.csv` that can be directly provided to the pipeline once renamed with a .csv extension e.g. `--input SRR_Acc_List.csv`.
+This downloads a text file called `SRR_Acc_List.txt` that can be directly provided to the pipeline once renamed with a .csv extension e.g. `--input SRR_Acc_List.csv`.
 
 ### Synapse ids
 

From cabff52754f5da2e0973f72af0ab06a46cc0654c Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 4 Nov 2022 09:55:09 +0000
Subject: [PATCH 226/852] Fix relative paths after module restructuring

---
 subworkflows/nf-core/srafastq/main.nf | 6 +++---
 workflows/sra.nf                      | 2 +-
 workflows/synapse.nf                  | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/subworkflows/nf-core/srafastq/main.nf b/subworkflows/nf-core/srafastq/main.nf
index f57b6fac..580fef18 100644
--- a/subworkflows/nf-core/srafastq/main.nf
+++ b/subworkflows/nf-core/srafastq/main.nf
@@ -1,6 +1,6 @@
-include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../modules/nf-core/modules/custom/sratoolsncbisettings/main'
-include { SRATOOLS_PREFETCH           } from '../../../modules/nf-core/modules/sratools/prefetch/main'
-include { SRATOOLS_FASTERQDUMP        } from '../../../modules/nf-core/modules/sratools/fasterqdump/main'
+include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../modules/nf-core/custom/sratoolsncbisettings/main'
+include { SRATOOLS_PREFETCH           } from '../../../modules/nf-core/sratools/prefetch/main'
+include { SRATOOLS_FASTERQDUMP        } from '../../../modules/nf-core/sratools/fasterqdump/main'
 
 /**
  * Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
diff --git a/workflows/sra.nf b/workflows/sra.nf
index 0dde4588..ef654b2d 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -34,7 +34,7 @@ include { SRAFASTQ                } from '../subworkflows/nf-core/srafastq/main'
 ========================================================================================
 */
 
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main'
+include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
 
 /*
 ========================================================================================
diff --git a/workflows/synapse.nf b/workflows/synapse.nf
index 2a673623..1203056a 100644
--- a/workflows/synapse.nf
+++ b/workflows/synapse.nf
@@ -31,7 +31,7 @@ include { SYNAPSE_MERGE_SAMPLESHEET } from '../modules/local/synapse_merge_sampl
 ========================================================================================
 */
 
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main'
+include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
 
 /*
 ========================================================================================

From 2b22ab6b92417ae5efd61b1a2a657fa1fe91b77e Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 4 Nov 2022 09:57:46 +0000
Subject: [PATCH 227/852] Fix PythonBlack

---
 bin/multiqc_mappings_config.py |  5 +--
 bin/sra_ids_to_runinfo.py      | 80 ++++++++--------------------------
 bin/sra_runinfo_to_ftp.py      | 36 ++++-----------
 3 files changed, 29 insertions(+), 92 deletions(-)

diff --git a/bin/multiqc_mappings_config.py b/bin/multiqc_mappings_config.py
index a7fc92ba..2fcdb49a 100755
--- a/bin/multiqc_mappings_config.py
+++ b/bin/multiqc_mappings_config.py
@@ -3,11 +3,10 @@
 import sys
 
 with open(sys.argv[1], "r") as fin, open(sys.argv[2], "w") as fout:
-    header = fin.readline().split(',')
+    header = fin.readline().split(",")
     config = "sample_names_rename_buttons:\n"
-    config += "\n".join(['  - ' + x.strip('"') for x in header])
+    config += "\n".join(["  - " + x.strip('"') for x in header])
     config += "sample_names_rename:\n"
     for line in fin:
         config += f"  - [{', '.join(line.strip().split(','))}]\n"
     fout.write(config)
-
diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index d85b0996..70627791 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -49,9 +49,7 @@
 )
 GEO_IDS = ("GSE18729", "GSM465244")
 ID_REGEX = re.compile(r"^([A-Z]+)([0-9]+)$")
-PREFIX_LIST = sorted(
-    {ID_REGEX.match(id).group(1) for id in SRA_IDS + ENA_IDS + DDBJ_IDS + GEO_IDS}
-)
+PREFIX_LIST = sorted({ID_REGEX.match(id).group(1) for id in SRA_IDS + ENA_IDS + DDBJ_IDS + GEO_IDS})
 
 
 # List of metadata fields fetched from the ENA API - can be overriden by options
@@ -193,10 +191,7 @@ def is_valid(cls, identifier):
 class DatabaseResolver:
     """Define a service class for resolving various identifiers to experiments."""
 
-    _GEO_PREFIXES = {
-        "GSE",
-        "GSM"
-    }
+    _GEO_PREFIXES = {"GSE", "GSM"}
     _SRA_PREFIXES = {
         "PRJNA",
         "SAMN",
@@ -207,11 +202,7 @@ class DatabaseResolver:
         "PRJDB",
         "SAMD",
     }
-    _ENA_PREFIXES = {
-        "ERR",
-        "SRR",
-        "DRR"
-    }
+    _ENA_PREFIXES = {"ERR", "SRR", "DRR"}
 
     @classmethod
     def expand_identifier(cls, identifier):
@@ -240,24 +231,14 @@ def expand_identifier(cls, identifier):
     def _content_check(cls, response, identifier):
         """Check that the response has content or terminate."""
         if response.status == 204:
-            logger.error(
-                f"There is no content for id {identifier}. Maybe you lack the right "
-                f"permissions?"
-            )
+            logger.error(f"There is no content for id {identifier}. Maybe you lack the right " f"permissions?")
             sys.exit(1)
 
     @classmethod
     def _id_to_srx(cls, identifier):
         """Resolve the identifier to SRA experiments."""
-        params = {
-            "id": identifier,
-            "db": "sra",
-            "rettype": "runinfo",
-            "retmode": "text"
-        }
-        response = fetch_url(
-            f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?{urlencode(params)}"
-        )
+        params = {"id": identifier, "db": "sra", "rettype": "runinfo", "retmode": "text"}
+        response = fetch_url(f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?{urlencode(params)}")
         cls._content_check(response, identifier)
         return [row["Experiment"] for row in open_table(response, delimiter=",")]
 
@@ -265,20 +246,13 @@ def _id_to_srx(cls, identifier):
     def _gse_to_srx(cls, identifier):
         """Resolve the identifier to SRA experiments."""
         ids = []
-        params = {
-            "id": identifier,
-            "db": "gds",
-            "rettype": "runinfo",
-            "retmode": "text"
-        }
-        response = fetch_url(
-            f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?{urlencode(params)}"
-        )
+        params = {"id": identifier, "db": "gds", "rettype": "runinfo", "retmode": "text"}
+        response = fetch_url(f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?{urlencode(params)}")
         cls._content_check(response, identifier)
         gsm_ids = [
             line.split("=")[1].strip()
             for line in response.text().splitlines()
-            if line.split('=')[1].strip().startswith('GSM')
+            if line.split("=")[1].strip().startswith("GSM")
         ]
         for gsm_id in gsm_ids:
             ids += cls._id_to_srx(gsm_id)
@@ -293,13 +267,9 @@ def _id_to_erx(cls, identifier):
             "result": "read_run",
             "fields": ",".join(fields),
         }
-        response = fetch_url(
-            f"https://www.ebi.ac.uk/ena/portal/api/filereport?{urlencode(params)}"
-        )
+        response = fetch_url(f"https://www.ebi.ac.uk/ena/portal/api/filereport?{urlencode(params)}")
         cls._content_check(response, identifier)
-        return [
-            row["experiment_accession"] for row in open_table(response, delimiter="\t")
-        ]
+        return [row["experiment_accession"] for row in open_table(response, delimiter="\t")]
 
 
 class ENAMetadataFetcher:
@@ -328,9 +298,7 @@ def open_experiment_table(self, accession):
 
         """
         params = {**self._params, "accession": accession}
-        response = fetch_url(
-            f"https://www.ebi.ac.uk/ena/portal/api/filereport?{urlencode(params)}"
-        )
+        response = fetch_url(f"https://www.ebi.ac.uk/ena/portal/api/filereport?{urlencode(params)}")
         self._content_check(response, accession)
         return open_table(response, delimiter="\t")
 
@@ -338,10 +306,7 @@ def open_experiment_table(self, accession):
     def _content_check(cls, response, identifier):
         """Check that the response has content or terminate."""
         if response.status == 204:
-            logger.error(
-                f"There is no content for id {identifier}. Maybe you lack the right "
-                f"permissions?"
-            )
+            logger.error(f"There is no content for id {identifier}. Maybe you lack the right " f"permissions?")
             sys.exit(1)
 
 
@@ -362,8 +327,7 @@ def open_table(response, delimiter=","):
 
 def parse_args(args=None):
     parser = argparse.ArgumentParser(
-        description="Download and create a run information metadata file from SRA / "
-        "ENA / DDBJ / GEO identifiers.",
+        description="Download and create a run information metadata file from SRA / " "ENA / DDBJ / GEO identifiers.",
         epilog="Example usage: python fetch_sra_runinfo.py <FILE_IN> <FILE_OUT>",
     )
     parser.add_argument(
@@ -383,8 +347,7 @@ def parse_args(args=None):
         "--ena_metadata_fields",
         type=str,
         default=",".join(ENA_METADATA_FIELDS),
-        help=f"Comma-separated list of ENA metadata fields to fetch "
-        f"(default: {','.join(ENA_METADATA_FIELDS)}).",
+        help=f"Comma-separated list of ENA metadata fields to fetch " f"(default: {','.join(ENA_METADATA_FIELDS)}).",
     )
     parser.add_argument(
         "-l",
@@ -431,9 +394,7 @@ def get_ena_fields():
     return [
         row["columnId"]
         for row in open_table(
-            fetch_url(
-                f"https://www.ebi.ac.uk/ena/portal/api/returnFields?{urlencode(params)}"
-            ),
+            fetch_url(f"https://www.ebi.ac.uk/ena/portal/api/returnFields?{urlencode(params)}"),
             delimiter="\t",
         )
     ]
@@ -453,16 +414,11 @@ def fetch_sra_runinfo(file_in, file_out, ena_metadata_fields):
             seen_ids.add(db_id)
             if not DatabaseIdentifierChecker.is_valid(db_id):
                 id_str = ", ".join([x + "*" for x in PREFIX_LIST])
-                logger.error(
-                    f"Please provide a valid database id starting with {id_str}!\n"
-                    f"Line: '{line.strip()}'"
-                )
+                logger.error(f"Please provide a valid database id starting with {id_str}!\n" f"Line: '{line.strip()}'")
                 sys.exit(1)
             ids = DatabaseResolver.expand_identifier(db_id)
             if not ids:
-                logger.error(
-                    f"No matches found for database id {db_id}!\nLine: '{line.strip()}'"
-                )
+                logger.error(f"No matches found for database id {db_id}!\nLine: '{line.strip()}'")
                 sys.exit(1)
             for accession in ids:
                 for row in ena_fetcher.open_experiment_table(accession):
diff --git a/bin/sra_runinfo_to_ftp.py b/bin/sra_runinfo_to_ftp.py
index d9400b2f..ef80ec80 100755
--- a/bin/sra_runinfo_to_ftp.py
+++ b/bin/sra_runinfo_to_ftp.py
@@ -62,10 +62,7 @@ def parse_sra_runinfo(file_in):
         reader = csv.DictReader(fin, delimiter="\t", skipinitialspace=True)
         header = list(reader.fieldnames)
         if missing := frozenset(columns).difference(frozenset(header)):
-            logger.critical(
-                f"The following expected columns are missing from {file_in}: "
-                f"{', '.join(missing)}."
-            )
+            logger.critical(f"The following expected columns are missing from {file_in}: " f"{', '.join(missing)}.")
             sys.exit(1)
         for row in reader:
             db_id = row["experiment_accession"]
@@ -73,14 +70,9 @@ def parse_sra_runinfo(file_in):
                 fq_files = row["fastq_ftp"].split(";")[-2:]
                 fq_md5 = row["fastq_md5"].split(";")[-2:]
                 if len(fq_files) == 1:
-                    assert fq_files[0].endswith(
-                        ".fastq.gz"
-                    ), f"Unexpected FastQ file format {file_in.name}."
+                    assert fq_files[0].endswith(".fastq.gz"), f"Unexpected FastQ file format {file_in.name}."
                     if row["library_layout"] != "SINGLE":
-                        logger.warning(
-                            f"The library layout '{row['library_layout']}' should be "
-                            f"'SINGLE'."
-                        )
+                        logger.warning(f"The library layout '{row['library_layout']}' should be " f"'SINGLE'.")
                     sample = {
                         "fastq_1": fq_files[0],
                         "fastq_2": None,
@@ -89,17 +81,10 @@ def parse_sra_runinfo(file_in):
                         "single_end": "true",
                     }
                 elif len(fq_files) == 2:
-                    assert fq_files[0].endswith(
-                        "_1.fastq.gz"
-                    ), f"Unexpected FastQ file format {file_in.name}."
-                    assert fq_files[1].endswith(
-                        "_2.fastq.gz"
-                    ), f"Unexpected FastQ file format {file_in.name}."
+                    assert fq_files[0].endswith("_1.fastq.gz"), f"Unexpected FastQ file format {file_in.name}."
+                    assert fq_files[1].endswith("_2.fastq.gz"), f"Unexpected FastQ file format {file_in.name}."
                     if row["library_layout"] != "PAIRED":
-                        logger.warning(
-                            f"The library layout '{row['library_layout']}' should be "
-                            f"'PAIRED'."
-                        )
+                        logger.warning(f"The library layout '{row['library_layout']}' should be " f"'PAIRED'.")
                     sample = {
                         "fastq_1": fq_files[0],
                         "fastq_2": fq_files[1],
@@ -124,8 +109,7 @@ def parse_sra_runinfo(file_in):
             else:
                 if sample in runinfo[db_id]:
                     logger.error(
-                        f"Input run info file contains duplicate rows!\n"
-                        f"{', '.join([row[col] for col in header])}"
+                        f"Input run info file contains duplicate rows!\n" f"{', '.join([row[col] for col in header])}"
                     )
                 else:
                     runinfo[db_id].append(sample)
@@ -146,9 +130,7 @@ def sra_runinfo_to_ftp(files_in, file_out):
                 logger.warning(f"Duplicate sample identifier found!\nID: '{db_id}'")
 
     # Create a combined header from all input files.
-    combined_header = header[0] + list(
-        set().union(chain.from_iterable(header)).difference(header[0])
-    )
+    combined_header = header[0] + list(set().union(chain.from_iterable(header)).difference(header[0]))
     combined_header.insert(0, "id")
 
     # Write samplesheet with paths to FastQ files and md5 sums.
@@ -159,7 +141,7 @@ def sra_runinfo_to_ftp(files_in, file_out):
             for db_id in sorted(samplesheet):
                 for idx, row in enumerate(samplesheet[db_id], start=1):
                     row["id"] = f"{db_id}"
-                    if 'run_accession' in row:
+                    if "run_accession" in row:
                         row["id"] = f"{db_id}_{row['run_accession']}"
                     writer.writerow(row)
 

From d67b3ef6eaf437c7a22da800fcb0d26f19d0a9a7 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 4 Nov 2022 10:19:08 +0000
Subject: [PATCH 228/852] Update regex for --input file extension

---
 nextflow_schema.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 4d02b3c5..435079b3 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -16,7 +16,7 @@
                     "type": "string",
                     "format": "file-path",
                     "mimetype": "text/csv",
-                    "pattern": "^\\S+\\.csv$",
+                    "pattern": "^\\S+\\.(csv|tsv|txt)$",
                     "schema": "assets/schema_input.json",
                     "fa_icon": "fas fa-file-excel",
                     "description": "File containing SRA/ENA/DDBJ identifiers one per line to download their associated metadata and FastQ files."

From 4747774e31434ac9688e668730f3517bab30d675 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 4 Nov 2022 10:59:03 +0000
Subject: [PATCH 229/852] Enable conda explicilty in profiles block

---
 nextflow.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nextflow.config b/nextflow.config
index 3f07ba06..f8f97ca3 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -72,6 +72,7 @@ profiles {
     debug { process.beforeScript = 'echo $HOSTNAME' }
     conda {
         params.enable_conda    = true
+        conda.enabled          = true
         docker.enabled         = false
         singularity.enabled    = false
         podman.enabled         = false

From 12e8b857b29bfeb37ff7d3841762190166832ef9 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 7 Nov 2022 11:48:22 +0000
Subject: [PATCH 230/852] Fix #114

---
 CHANGELOG.md                        |  5 +-
 modules/local/sra_to_samplesheet.nf | 26 ++++-----
 workflows/sra.nf                    | 86 ++++++++++++++++++-----------
 3 files changed, 71 insertions(+), 46 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 993bc934..679644f1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+- [#111](https://github.com/nf-core/fetchngs/issues/111) - Change input mimetype to csv
+- [#114](https://github.com/nf-core/fetchngs/issues/114) - Final samplesheet is not created when `--skip_fastq_download` is provided
+- [#118](https://github.com/nf-core/fetchngs/issues/118) - Allow input pattern validation for csv/tsv/txt
+- [#121](https://github.com/nf-core/fetchngs/issues/121) - Add `tower.yml` to render samplesheet as Report in Tower
 - Fetch `SRR` and `DRR` metadata from ENA API instead of NCBI API to bypass frequent breaking changes
 - Updated pipeline template to [nf-core/tools 2.6](https://github.com/nf-core/tools/releases/tag/2.6)
 
@@ -26,7 +30,6 @@ This downloads a text file called `SRR_Acc_List.txt` that can be directly provid
 
 ### Enhancements & fixes
 
-- [#121](https://github.com/nf-core/fetchngs/pull/123) - Add `tower.yml` to render Reports in Tower
 - [#97](https://github.com/nf-core/fetchngs/pull/97) - Add support for generating nf-core/taxprofiler compatible samplesheets.
 - [#99](https://github.com/nf-core/fetchngs/issues/99) - SRA_IDS_TO_RUNINFO fails due to bad request
 - Add `enum` field for `--nf_core_pipeline` to parameter schema so only accept supported pipelines are accepted
diff --git a/modules/local/sra_to_samplesheet.nf b/modules/local/sra_to_samplesheet.nf
index 4b448e89..6dce588b 100644
--- a/modules/local/sra_to_samplesheet.nf
+++ b/modules/local/sra_to_samplesheet.nf
@@ -6,9 +6,9 @@ process SRA_TO_SAMPLESHEET {
     memory 100.MB
 
     input:
-    tuple val(meta), path(fastq)
-    val   pipeline
-    val   mapping_fields
+    val meta
+    val pipeline
+    val mapping_fields
 
     output:
     tuple val(meta), path("*samplesheet.csv"), emit: samplesheet
@@ -20,19 +20,19 @@ process SRA_TO_SAMPLESHEET {
     //
 
     //  Remove custom keys needed to download the data
-    def meta_map = meta.clone()
-    meta_map.remove("id")
-    meta_map.remove("fastq_1")
-    meta_map.remove("fastq_2")
-    meta_map.remove("md5_1")
-    meta_map.remove("md5_2")
-    meta_map.remove("single_end")
+    def meta_clone = meta.clone()
+    meta_clone.remove("id")
+    meta_clone.remove("fastq_1")
+    meta_clone.remove("fastq_2")
+    meta_clone.remove("md5_1")
+    meta_clone.remove("md5_2")
+    meta_clone.remove("single_end")
 
     // Add relevant fields to the beginning of the map
     pipeline_map = [
         sample  : "${meta.id.split('_')[0..-2].join('_')}",
-        fastq_1 : "${params.outdir}/fastq/${fastq[0]}",
-        fastq_2 : meta.single_end ? '' : "${params.outdir}/fastq/${fastq[1]}"
+        fastq_1 : meta.fastq_1,
+        fastq_2 : meta.fastq_2
     ]
 
     // Add nf-core pipeline specific entries
@@ -43,7 +43,7 @@ process SRA_TO_SAMPLESHEET {
             pipeline_map << [ fasta: '' ]
         }
     }
-    pipeline_map << meta_map
+    pipeline_map << meta_clone
 
     // Create a samplesheet
     samplesheet  = pipeline_map.keySet().collect{ '"' + it + '"'}.join(",") + '\n'
diff --git a/workflows/sra.nf b/workflows/sra.nf
index ef654b2d..ebb15602 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -80,19 +80,27 @@ workflow SRA {
         .splitCsv(header:true, sep:'\t')
         .map {
             meta ->
-                meta.single_end = meta.single_end.toBoolean()
-                [ meta, [ meta.fastq_1, meta.fastq_2 ] ]
+                def meta_clone = meta.clone()
+                meta_clone.single_end = meta_clone.single_end.toBoolean()
+                return meta_clone
         }
         .unique()
-        .branch {
-            ftp: it[0].fastq_1  && !params.force_sratools_download
-            sra: !it[0].fastq_1 || params.force_sratools_download
-        }
-        .set { ch_sra_reads }
+        .set { ch_sra_metadata }
     ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first())
 
     if (!params.skip_fastq_download) {
 
+        ch_sra_metadata
+            .map { 
+                meta -> 
+                    [ meta, [ meta.fastq_1, meta.fastq_2 ] ] 
+            }
+            .branch {
+                ftp: it[0].fastq_1  && !params.force_sratools_download
+                sra: !it[0].fastq_1 || params.force_sratools_download
+            }
+            .set { ch_sra_reads }
+
         //
         // MODULE: If FTP link is provided in run information then download FastQ directly via FTP and validate with md5sums
         //
@@ -109,33 +117,47 @@ workflow SRA {
         )
         ch_versions = ch_versions.mix(SRAFASTQ.out.versions.first())
 
-        //
-        // MODULE: Stage FastQ files downloaded by SRA together and auto-create a samplesheet
-        //
-        SRA_TO_SAMPLESHEET (
-            SRA_FASTQ_FTP.out.fastq.mix(SRAFASTQ.out.reads),
-            params.nf_core_pipeline ?: '',
-            params.sample_mapping_fields
-        )
+        SRA_FASTQ_FTP
+            .out
+            .fastq
+            .mix(SRAFASTQ.out.reads)
+            .map { 
+                meta, fastq ->
+                    def reads = meta.single_end ? [ fastq ] : fastq
+                    def meta_clone = meta.clone()
+                    meta_clone.fastq_1 = reads[0] ? "${params.outdir}/fastq/${reads[0].getName()}" : ''
+                    meta_clone.fastq_2 = reads[1] && !meta.single_end ? "${params.outdir}/fastq/${reads[1].getName()}" : ''
+                    return meta_clone
+            }
+            .set { ch_sra_metadata }
+    }
 
-        //
-        // MODULE: Create a merged samplesheet across all samples for the pipeline
-        //
-        SRA_MERGE_SAMPLESHEET (
-            SRA_TO_SAMPLESHEET.out.samplesheet.collect{it[1]},
-            SRA_TO_SAMPLESHEET.out.mappings.collect{it[1]}
-        )
-        ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions)
+    //
+    // MODULE: Stage FastQ files downloaded by SRA together and auto-create a samplesheet
+    //
+    SRA_TO_SAMPLESHEET (
+        ch_sra_metadata,
+        params.nf_core_pipeline ?: '',
+        params.sample_mapping_fields
+    )
 
-        //
-        // MODULE: Create a MutiQC config file with sample name mappings
-        //
-        if (params.sample_mapping_fields) {
-            MULTIQC_MAPPINGS_CONFIG (
-                SRA_MERGE_SAMPLESHEET.out.mappings
-            )
-            ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions)
-        }
+    //
+    // MODULE: Create a merged samplesheet across all samples for the pipeline
+    //
+    SRA_MERGE_SAMPLESHEET (
+        SRA_TO_SAMPLESHEET.out.samplesheet.collect{it[1]},
+        SRA_TO_SAMPLESHEET.out.mappings.collect{it[1]}
+    )
+    ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions)
+
+    //
+    // MODULE: Create a MutiQC config file with sample name mappings
+    //
+    if (params.sample_mapping_fields) {
+        MULTIQC_MAPPINGS_CONFIG (
+            SRA_MERGE_SAMPLESHEET.out.mappings
+        )
+        ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions)
     }
 
     //

From 317262243aa5e120441ec05dadac0636cf8c86bc Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 7 Nov 2022 19:30:29 +0000
Subject: [PATCH 231/852] Fix #119

---
 CHANGELOG.md                                     |  3 ++-
 conf/modules.config                              | 13 +++----------
 modules/nf-core/sratools/fasterqdump/main.nf     | 16 ++++++++++------
 .../main.nf                                      |  2 +-
 .../meta.yml                                     |  3 ++-
 workflows/sra.nf                                 | 10 +++++-----
 6 files changed, 23 insertions(+), 24 deletions(-)
 rename subworkflows/nf-core/{srafastq => fastq_download_prefetch_fasterqdump_sratools}/main.nf (96%)
 rename subworkflows/nf-core/{srafastq => fastq_download_prefetch_fasterqdump_sratools}/meta.yml (93%)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 679644f1..e12fa79a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,13 +3,14 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[1.8](https://github.com/nf-core/fetchngs/releases/tag/1.8)] - 2022-11-07
+## [[1.8](https://github.com/nf-core/fetchngs/releases/tag/1.8)] - 2022-11-08
 
 ### Enhancements & fixes
 
 - [#111](https://github.com/nf-core/fetchngs/issues/111) - Change input mimetype to csv
 - [#114](https://github.com/nf-core/fetchngs/issues/114) - Final samplesheet is not created when `--skip_fastq_download` is provided
 - [#118](https://github.com/nf-core/fetchngs/issues/118) - Allow input pattern validation for csv/tsv/txt
+- [#119](https://github.com/nf-core/fetchngs/issues/119) - `--force_sratools_download` results in different fastq names compared to FTP download 
 - [#121](https://github.com/nf-core/fetchngs/issues/121) - Add `tower.yml` to render samplesheet as Report in Tower
 - Fetch `SRR` and `DRR` metadata from ENA API instead of NCBI API to bypass frequent breaking changes
 - Updated pipeline template to [nf-core/tools 2.6](https://github.com/nf-core/tools/releases/tag/2.6)
diff --git a/conf/modules.config b/conf/modules.config
index 82a5f75c..c42f4d60 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -78,16 +78,9 @@ if (params.input_type == 'sra') {
 
         withName: SRATOOLS_FASTERQDUMP {
             publishDir = [
-                [
-                    path: { "${params.outdir}/fastq" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.fastq.gz"
-                ],
-                [
-                    path: { "${params.outdir}/fastq/md5" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.md5"
-                ]
+                path: { "${params.outdir}/fastq" },
+                mode: params.publish_dir_mode,
+                pattern: "*.fastq.gz"
             ]
         }
 
diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf
index 18f46e51..16454a54 100644
--- a/modules/nf-core/sratools/fasterqdump/main.nf
+++ b/modules/nf-core/sratools/fasterqdump/main.nf
@@ -12,8 +12,8 @@ process SRATOOLS_FASTERQDUMP {
     path ncbi_settings
 
     output:
-    tuple val(meta), path(output), emit: reads
-    path "versions.yml"          , emit: versions
+    tuple val(meta), path(fastq), emit: reads
+    path "versions.yml"         , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -21,16 +21,20 @@ process SRATOOLS_FASTERQDUMP {
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
-    // Paired-end data extracted by fasterq-dump (--split-3 the default) always creates
-    // *_1.fastq *_2.fastq files but sometimes also an additional *.fastq file
-    // for unpaired reads which we ignore here.
-    output = meta.single_end ? '*.fastq.gz' : '*_{1,2}.fastq.gz'
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    // WARNING: Paired-end data extracted by fasterq-dump (--split-3 the default) 
+        // always creates *_1.fastq *_2.fastq files but sometimes also
+        // an additional *.fastq file for unpaired reads which we ignore here.
+    fastq = meta.single_end ? '*.fastq.gz' : '*_{1,2}.fastq.gz'
+    def outfile = meta.single_end ? "${prefix}.fastq" : prefix
     """
     export NCBI_SETTINGS="\$PWD/${ncbi_settings}"
 
     fasterq-dump \\
         $args \\
         --threads $task.cpus \\
+        --outfile $outfile \\
         ${sra.name}
 
     pigz \\
diff --git a/subworkflows/nf-core/srafastq/main.nf b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf
similarity index 96%
rename from subworkflows/nf-core/srafastq/main.nf
rename to subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf
index 580fef18..cacde6f5 100644
--- a/subworkflows/nf-core/srafastq/main.nf
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf
@@ -5,7 +5,7 @@ include { SRATOOLS_FASTERQDUMP        } from '../../../modules/nf-core/sratools/
 /**
  * Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
  */
-workflow SRAFASTQ {
+workflow FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS {
     take:
     sra_ids  // channel: [ val(meta), val(id) ]
 
diff --git a/subworkflows/nf-core/srafastq/meta.yml b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml
similarity index 93%
rename from subworkflows/nf-core/srafastq/meta.yml
rename to subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml
index 873ccaca..f032628b 100644
--- a/subworkflows/nf-core/srafastq/meta.yml
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml
@@ -1,4 +1,4 @@
-name: sra_fastq
+name: fastq_download_prefetch_fasterqdump_sratools
 description: Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
 keywords:
   - SRA
@@ -38,3 +38,4 @@ output:
       pattern: "versions.yml"
 authors:
   - "@Midnighter"
+  - "@drpatelh"
diff --git a/workflows/sra.nf b/workflows/sra.nf
index ebb15602..9f38e7f8 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -26,8 +26,6 @@ include { SRA_TO_SAMPLESHEET      } from '../modules/local/sra_to_samplesheet'
 include { SRA_MERGE_SAMPLESHEET   } from '../modules/local/sra_merge_samplesheet'
 include { MULTIQC_MAPPINGS_CONFIG } from '../modules/local/multiqc_mappings_config'
 
-include { SRAFASTQ                } from '../subworkflows/nf-core/srafastq/main'
-
 /*
 ========================================================================================
     IMPORT NF-CORE MODULES/SUBWORKFLOWS
@@ -36,6 +34,8 @@ include { SRAFASTQ                } from '../subworkflows/nf-core/srafastq/main'
 
 include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
 
+include { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS } from '../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main'
+
 /*
 ========================================================================================
     RUN MAIN WORKFLOW
@@ -112,15 +112,15 @@ workflow SRA {
         //
         // SUBWORKFLOW: Download sequencing reads without FTP links using sra-tools.
         //
-        SRAFASTQ (
+        FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS (
             ch_sra_reads.sra.map { meta, reads -> [ meta, meta.run_accession ] }
         )
-        ch_versions = ch_versions.mix(SRAFASTQ.out.versions.first())
+        ch_versions = ch_versions.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.versions.first())
 
         SRA_FASTQ_FTP
             .out
             .fastq
-            .mix(SRAFASTQ.out.reads)
+            .mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads)
             .map { 
                 meta, fastq ->
                     def reads = meta.single_end ? [ fastq ] : fastq

From 0ff28b46c324397ab3013ca41053310b626535ff Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 7 Nov 2022 19:31:02 +0000
Subject: [PATCH 232/852] Bump pipeline version to 1.8

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index f8f97ca3..633a0fb2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -174,7 +174,7 @@ manifest {
     description     = 'Pipeline to fetch metadata and raw FastQ files from public databases'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
-    version         = '1.8dev'
+    version         = '1.8'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
 

From 53858ba59dee0bc79ff146aa1382d2b2e5433e24 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 7 Nov 2022 21:20:11 +0000
Subject: [PATCH 233/852] Re-install subworkflow from nf-core/modules

---
 modules.json                                     |  8 ++++++++
 .../main.nf                                      | 16 ++++++++--------
 .../meta.yml                                     |  2 +-
 3 files changed, 17 insertions(+), 9 deletions(-)

diff --git a/modules.json b/modules.json
index c687eccd..fc957282 100644
--- a/modules.json
+++ b/modules.json
@@ -22,6 +22,14 @@
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     }
                 }
+            },
+            "subworkflows": {
+                "nf-core": {
+                    "fastq_download_prefetch_fasterqdump_sratools": {
+                        "branch": "master",
+                        "git_sha": "03711bcb7fa2a7088eb54abb1fca326d30e602c2"
+                    }
+                }
             }
         }
     }
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf
index cacde6f5..1e1d0d7b 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf
@@ -2,12 +2,12 @@ include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../modules/nf-core/custom/sr
 include { SRATOOLS_PREFETCH           } from '../../../modules/nf-core/sratools/prefetch/main'
 include { SRATOOLS_FASTERQDUMP        } from '../../../modules/nf-core/sratools/fasterqdump/main'
 
-/**
- * Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
- */
+//
+// Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
+//
 workflow FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS {
     take:
-    sra_ids  // channel: [ val(meta), val(id) ]
+    ch_sra_ids  // channel: [ val(meta), val(id) ]
 
     main:
 
@@ -18,19 +18,19 @@ workflow FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS {
     //
     CUSTOM_SRATOOLSNCBISETTINGS()
     def settings = CUSTOM_SRATOOLSNCBISETTINGS.out.ncbi_settings  // value channel: path(settings)
-    ch_versions = ch_versions.mix( CUSTOM_SRATOOLSNCBISETTINGS.out.versions )
+    ch_versions = ch_versions.mix(CUSTOM_SRATOOLSNCBISETTINGS.out.versions)
 
     //
     // Prefetch sequencing reads in SRA format.
     //
-    SRATOOLS_PREFETCH ( sra_ids, settings )
-    ch_versions = ch_versions.mix( SRATOOLS_PREFETCH.out.versions.first() )
+    SRATOOLS_PREFETCH ( ch_sra_ids, settings )
+    ch_versions = ch_versions.mix(SRATOOLS_PREFETCH.out.versions.first())
 
     //
     // Convert the SRA format into one or more compressed FASTQ files.
     //
     SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra, settings )
-    ch_versions = ch_versions.mix( SRATOOLS_FASTERQDUMP.out.versions.first() )
+    ch_versions = ch_versions.mix(SRATOOLS_FASTERQDUMP.out.versions.first())
 
     emit:
     reads    = SRATOOLS_FASTERQDUMP.out.reads  // channel: [ val(meta), [ reads ] ]
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml
index f032628b..c385ca21 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml
@@ -4,7 +4,7 @@ keywords:
   - SRA
   - NCBI
   - sequencing
-  - FASTQ
+  - fastq
   - prefetch
   - fasterq-dump
 modules:

From c791a37cd0fed39703394e652eb3a5c602654a7d Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 7 Nov 2022 21:24:53 +0000
Subject: [PATCH 234/852] Update sratools/fasterqdump manually

---
 CHANGELOG.md                                 | 2 +-
 modules.json                                 | 2 +-
 modules/nf-core/sratools/fasterqdump/main.nf | 6 +++---
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e12fa79a..b57bfefc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,7 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#111](https://github.com/nf-core/fetchngs/issues/111) - Change input mimetype to csv
 - [#114](https://github.com/nf-core/fetchngs/issues/114) - Final samplesheet is not created when `--skip_fastq_download` is provided
 - [#118](https://github.com/nf-core/fetchngs/issues/118) - Allow input pattern validation for csv/tsv/txt
-- [#119](https://github.com/nf-core/fetchngs/issues/119) - `--force_sratools_download` results in different fastq names compared to FTP download 
+- [#119](https://github.com/nf-core/fetchngs/issues/119) - `--force_sratools_download` results in different fastq names compared to FTP download
 - [#121](https://github.com/nf-core/fetchngs/issues/121) - Add `tower.yml` to render samplesheet as Report in Tower
 - Fetch `SRR` and `DRR` metadata from ENA API instead of NCBI API to bypass frequent breaking changes
 - Updated pipeline template to [nf-core/tools 2.6](https://github.com/nf-core/tools/releases/tag/2.6)
diff --git a/modules.json b/modules.json
index fc957282..512b3fea 100644
--- a/modules.json
+++ b/modules.json
@@ -15,7 +15,7 @@
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "03711bcb7fa2a7088eb54abb1fca326d30e602c2"
                     },
                     "sratools/prefetch": {
                         "branch": "master",
diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf
index 16454a54..1ffb21f0 100644
--- a/modules/nf-core/sratools/fasterqdump/main.nf
+++ b/modules/nf-core/sratools/fasterqdump/main.nf
@@ -23,9 +23,9 @@ process SRATOOLS_FASTERQDUMP {
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
-    // WARNING: Paired-end data extracted by fasterq-dump (--split-3 the default) 
-        // always creates *_1.fastq *_2.fastq files but sometimes also
-        // an additional *.fastq file for unpaired reads which we ignore here.
+    // WARNING: Paired-end data extracted by fasterq-dump (--split-3 the default)
+    // always creates *_1.fastq *_2.fastq files but sometimes also
+    // an additional *.fastq file for unpaired reads which we ignore here.
     fastq = meta.single_end ? '*.fastq.gz' : '*_{1,2}.fastq.gz'
     def outfile = meta.single_end ? "${prefix}.fastq" : prefix
     """

From fa869e98f7c6fdc38fabc96ac52bac30904c0b3a Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 8 Nov 2022 09:51:22 +0000
Subject: [PATCH 235/852] Bump pipeline version to 1.9dev

---
 CHANGELOG.md    | 4 ++++
 nextflow.config | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b57bfefc..5fd50bd1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unpublished Version / DEV]
+
+### Enhancements & fixes
+
 ## [[1.8](https://github.com/nf-core/fetchngs/releases/tag/1.8)] - 2022-11-08
 
 ### Enhancements & fixes
diff --git a/nextflow.config b/nextflow.config
index 633a0fb2..94cc7de4 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -174,7 +174,7 @@ manifest {
     description     = 'Pipeline to fetch metadata and raw FastQ files from public databases'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
-    version         = '1.8'
+    version         = '1.9dev'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
 

From afd22a4581d52f513db355e4f61b5e1e918e0721 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 20 Dec 2022 17:58:18 +0000
Subject: [PATCH 236/852] Update all modules and subworkflows

---
 modules.json                                           | 10 ++++++----
 modules/local/multiqc_mappings_config.nf               |  2 +-
 modules/local/sra_fastq_ftp.nf                         |  2 +-
 modules/local/sra_ids_to_runinfo.nf                    |  2 +-
 modules/local/sra_merge_samplesheet.nf                 |  2 +-
 modules/local/sra_runinfo_to_ftp.nf                    |  2 +-
 modules/local/synapse_get.nf                           |  2 +-
 modules/local/synapse_list.nf                          |  2 +-
 modules/local/synapse_merge_samplesheet.nf             |  2 +-
 modules/local/synapse_show.nf                          |  2 +-
 .../templates/dumpsoftwareversions.py                  |  3 +--
 modules/nf-core/custom/sratoolsncbisettings/main.nf    |  2 +-
 modules/nf-core/sratools/fasterqdump/main.nf           |  2 +-
 modules/nf-core/sratools/prefetch/main.nf              |  2 +-
 14 files changed, 19 insertions(+), 18 deletions(-)

diff --git a/modules.json b/modules.json
index e125fc48..c8cd187a 100644
--- a/modules.json
+++ b/modules.json
@@ -13,16 +13,17 @@
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"]
+                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "03711bcb7fa2a7088eb54abb1fca326d30e602c2"
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/prefetch": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"]
+                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     }
                 }
             },
@@ -30,7 +31,8 @@
                 "nf-core": {
                     "fastq_download_prefetch_fasterqdump_sratools": {
                         "branch": "master",
-                        "git_sha": "03711bcb7fa2a7088eb54abb1fca326d30e602c2"
+                        "git_sha": "03711bcb7fa2a7088eb54abb1fca326d30e602c2",
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }
diff --git a/modules/local/multiqc_mappings_config.nf b/modules/local/multiqc_mappings_config.nf
index 31f06dae..4f6c95bd 100644
--- a/modules/local/multiqc_mappings_config.nf
+++ b/modules/local/multiqc_mappings_config.nf
@@ -1,7 +1,7 @@
 
 process MULTIQC_MAPPINGS_CONFIG {
 
-    conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
+    conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
         'quay.io/biocontainers/python:3.9--1' }"
diff --git a/modules/local/sra_fastq_ftp.nf b/modules/local/sra_fastq_ftp.nf
index 5e4f6a05..464a327e 100644
--- a/modules/local/sra_fastq_ftp.nf
+++ b/modules/local/sra_fastq_ftp.nf
@@ -4,7 +4,7 @@ process SRA_FASTQ_FTP {
     label 'process_low'
     label 'error_retry'
 
-    conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
+    conda "bioconda::sra-tools=2.11.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' :
         'quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
diff --git a/modules/local/sra_ids_to_runinfo.nf b/modules/local/sra_ids_to_runinfo.nf
index 57fdb10e..49c83554 100644
--- a/modules/local/sra_ids_to_runinfo.nf
+++ b/modules/local/sra_ids_to_runinfo.nf
@@ -3,7 +3,7 @@ process SRA_IDS_TO_RUNINFO {
     tag "$id"
     label 'error_retry'
 
-    conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
+    conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
         'quay.io/biocontainers/python:3.9--1' }"
diff --git a/modules/local/sra_merge_samplesheet.nf b/modules/local/sra_merge_samplesheet.nf
index ca9c0068..4b94a823 100644
--- a/modules/local/sra_merge_samplesheet.nf
+++ b/modules/local/sra_merge_samplesheet.nf
@@ -1,6 +1,6 @@
 process SRA_MERGE_SAMPLESHEET {
 
-    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
         'ubuntu:20.04' }"
diff --git a/modules/local/sra_runinfo_to_ftp.nf b/modules/local/sra_runinfo_to_ftp.nf
index 13fa6c3e..3a060f7b 100644
--- a/modules/local/sra_runinfo_to_ftp.nf
+++ b/modules/local/sra_runinfo_to_ftp.nf
@@ -1,7 +1,7 @@
 
 process SRA_RUNINFO_TO_FTP {
 
-    conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
+    conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
         'quay.io/biocontainers/python:3.9--1' }"
diff --git a/modules/local/synapse_get.nf b/modules/local/synapse_get.nf
index b494bafd..f43e4d5e 100644
--- a/modules/local/synapse_get.nf
+++ b/modules/local/synapse_get.nf
@@ -4,7 +4,7 @@ process SYNAPSE_GET {
     label 'process_low'
     label 'error_retry'
 
-    conda (params.enable_conda ? "bioconda::synapseclient=2.6.0" : null)
+    conda "bioconda::synapseclient=2.6.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/synapseclient:2.6.0--pyh5e36f6f_0' :
         'quay.io/biocontainers/synapseclient:2.6.0--pyh5e36f6f_0' }"
diff --git a/modules/local/synapse_list.nf b/modules/local/synapse_list.nf
index c3861bff..f42357ab 100644
--- a/modules/local/synapse_list.nf
+++ b/modules/local/synapse_list.nf
@@ -3,7 +3,7 @@ process SYNAPSE_LIST {
     tag "$id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::synapseclient=2.6.0" : null)
+    conda "bioconda::synapseclient=2.6.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/synapseclient:2.6.0--pyh5e36f6f_0' :
         'quay.io/biocontainers/synapseclient:2.6.0--pyh5e36f6f_0' }"
diff --git a/modules/local/synapse_merge_samplesheet.nf b/modules/local/synapse_merge_samplesheet.nf
index 68bfd68b..f46a1fbf 100644
--- a/modules/local/synapse_merge_samplesheet.nf
+++ b/modules/local/synapse_merge_samplesheet.nf
@@ -1,7 +1,7 @@
 
 process SYNAPSE_MERGE_SAMPLESHEET {
 
-    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
         'ubuntu:20.04' }"
diff --git a/modules/local/synapse_show.nf b/modules/local/synapse_show.nf
index a7a12767..0bd6cc12 100644
--- a/modules/local/synapse_show.nf
+++ b/modules/local/synapse_show.nf
@@ -3,7 +3,7 @@ process SYNAPSE_SHOW {
     tag "$id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::synapseclient=2.6.0" : null)
+    conda "bioconda::synapseclient=2.6.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/synapseclient:2.6.0--pyh5e36f6f_0' :
         'quay.io/biocontainers/synapseclient:2.6.0--pyh5e36f6f_0' }"
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
index e55b8d43..da033408 100755
--- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
@@ -4,11 +4,10 @@
 """Provide functions to merge multiple versions.yml files."""
 
 
+import yaml
 import platform
 from textwrap import dedent
 
-import yaml
-
 
 def _make_versions_html(versions):
     """Generate a tabular HTML output of all versions for MultiQC."""
diff --git a/modules/nf-core/custom/sratoolsncbisettings/main.nf b/modules/nf-core/custom/sratoolsncbisettings/main.nf
index 21bf3005..36be10d3 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/main.nf
+++ b/modules/nf-core/custom/sratoolsncbisettings/main.nf
@@ -2,7 +2,7 @@ process CUSTOM_SRATOOLSNCBISETTINGS {
     tag 'ncbi-settings'
     label 'process_low'
 
-    conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
+    conda "bioconda::sra-tools=2.11.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' :
         'quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf
index 1ffb21f0..ca5ee763 100644
--- a/modules/nf-core/sratools/fasterqdump/main.nf
+++ b/modules/nf-core/sratools/fasterqdump/main.nf
@@ -2,7 +2,7 @@ process SRATOOLS_FASTERQDUMP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0 conda-forge::pigz=2.6' : null)
+    conda "bioconda::sra-tools=2.11.0 conda-forge::pigz=2.6"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' :
         'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' }"
diff --git a/modules/nf-core/sratools/prefetch/main.nf b/modules/nf-core/sratools/prefetch/main.nf
index 3426ae12..57e8a3c9 100644
--- a/modules/nf-core/sratools/prefetch/main.nf
+++ b/modules/nf-core/sratools/prefetch/main.nf
@@ -2,7 +2,7 @@ process SRATOOLS_PREFETCH {
     tag "$id"
     label 'process_low'
 
-    conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
+    conda "bioconda::sra-tools=2.11.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' :
         'quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"

From e4a30d2a4c0160f70e2b5f6e1bf9fc93e703ff66 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 20 Dec 2022 20:01:33 +0000
Subject: [PATCH 237/852] Add --nf_core_rnaseq_strandedness and support for
 nf-core/atacseq

---
 CHANGELOG.md                            |  3 ++
 README.md                               |  3 +-
 docs/usage.md                           |  5 +-
 modules/local/sra_to_samplesheet.nf     |  5 +-
 modules/local/synapse_to_samplesheet.nf |  7 ++-
 nextflow.config                         | 61 +++++++++++++------------
 nextflow_schema.json                    | 35 ++++++++++++--
 workflows/sra.nf                        |  1 +
 workflows/synapse.nf                    |  3 +-
 9 files changed, 83 insertions(+), 40 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c80fbebf..04968c93 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,7 +7,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+- Bumped minimum Nextflow version from `21.10.3` -> `22.10.1`
 - Updated pipeline template to [nf-core/tools 2.7.2](https://github.com/nf-core/tools/releases/tag/2.7.2)
+- Added support for generating nf-core/atacseq compatible samplesheets
+- Added `--nf_core_rnaseq_strandedness` parameter to specify value for `strandedness` entry added to samplesheet created when using `--nf_core_pipeline rnaseq`. The default is `auto` which can be used with nf-core/rnaseq v3.10 onwards to auto-detect strandedness during the pipeline execution.
 
 ## [[1.8](https://github.com/nf-core/fetchngs/releases/tag/1.8)] - 2022-11-08
 
diff --git a/README.md b/README.md
index 161d0218..fdc60a60 100644
--- a/README.md
+++ b/README.md
@@ -55,10 +55,11 @@ This downloads a text file called `SRR_Acc_List.txt` that can be directly provid
 The columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include:
 
 - [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input)
+- [nf-core/atacseq](https://nf-co.re/atacseq/usage#samplesheet-input)
 - Ilumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format)
 - [nf-core/taxprofiler](https://nf-co.re/nf-core/taxprofiler)
 
-You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core.
+See [usage docs](https://nf-co.re/fetchngs/1.8/usage#samplesheet-format) for more details.
 
 ## Quick Start
 
diff --git a/docs/usage.md b/docs/usage.md
index f78879d4..9172b403 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -58,10 +58,13 @@ The final sample information for the FastQ files used for samplesheet generation
 As a bonus, the columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include:
 
 - [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input)
+- [nf-core/atacseq](https://nf-co.re/atacseq/usage#samplesheet-input)
 - Ilumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format)
 - [nf-core/taxprofiler](https://nf-co.re/nf-core/taxprofiler)
 
-You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core. It is highly recommended that you double-check that all of the identifiers you defined using `--input` are represented in the samplesheet. Also, public databases don't reliably hold information such as strandedness information so you may need to amend these entries too if for example your samplesheet was created by providing `--nf_core_pipeline rnaseq`.
+You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core. It is highly recommended that you double-check that all of the identifiers required by the downstream nf-core pipeline are accurately represented in the samplesheet. For example, the nf-core/atacseq pipeline requires a `replicate` column to be provided in it's input samplehsheet, however, public databases don't reliably hold information regarding replicates so you may need to amend these entries if your samplesheet was created by providing `--nf_core_pipeline atacseq`.
+
+From v1.9 of this pipeline the default `strandedness` in the output samplesheet will be set to `auto` when using `--nf_core_pipeline rnaseq`. This will only work with v3.10 onwards of nf-core/rnaseq which permits the auto-detection of strandedness during the pipeline execution. You can change this behaviour with the `--nf_core_rnaseq_strandedness` parameter which is set to `auto` by default.
 
 ### Bypass `FTP` data download
 
diff --git a/modules/local/sra_to_samplesheet.nf b/modules/local/sra_to_samplesheet.nf
index 6dce588b..92edf5df 100644
--- a/modules/local/sra_to_samplesheet.nf
+++ b/modules/local/sra_to_samplesheet.nf
@@ -8,6 +8,7 @@ process SRA_TO_SAMPLESHEET {
     input:
     val meta
     val pipeline
+    val strandedness
     val mapping_fields
 
     output:
@@ -38,7 +39,9 @@ process SRA_TO_SAMPLESHEET {
     // Add nf-core pipeline specific entries
     if (pipeline) {
         if (pipeline == 'rnaseq') {
-            pipeline_map << [ strandedness: 'unstranded' ]
+            pipeline_map << [ strandedness: strandedness ]
+        } else if (pipeline == 'atacseq') {
+            pipeline_map << [ replicate: 1 ]
         } else if (pipeline == 'taxprofiler') {
             pipeline_map << [ fasta: '' ]
         }
diff --git a/modules/local/synapse_to_samplesheet.nf b/modules/local/synapse_to_samplesheet.nf
index 2e7945ed..393203de 100644
--- a/modules/local/synapse_to_samplesheet.nf
+++ b/modules/local/synapse_to_samplesheet.nf
@@ -8,6 +8,7 @@ process SYNAPSE_TO_SAMPLESHEET {
     input:
     tuple val(meta), path(fastq)
     val pipeline
+    val strandedness
 
     output:
     tuple val(meta), path("*.csv"), emit: samplesheet
@@ -35,7 +36,11 @@ process SYNAPSE_TO_SAMPLESHEET {
     // Add nf-core pipeline specific entries
     if (pipeline) {
         if (pipeline == 'rnaseq') {
-            pipeline_map << [ strandedness: 'unstranded' ]
+            pipeline_map << [ strandedness: strandedness ]
+        } else if (pipeline == 'atacseq') {
+            pipeline_map << [ replicate: 1 ]
+        } else if (pipeline == 'taxprofiler') {
+            pipeline_map << [ fasta: '' ]
         }
     }
     pipeline_map << meta_map
diff --git a/nextflow.config b/nextflow.config
index 0dfff0e4..c212bcd3 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -10,43 +10,44 @@
 params {
 
     // Input options
-    input                      = null
-    input_type                 = 'sra'
-    nf_core_pipeline           = null
-    ena_metadata_fields        = null
-    sample_mapping_fields      = 'experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description,description'
-    synapse_config             = null
-    force_sratools_download    = false
-    skip_fastq_download        = false
+    input                       = null
+    input_type                  = 'sra'
+    nf_core_pipeline            = null
+    nf_core_rnaseq_strandedness = 'auto'
+    ena_metadata_fields         = null
+    sample_mapping_fields       = 'experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description,description'
+    synapse_config              = null
+    force_sratools_download     = false
+    skip_fastq_download         = false
 
     // Boilerplate options
-    outdir                     = null
-    tracedir                   = "${params.outdir}/pipeline_info"
-    publish_dir_mode           = 'copy'
-    email                      = null
-    email_on_fail              = null
-    plaintext_email            = false
-    monochrome_logs            = false
-    hook_url                   = null
-    help                       = false
-    version                    = false
-    validate_params            = true
-    show_hidden_params         = false
-    schema_ignore_params       = 'genomes,igenomes_base'
+    outdir                      = null
+    tracedir                    = "${params.outdir}/pipeline_info"
+    publish_dir_mode            = 'copy'
+    email                       = null
+    email_on_fail               = null
+    plaintext_email             = false
+    monochrome_logs             = false
+    hook_url                    = null
+    help                        = false
+    version                     = false
+    validate_params             = true
+    show_hidden_params          = false
+    schema_ignore_params        = 'genomes,igenomes_base'
 
     // Config options
-    custom_config_version      = 'master'
-    custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
-    config_profile_description = null
-    config_profile_contact     = null
-    config_profile_url         = null
-    config_profile_name        = null
+    custom_config_version       = 'master'
+    custom_config_base          = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
+    config_profile_description  = null
+    config_profile_contact      = null
+    config_profile_url          = null
+    config_profile_name         = null
 
     // Max resource options
     // Defaults only, expecting to be overwritten
-    max_memory                 = '128.GB'
-    max_cpus                   = 16
-    max_time                   = '240.h'
+    max_memory                  = '128.GB'
+    max_cpus                    = 16
+    max_time                    = '240.h'
 
 }
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index c7e223bc..278a58a1 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -10,7 +10,10 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["input", "outdir"],
+            "required": [
+                "input",
+                "outdir"
+            ],
             "properties": {
                 "input": {
                     "type": "string",
@@ -26,7 +29,10 @@
                     "default": "sra",
                     "description": "Specifies the type of identifier provided via `--input` - available options are 'sra' and 'synapse'.",
                     "fa_icon": "fas fa-keyboard",
-                    "enum": ["sra", "synapse"]
+                    "enum": [
+                        "sra",
+                        "synapse"
+                    ]
                 },
                 "ena_metadata_fields": {
                     "type": "string",
@@ -43,8 +49,20 @@
                 "nf_core_pipeline": {
                     "type": "string",
                     "fa_icon": "fab fa-apple",
-                    "description": "Name of supported nf-core pipeline e.g.  'rnaseq'. A samplesheet for direct use with the pipeline will be created with the appropriate columns.",
-                    "enum": ["rnaseq", "viralrecon", "taxprofiler"]
+                    "description": "Name of supported nf-core pipeline e.g. 'rnaseq'. A samplesheet for direct use with the pipeline will be created with the appropriate columns.",
+                    "enum": [
+                        "rnaseq",
+                        "atacseq",
+                        "viralrecon",
+                        "taxprofiler"
+                    ]
+                },
+                "nf_core_rnaseq_strandedness": {
+                    "type": "string",
+                    "fa_icon": "fas fa-car",
+                    "description": "Value for 'strandedness' entry added to samplesheet created when using '--nf_core_pipeline rnaseq'.",
+                    "help_text": "The default is 'auto' which can be used with nf-core/rnaseq v3.10 onwards to auto-detect strandedness during the pipeline execution.",
+                    "default": "auto"
                 },
                 "force_sratools_download": {
                     "type": "boolean",
@@ -186,7 +204,14 @@
                     "description": "Method used to save pipeline results to output directory.",
                     "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                     "fa_icon": "fas fa-copy",
-                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
+                    "enum": [
+                        "symlink",
+                        "rellink",
+                        "link",
+                        "copy",
+                        "copyNoFollow",
+                        "move"
+                    ],
                     "hidden": true
                 },
                 "email_on_fail": {
diff --git a/workflows/sra.nf b/workflows/sra.nf
index 9f38e7f8..1085598b 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -138,6 +138,7 @@ workflow SRA {
     SRA_TO_SAMPLESHEET (
         ch_sra_metadata,
         params.nf_core_pipeline ?: '',
+        params.nf_core_rnaseq_strandedness ?: 'auto',
         params.sample_mapping_fields
     )
 
diff --git a/workflows/synapse.nf b/workflows/synapse.nf
index 1203056a..f2138a60 100644
--- a/workflows/synapse.nf
+++ b/workflows/synapse.nf
@@ -115,7 +115,8 @@ workflow SYNAPSE {
     //
     SYNAPSE_TO_SAMPLESHEET (
         ch_fastq,
-        params.nf_core_pipeline ?: ''
+        params.nf_core_pipeline ?: '',
+        params.nf_core_rnaseq_strandedness ?: 'auto'
     )
 
     //

From b50e1f64728f51a7a1d12c6f6ce2a00db8bef99f Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 20 Dec 2022 20:02:46 +0000
Subject: [PATCH 238/852] Bump pipeline version to 1.9

---
 CHANGELOG.md    | 2 +-
 nextflow.config | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 04968c93..37f9ea6d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unpublished Version / DEV]
+## [[1.9](https://github.com/nf-core/rnaseq/releases/tag/1.9)] - 2022-12-21
 
 ### Enhancements & fixes
 
diff --git a/nextflow.config b/nextflow.config
index c212bcd3..d6686ae4 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -177,7 +177,7 @@ manifest {
     description     = """Pipeline to fetch metadata and raw FastQ files from public databases"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '1.9dev'
+    version         = '1.9'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
 

From 4f84832800e7c8ca1819d47efbddff8d7248e682 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 20 Dec 2022 21:52:58 +0000
Subject: [PATCH 239/852] Fix prettier

---
 nextflow_schema.json | 26 ++++----------------------
 1 file changed, 4 insertions(+), 22 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 278a58a1..696914e4 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -10,10 +10,7 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": [
-                "input",
-                "outdir"
-            ],
+            "required": ["input", "outdir"],
             "properties": {
                 "input": {
                     "type": "string",
@@ -29,10 +26,7 @@
                     "default": "sra",
                     "description": "Specifies the type of identifier provided via `--input` - available options are 'sra' and 'synapse'.",
                     "fa_icon": "fas fa-keyboard",
-                    "enum": [
-                        "sra",
-                        "synapse"
-                    ]
+                    "enum": ["sra", "synapse"]
                 },
                 "ena_metadata_fields": {
                     "type": "string",
@@ -50,12 +44,7 @@
                     "type": "string",
                     "fa_icon": "fab fa-apple",
                     "description": "Name of supported nf-core pipeline e.g. 'rnaseq'. A samplesheet for direct use with the pipeline will be created with the appropriate columns.",
-                    "enum": [
-                        "rnaseq",
-                        "atacseq",
-                        "viralrecon",
-                        "taxprofiler"
-                    ]
+                    "enum": ["rnaseq", "atacseq", "viralrecon", "taxprofiler"]
                 },
                 "nf_core_rnaseq_strandedness": {
                     "type": "string",
@@ -204,14 +193,7 @@
                     "description": "Method used to save pipeline results to output directory.",
                     "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                     "fa_icon": "fas fa-copy",
-                    "enum": [
-                        "symlink",
-                        "rellink",
-                        "link",
-                        "copy",
-                        "copyNoFollow",
-                        "move"
-                    ],
+                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
                     "hidden": true
                 },
                 "email_on_fail": {

From 4f516556abd9af888eb9e747d16c39ed451c1153 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Wed, 21 Dec 2022 12:15:14 +0000
Subject: [PATCH 240/852] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 37f9ea6d..54242118 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[1.9](https://github.com/nf-core/rnaseq/releases/tag/1.9)] - 2022-12-21
+## [[1.9](https://github.com/nf-core/fetchngs/releases/tag/1.9)] - 2022-12-21
 
 ### Enhancements & fixes
 

From d47b62035b0e8ae0d43c21436de82dbf53ebfec0 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 21 Dec 2022 15:41:03 +0000
Subject: [PATCH 241/852] Bump pipeline version to 1.10dev

---
 CHANGELOG.md    | 4 ++++
 nextflow.config | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 54242118..6765ac12 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unpublished Version / DEV]
+
+### Enhancements & fixes
+
 ## [[1.9](https://github.com/nf-core/fetchngs/releases/tag/1.9)] - 2022-12-21
 
 ### Enhancements & fixes
diff --git a/nextflow.config b/nextflow.config
index d6686ae4..1ead02d0 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -177,7 +177,7 @@ manifest {
     description     = """Pipeline to fetch metadata and raw FastQ files from public databases"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '1.9'
+    version         = '1.10dev'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
 

From 9a88c5ca48afc5a6d9af4283736a1ad0c455419c Mon Sep 17 00:00:00 2001
From: Rob Syme <rob.syme@gmail.com>
Date: Mon, 3 Apr 2023 15:44:44 +0100
Subject: [PATCH 242/852] Update module versions

Changelog update
---
 CHANGELOG.md                                                | 1 +
 modules.json                                                | 4 ++--
 modules/nf-core/custom/dumpsoftwareversions/main.nf         | 6 +++---
 .../dumpsoftwareversions/templates/dumpsoftwareversions.py  | 0
 .../sratools/prefetch/templates/retry_with_backoff.sh       | 2 ++
 5 files changed, 8 insertions(+), 5 deletions(-)
 mode change 100755 => 100644 modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6765ac12..cadb21a6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unpublished Version / DEV]
+- Bumped modules version to allow for sratools download of sralite format files.
 
 ### Enhancements & fixes
 
diff --git a/modules.json b/modules.json
index c8cd187a..bd085eba 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "7101db4432d3268b7fcb5b8f75fa0a022dc5561b",
                         "installed_by": ["modules"]
                     },
                     "custom/sratoolsncbisettings": {
@@ -22,7 +22,7 @@
                     },
                     "sratools/prefetch": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "cded1570b7cb0ea128a5c89dd6ec3a62035c1526",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     }
                 }
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
index 3df21765..800a6099 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     label 'process_single'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda "bioconda::multiqc=1.13"
+    conda "bioconda::multiqc=1.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
 
     input:
     path versions
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
old mode 100755
new mode 100644
diff --git a/modules/nf-core/sratools/prefetch/templates/retry_with_backoff.sh b/modules/nf-core/sratools/prefetch/templates/retry_with_backoff.sh
index cec0ab43..e08dbb6a 100755
--- a/modules/nf-core/sratools/prefetch/templates/retry_with_backoff.sh
+++ b/modules/nf-core/sratools/prefetch/templates/retry_with_backoff.sh
@@ -47,6 +47,8 @@ retry_with_backoff !{args2} \
     !{args} \
     !{id}
 
+[ -f !{id}.sralite ] && { mkdir -p !{id}; mv "!{id}.sralite" !{id}/; }
+
 vdb-validate !{id}
 
 cat <<-END_VERSIONS > versions.yml

From ef7effc9beb884ba7e1aff6d05f4b8f69c71ecdb Mon Sep 17 00:00:00 2001
From: Rob Syme <rob.syme@gmail.com>
Date: Mon, 3 Apr 2023 16:46:19 +0100
Subject: [PATCH 243/852] Prettier fix

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index cadb21a6..05e123b6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unpublished Version / DEV]
+
 - Bumped modules version to allow for sratools download of sralite format files.
 
 ### Enhancements & fixes

From 7885fcd294f3ff2134a73599e5e131d1731fbee2 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 25 Apr 2023 11:09:17 +0100
Subject: [PATCH 244/852] Update all nf-core subworkflows

---
 modules.json                                                    | 2 +-
 .../fastq_download_prefetch_fasterqdump_sratools/meta.yml       | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules.json b/modules.json
index bd085eba..6a0c61a8 100644
--- a/modules.json
+++ b/modules.json
@@ -31,7 +31,7 @@
                 "nf-core": {
                     "fastq_download_prefetch_fasterqdump_sratools": {
                         "branch": "master",
-                        "git_sha": "03711bcb7fa2a7088eb54abb1fca326d30e602c2",
+                        "git_sha": "ca2bf9212707e83717934ec6c5d4cab42b39ca69",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml
index c385ca21..ed93a54a 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml
@@ -1,3 +1,4 @@
+# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
 name: fastq_download_prefetch_fasterqdump_sratools
 description: Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
 keywords:

From aba1d0bdac2cb906b7d6f54579fcfb73f51cdb63 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 25 Apr 2023 23:04:08 +0100
Subject: [PATCH 245/852] Add fasterq-dump options to --split-files

---
 conf/modules.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conf/modules.config b/conf/modules.config
index c42f4d60..f5cb1c77 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -77,6 +77,7 @@ if (params.input_type == 'sra') {
         }
 
         withName: SRATOOLS_FASTERQDUMP {
+            ext.args = '--split-files --include-technical'
             publishDir = [
                 path: { "${params.outdir}/fastq" },
                 mode: params.publish_dir_mode,

From fff5da74cd08870fc08388ad086b388366afd6f0 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 25 Apr 2023 23:50:05 +0100
Subject: [PATCH 246/852] Use generic glob for output fastq files from
 fasterq-dump

---
 modules/nf-core/sratools/fasterqdump/main.nf | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf
index ca5ee763..2336c318 100644
--- a/modules/nf-core/sratools/fasterqdump/main.nf
+++ b/modules/nf-core/sratools/fasterqdump/main.nf
@@ -12,8 +12,8 @@ process SRATOOLS_FASTERQDUMP {
     path ncbi_settings
 
     output:
-    tuple val(meta), path(fastq), emit: reads
-    path "versions.yml"         , emit: versions
+    tuple val(meta), path('*.fastq.gz'), emit: reads
+    path "versions.yml"                , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,11 +22,6 @@ process SRATOOLS_FASTERQDUMP {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-
-    // WARNING: Paired-end data extracted by fasterq-dump (--split-3 the default)
-    // always creates *_1.fastq *_2.fastq files but sometimes also
-    // an additional *.fastq file for unpaired reads which we ignore here.
-    fastq = meta.single_end ? '*.fastq.gz' : '*_{1,2}.fastq.gz'
     def outfile = meta.single_end ? "${prefix}.fastq" : prefix
     """
     export NCBI_SETTINGS="\$PWD/${ncbi_settings}"

From 37f0a785bc2d7d2c40ba4b3173cbc5bcd57305bb Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 25 Apr 2023 23:57:32 +0100
Subject: [PATCH 247/852] Update CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 05e123b6..3a443a96 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unpublished Version / DEV]
 
+- [#144](https://github.com/nf-core/fetchngs/issues/144) - Add support to download 10X Genomics data
 - Bumped modules version to allow for sratools download of sralite format files.
 
 ### Enhancements & fixes

From 0dcc5f37f0968a9784da03047b645d0bdfc53a6e Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 26 Apr 2023 00:29:00 +0100
Subject: [PATCH 248/852] Log contents of reads variable

---
 workflows/sra.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/workflows/sra.nf b/workflows/sra.nf
index 1085598b..ba39d233 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -124,6 +124,7 @@ workflow SRA {
             .map { 
                 meta, fastq ->
                     def reads = meta.single_end ? [ fastq ] : fastq
+                    log.info "$meta.id: $reads"
                     def meta_clone = meta.clone()
                     meta_clone.fastq_1 = reads[0] ? "${params.outdir}/fastq/${reads[0].getName()}" : ''
                     meta_clone.fastq_2 = reads[1] && !meta.single_end ? "${params.outdir}/fastq/${reads[1].getName()}" : ''

From 2d653037d127f03d8a4228833a8ac3041babe818 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 26 Apr 2023 00:35:43 +0100
Subject: [PATCH 249/852] Add more logging

---
 workflows/sra.nf | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/workflows/sra.nf b/workflows/sra.nf
index ba39d233..2a704395 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -116,6 +116,8 @@ workflow SRA {
             ch_sra_reads.sra.map { meta, reads -> [ meta, meta.run_accession ] }
         )
         ch_versions = ch_versions.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.versions.first())
+        
+        FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads.view()
 
         SRA_FASTQ_FTP
             .out
@@ -124,7 +126,7 @@ workflow SRA {
             .map { 
                 meta, fastq ->
                     def reads = meta.single_end ? [ fastq ] : fastq
-                    log.info "$meta.id: $reads"
+                    log.info "$meta.id: $meta.single_end: $reads"
                     def meta_clone = meta.clone()
                     meta_clone.fastq_1 = reads[0] ? "${params.outdir}/fastq/${reads[0].getName()}" : ''
                     meta_clone.fastq_2 = reads[1] && !meta.single_end ? "${params.outdir}/fastq/${reads[1].getName()}" : ''

From 1867a80f45c5bd58f28bdb00ed5ffc94ef5a2082 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 26 Apr 2023 01:02:44 +0100
Subject: [PATCH 250/852] Fix logic to factor for reads being a nested list

---
 workflows/sra.nf | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/workflows/sra.nf b/workflows/sra.nf
index 2a704395..38915944 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -116,8 +116,6 @@ workflow SRA {
             ch_sra_reads.sra.map { meta, reads -> [ meta, meta.run_accession ] }
         )
         ch_versions = ch_versions.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.versions.first())
-        
-        FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads.view()
 
         SRA_FASTQ_FTP
             .out
@@ -125,12 +123,10 @@ workflow SRA {
             .mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads)
             .map { 
                 meta, fastq ->
-                    def reads = meta.single_end ? [ fastq ] : fastq
-                    log.info "$meta.id: $meta.single_end: $reads"
-                    def meta_clone = meta.clone()
-                    meta_clone.fastq_1 = reads[0] ? "${params.outdir}/fastq/${reads[0].getName()}" : ''
-                    meta_clone.fastq_2 = reads[1] && !meta.single_end ? "${params.outdir}/fastq/${reads[1].getName()}" : ''
-                    return meta_clone
+                    def reads = fastq instanceof List ? fastq.flatten() : [ fastq ]
+                    def fastq_1 = reads[0] ? "${params.outdir}/fastq/${reads[0].getName()}" : ''
+                    def fastq_2 = reads[1] && !meta.single_end ? "${params.outdir}/fastq/${reads[1].getName()}" : ''
+                    return [ meta + [ fastq_1: fastq_1, fastq_2: fastq_2 ], fastq ]
             }
             .set { ch_sra_metadata }
     }

From 399081edcf83af28a137a29344f7c5b4a6f9e78b Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 26 Apr 2023 01:11:41 +0100
Subject: [PATCH 251/852] Remove fastq files from channel

---
 workflows/sra.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/sra.nf b/workflows/sra.nf
index 38915944..d2ce0c2b 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -126,7 +126,7 @@ workflow SRA {
                     def reads = fastq instanceof List ? fastq.flatten() : [ fastq ]
                     def fastq_1 = reads[0] ? "${params.outdir}/fastq/${reads[0].getName()}" : ''
                     def fastq_2 = reads[1] && !meta.single_end ? "${params.outdir}/fastq/${reads[1].getName()}" : ''
-                    return [ meta + [ fastq_1: fastq_1, fastq_2: fastq_2 ], fastq ]
+                    return [ meta + [ fastq_1: fastq_1, fastq_2: fastq_2 ] ]
             }
             .set { ch_sra_metadata }
     }

From 935de8cf64c67b3542b4c2a233ca3c1392119ea1 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 26 Apr 2023 01:35:19 +0100
Subject: [PATCH 252/852] Revert to cloning map because adding entries returns
 a list

---
 workflows/sra.nf | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/workflows/sra.nf b/workflows/sra.nf
index d2ce0c2b..52479771 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -124,9 +124,10 @@ workflow SRA {
             .map { 
                 meta, fastq ->
                     def reads = fastq instanceof List ? fastq.flatten() : [ fastq ]
-                    def fastq_1 = reads[0] ? "${params.outdir}/fastq/${reads[0].getName()}" : ''
-                    def fastq_2 = reads[1] && !meta.single_end ? "${params.outdir}/fastq/${reads[1].getName()}" : ''
-                    return [ meta + [ fastq_1: fastq_1, fastq_2: fastq_2 ] ]
+                    def meta_clone = meta.clone()
+                    meta_clone.fastq_1 = reads[0] ? "${params.outdir}/fastq/${reads[0].getName()}" : ''
+                    meta_clone.fastq_2 = reads[1] && !meta.single_end ? "${params.outdir}/fastq/${reads[1].getName()}" : ''
+                    return meta_clone
             }
             .set { ch_sra_metadata }
     }

From aa82d896b7a7f70700d23df8bb964f64ba388c3e Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 26 Apr 2023 10:54:54 +0100
Subject: [PATCH 253/852] Add full-sized data for 10x to test_full

---
 conf/test_full.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/test_full.config b/conf/test_full.config
index 2f0303ea..c16fda7f 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -15,5 +15,5 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv'
+    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test_full.csv'
 }

From b47cab18718eaebe8b592d53a39e87653d12b727 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 26 Apr 2023 12:33:05 +0100
Subject: [PATCH 254/852] Re-install sratools/fasterqdump from nf-core/modules

---
 modules.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules.json b/modules.json
index 6a0c61a8..f6d1001c 100644
--- a/modules.json
+++ b/modules.json
@@ -17,7 +17,7 @@
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "10cb20f6a130d104fef335a8290f3ffce650f28d",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/prefetch": {

From d6125e1f0722a65e5e6dce95ff9381713c2f0447 Mon Sep 17 00:00:00 2001
From: Esha Joshi <eshajoshi@eshas-mbp.home>
Date: Tue, 2 May 2023 19:51:10 -0400
Subject: [PATCH 255/852] fix: remove default ena meta fields to match api spec
 v2.0

---
 bin/sra_ids_to_runinfo.py | 2 --
 nextflow.config           | 2 +-
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index 70627791..5da7c708 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -64,7 +64,6 @@
     "secondary_sample_accession",
     "study_accession",
     "secondary_study_accession",
-    "parent_study",
     "submission_accession",
     "run_alias",
     "experiment_alias",
@@ -84,7 +83,6 @@
     "sample_title",
     "experiment_title",
     "study_title",
-    "description",
     "sample_description",
     "fastq_md5",
     "fastq_bytes",
diff --git a/nextflow.config b/nextflow.config
index d6686ae4..d3a1f3f0 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -15,7 +15,7 @@ params {
     nf_core_pipeline            = null
     nf_core_rnaseq_strandedness = 'auto'
     ena_metadata_fields         = null
-    sample_mapping_fields       = 'experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description,description'
+    sample_mapping_fields       = 'experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description'
     synapse_config              = null
     force_sratools_download     = false
     skip_fastq_download         = false

From 24ff80b4e01e75de776fb3d585c5cacf5bbc2bc1 Mon Sep 17 00:00:00 2001
From: Esha Joshi <eshajoshi@eshas-mbp.home>
Date: Tue, 2 May 2023 21:01:44 -0400
Subject: [PATCH 256/852] feat: improve error handling for meta field
 validation

---
 bin/sra_ids_to_runinfo.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index 5da7c708..a0f6fcb3 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -57,7 +57,6 @@
 # Full list of accepted fields can be obtained here:
 # https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run
 ENA_METADATA_FIELDS = (
-    "accession",
     "run_accession",
     "experiment_accession",
     "sample_accession",
@@ -364,10 +363,12 @@ def validate_fields_parameter(param, valid_vals, param_desc):
     if len(set(user_vals) & set(valid_vals)) == len(user_vals):
         return user_vals
     else:
+        invalid_vals = [x for x in user_vals if x not in valid_vals]
         logger.error(
             f"Please provide a valid value for {param_desc}!\n"
             f"Provided values = {param}\n"
-            f"Accepted values = {','.join(valid_vals)}"
+            f"Accepted values = {','.join(valid_vals)}\n"
+            f"The following values are invalid: {','.join(invalid_vals)}\n"
         )
         sys.exit(1)
 

From 9e454f2ee24215b16505ac4487b26f85898896b1 Mon Sep 17 00:00:00 2001
From: Esha Joshi <eshajoshi@eshas-mbp.home>
Date: Tue, 2 May 2023 21:10:05 -0400
Subject: [PATCH 257/852] fix: update default mapping fields in schema and
 specify API version

---
 nextflow_schema.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 696914e4..563c5e7b 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -32,13 +32,13 @@
                     "type": "string",
                     "fa_icon": "fas fa-columns",
                     "description": "Comma-separated list of ENA metadata fields to fetch before downloading data.",
-                    "help_text": "The default list of fields used by the pipeline can be found at the top of the [`bin/sra_ids_to_runinfo.py`](https://github.com/nf-core/fetchngs/blob/master/bin/sra_ids_to_runinfo.py) script within the pipeline repo. This pipeline requires a minimal set of fields to download FastQ files i.e. `'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'`. Full list of accepted metadata fields can be obtained from the [ENA API](https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run])."
+                    "help_text": "The default list of fields used by the pipeline can be found at the top of the [`bin/sra_ids_to_runinfo.py`](https://github.com/nf-core/fetchngs/blob/master/bin/sra_ids_to_runinfo.py) script within the pipeline repo. This pipeline requires a minimal set of fields to download FastQ files i.e. `'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'`. Full list of accepted metadata fields can be obtained from the [ENA API v2.0](https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run])."
                 },
                 "sample_mapping_fields": {
                     "type": "string",
                     "fa_icon": "fas fa-globe-americas",
                     "description": "Comma-separated list of ENA metadata fields used to create a separate 'id_mappings.csv' and 'multiqc_config.yml' with selected fields that can be used to rename samples in general and in MultiQC.",
-                    "default": "experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description,description"
+                    "default": "experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description"
                 },
                 "nf_core_pipeline": {
                     "type": "string",

From b1019a595181db0db77b766eb85f050642be6e9e Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 4 May 2023 22:24:11 +0100
Subject: [PATCH 258/852] Remove Sys.exit calls and quay.io in Docker
 definition from local modules

---
 docs/usage.md                              | 11 +++++------
 lib/WorkflowMain.groovy                    | 10 ++++------
 lib/WorkflowSra.groovy                     | 13 +++++++------
 main.nf                                    |  4 ++--
 modules/local/multiqc_mappings_config.nf   |  2 +-
 modules/local/sra_fastq_ftp.nf             |  2 +-
 modules/local/sra_ids_to_runinfo.nf        |  2 +-
 modules/local/sra_merge_samplesheet.nf     |  2 +-
 modules/local/sra_runinfo_to_ftp.nf        |  2 +-
 modules/local/synapse_get.nf               |  6 +++---
 modules/local/synapse_list.nf              |  6 +++---
 modules/local/synapse_merge_samplesheet.nf |  2 +-
 modules/local/synapse_show.nf              |  6 +++---
 nextflow.config                            |  2 +-
 workflows/sra.nf                           |  4 ++--
 15 files changed, 36 insertions(+), 38 deletions(-)

diff --git a/docs/usage.md b/docs/usage.md
index 807abb75..55e47133 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -75,7 +75,7 @@ If FTP connections are blocked on your network use the [`--force_sratools_downlo
 The typical command for running the pipeline is as follows:
 
 ```bash
-nextflow run nf-core/fetchngs --input ids.csv --outdir <OUTDIR> -profile docker
+nextflow run nf-core/fetchngs --input ./ids.csv --outdir ./results -profile docker
 ```
 
 This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
@@ -94,7 +94,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than
 Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.
 
 > ⚠️ Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
-> The above pipeline run specified with a params file in yaml format:
+
+The above pipeline run specified with a params file in yaml format:
 
 ```bash
 nextflow run nf-core/fetchngs -profile docker -params-file params.yaml
@@ -103,10 +104,8 @@ nextflow run nf-core/fetchngs -profile docker -params-file params.yaml
 with `params.yaml` containing:
 
 ```yaml
-input: './samplesheet.csv'
+input: './ids.csv'
 outdir: './results/'
-genome: 'GRCh37'
-input: 'data'
 <...>
 ```
 
@@ -189,7 +188,7 @@ To change the resource requests, please see the [max resources](https://nf-co.re
 
 ### Custom Containers
 
-In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date.
+In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version may be out of date.
 
 To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website.
 
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index 24d82c4e..13fd6d82 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -94,7 +94,7 @@ class WorkflowMain {
     }
 
     // Check if input ids are from the SRA
-    public static Boolean isSraId(input, log) {
+    public static Boolean isSraId(input) {
         def is_sra = false
         def total_ids = 0
         def no_match_ids = []
@@ -111,15 +111,14 @@ class WorkflowMain {
             if (num_match == total_ids) {
                 is_sra = true
             } else {
-                log.error "Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / DDBJ or Synapse ids!"
-                System.exit(1)
+                Nextflow.error("Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / DDBJ or Synapse ids!")
             }
         }
         return is_sra
     }
 
     // Check if input ids are from the Synapse platform
-    public static Boolean isSynapseId(input, log) {
+    public static Boolean isSynapseId(input) {
         def is_synapse = false
         def total_ids = 0
         def no_match_ids = []
@@ -136,8 +135,7 @@ class WorkflowMain {
             if (num_match == total_ids) {
                 is_synapse = true
             } else {
-                log.error "Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / DDBJ or Synapse ids!"
-                System.exit(1)
+                Nextflow.error("Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / DDBJ or Synapse ids!")
             }
         }
         return is_synapse
diff --git a/lib/WorkflowSra.groovy b/lib/WorkflowSra.groovy
index 90d86f1c..061f7ffb 100755
--- a/lib/WorkflowSra.groovy
+++ b/lib/WorkflowSra.groovy
@@ -2,17 +2,18 @@
 // This file holds several functions specific to the workflow/sra.nf in the nf-core/fetchngs pipeline
 //
 
+import nextflow.Nextflow
+
 class WorkflowSra {
 
     //
     // Check and validate parameters
     //
-    public static void initialise(params, log, valid_params) {
+    public static void initialise(params, valid_params) {
         // Check minimal ENA fields are provided to download FastQ files
         def ena_metadata_fields = params.ena_metadata_fields ? params.ena_metadata_fields.split(',').collect{ it.trim().toLowerCase() } : valid_params['ena_metadata_fields']
         if (!ena_metadata_fields.containsAll(valid_params['ena_metadata_fields'])) {
-            log.error "Invalid option: '${params.ena_metadata_fields}'. Minimally required fields for '--ena_metadata_fields': '${valid_params['ena_metadata_fields'].join(',')}'"
-            System.exit(1)
+            Nextflow.error("Invalid option: '${params.ena_metadata_fields}'. Minimally required fields for '--ena_metadata_fields': '${valid_params['ena_metadata_fields'].join(',')}'")
         }
     }
 
@@ -31,18 +32,18 @@ class WorkflowSra {
     }
 
     // Fail pipeline if input ids are from the GEO
-    public static void isGeoFail(ids, log) {
+    public static void isGeoFail(ids) {
         def pattern = /^(GS[EM])(\d+)$/
         for (id in ids) {
             if (id =~ pattern) {
-                log.error "===================================================================================\n" +
+                def error_string = "===================================================================================\n" +
                     "  GEO id detected: ${id}\n" +
                     "  Support for GEO ids was dropped in v1.7 due to breaking changes in the NCBI API.\n" +
                     "  Please remove any GEO ids from the input samplesheet.\n\n" +
                     "  Please see:\n" +
                     "  https://github.com/nf-core/fetchngs/pull/102\n" +
                     "==================================================================================="
-                System.exit(1)
+                Nextflow.error(error_string)
             }
         }
     }
diff --git a/main.nf b/main.nf
index 2c4b52f2..e7d67165 100644
--- a/main.nf
+++ b/main.nf
@@ -39,9 +39,9 @@ Channel
 
 // Auto-detect input id type
 def input_type = ''
-if (WorkflowMain.isSraId(ch_input, log)) {
+if (WorkflowMain.isSraId(ch_input)) {
     input_type = 'sra'
-} else if (WorkflowMain.isSynapseId(ch_input, log)) {
+} else if (WorkflowMain.isSynapseId(ch_input)) {
     input_type = 'synapse'
 } else {
     exit 1, 'Ids provided via --input not recognised please make sure they are either SRA / ENA / DDBJ or Synapse ids!'
diff --git a/modules/local/multiqc_mappings_config.nf b/modules/local/multiqc_mappings_config.nf
index 4f6c95bd..8efe1caa 100644
--- a/modules/local/multiqc_mappings_config.nf
+++ b/modules/local/multiqc_mappings_config.nf
@@ -4,7 +4,7 @@ process MULTIQC_MAPPINGS_CONFIG {
     conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
-        'quay.io/biocontainers/python:3.9--1' }"
+        'biocontainers/python:3.9--1' }"
 
     input:
     path csv
diff --git a/modules/local/sra_fastq_ftp.nf b/modules/local/sra_fastq_ftp.nf
index 464a327e..2b7769ff 100644
--- a/modules/local/sra_fastq_ftp.nf
+++ b/modules/local/sra_fastq_ftp.nf
@@ -7,7 +7,7 @@ process SRA_FASTQ_FTP {
     conda "bioconda::sra-tools=2.11.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' :
-        'quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
+        'biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
 
     input:
     tuple val(meta), val(fastq)
diff --git a/modules/local/sra_ids_to_runinfo.nf b/modules/local/sra_ids_to_runinfo.nf
index 49c83554..7d47f5e3 100644
--- a/modules/local/sra_ids_to_runinfo.nf
+++ b/modules/local/sra_ids_to_runinfo.nf
@@ -6,7 +6,7 @@ process SRA_IDS_TO_RUNINFO {
     conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
-        'quay.io/biocontainers/python:3.9--1' }"
+        'biocontainers/python:3.9--1' }"
 
     input:
     val id
diff --git a/modules/local/sra_merge_samplesheet.nf b/modules/local/sra_merge_samplesheet.nf
index 4b94a823..66d697aa 100644
--- a/modules/local/sra_merge_samplesheet.nf
+++ b/modules/local/sra_merge_samplesheet.nf
@@ -3,7 +3,7 @@ process SRA_MERGE_SAMPLESHEET {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"
+        'docker.io/library/ubuntu:20.04' }"
 
     input:
     path ('samplesheets/*')
diff --git a/modules/local/sra_runinfo_to_ftp.nf b/modules/local/sra_runinfo_to_ftp.nf
index 3a060f7b..9c83cf53 100644
--- a/modules/local/sra_runinfo_to_ftp.nf
+++ b/modules/local/sra_runinfo_to_ftp.nf
@@ -4,7 +4,7 @@ process SRA_RUNINFO_TO_FTP {
     conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
-        'quay.io/biocontainers/python:3.9--1' }"
+        'biocontainers/python:3.9--1' }"
 
     input:
     path runinfo
diff --git a/modules/local/synapse_get.nf b/modules/local/synapse_get.nf
index f43e4d5e..c8a6d7a4 100644
--- a/modules/local/synapse_get.nf
+++ b/modules/local/synapse_get.nf
@@ -4,10 +4,10 @@ process SYNAPSE_GET {
     label 'process_low'
     label 'error_retry'
 
-    conda "bioconda::synapseclient=2.6.0"
+    conda "bioconda::synapseclient=2.7.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/synapseclient:2.6.0--pyh5e36f6f_0' :
-        'quay.io/biocontainers/synapseclient:2.6.0--pyh5e36f6f_0' }"
+        'https://depot.galaxyproject.org/singularity/synapseclient:2.7.1--pyh7cba7a3_0' :
+        'biocontainers/synapseclient:2.7.1--pyh7cba7a3_0' }"
 
     input:
     val meta
diff --git a/modules/local/synapse_list.nf b/modules/local/synapse_list.nf
index f42357ab..0c03f8b2 100644
--- a/modules/local/synapse_list.nf
+++ b/modules/local/synapse_list.nf
@@ -3,10 +3,10 @@ process SYNAPSE_LIST {
     tag "$id"
     label 'process_low'
 
-    conda "bioconda::synapseclient=2.6.0"
+    conda "bioconda::synapseclient=2.7.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/synapseclient:2.6.0--pyh5e36f6f_0' :
-        'quay.io/biocontainers/synapseclient:2.6.0--pyh5e36f6f_0' }"
+        'https://depot.galaxyproject.org/singularity/synapseclient:2.7.1--pyh7cba7a3_0' :
+        'biocontainers/synapseclient:2.7.1--pyh7cba7a3_0' }"
 
     input:
     val id
diff --git a/modules/local/synapse_merge_samplesheet.nf b/modules/local/synapse_merge_samplesheet.nf
index f46a1fbf..bfe89693 100644
--- a/modules/local/synapse_merge_samplesheet.nf
+++ b/modules/local/synapse_merge_samplesheet.nf
@@ -4,7 +4,7 @@ process SYNAPSE_MERGE_SAMPLESHEET {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"
+        'docker.io/library/ubuntu:20.04' }"
 
     input:
     path ('samplesheets/*')
diff --git a/modules/local/synapse_show.nf b/modules/local/synapse_show.nf
index 0bd6cc12..e1f756a5 100644
--- a/modules/local/synapse_show.nf
+++ b/modules/local/synapse_show.nf
@@ -3,10 +3,10 @@ process SYNAPSE_SHOW {
     tag "$id"
     label 'process_low'
 
-    conda "bioconda::synapseclient=2.6.0"
+    conda "bioconda::synapseclient=2.7.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/synapseclient:2.6.0--pyh5e36f6f_0' :
-        'quay.io/biocontainers/synapseclient:2.6.0--pyh5e36f6f_0' }"
+        'https://depot.galaxyproject.org/singularity/synapseclient:2.7.1--pyh7cba7a3_0' :
+        'biocontainers/synapseclient:2.7.1--pyh7cba7a3_0' }"
 
     input:
     val id
diff --git a/nextflow.config b/nextflow.config
index 6731df72..74ae84d6 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -73,7 +73,7 @@ profiles {
     debug {
         dumpHashes             = true
         process.beforeScript   = 'echo $HOSTNAME'
-        cleanup = false
+        cleanup                = false
     }
     conda {
         conda.enabled          = true
diff --git a/workflows/sra.nf b/workflows/sra.nf
index 52479771..e3ac447f 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -11,7 +11,7 @@ def valid_params = [
 def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
 
 // Validate input parameters
-WorkflowSra.initialise(params, log, valid_params)
+WorkflowSra.initialise(params, valid_params)
 
 /*
 ========================================================================================
@@ -55,7 +55,7 @@ workflow SRA {
     //
     ids
         .collect()
-        .map { WorkflowSra.isGeoFail(it, log) }
+        .map { WorkflowSra.isGeoFail(it) }
 
     //
     // MODULE: Get SRA run information for public database ids

From e7623943f86fa8131da3b3de9c1848ce65249fe7 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 4 May 2023 22:37:18 +0100
Subject: [PATCH 259/852] Run nf-core modules update to fix quay.io container
 definitions

---
 modules.json                                              | 8 ++++----
 modules/nf-core/custom/dumpsoftwareversions/main.nf       | 2 +-
 modules/nf-core/custom/sratoolsncbisettings/main.nf       | 2 +-
 modules/nf-core/sratools/prefetch/main.nf                 | 2 +-
 .../fastq_download_prefetch_fasterqdump_sratools/meta.yml | 2 +-
 5 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/modules.json b/modules.json
index 02ca48e7..dea81e71 100644
--- a/modules.json
+++ b/modules.json
@@ -7,12 +7,12 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/fasterqdump": {
@@ -22,7 +22,7 @@
                     },
                     "sratools/prefetch": {
                         "branch": "master",
-                        "git_sha": "cded1570b7cb0ea128a5c89dd6ec3a62035c1526",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     }
                 }
@@ -31,7 +31,7 @@
                 "nf-core": {
                     "fastq_download_prefetch_fasterqdump_sratools": {
                         "branch": "master",
-                        "git_sha": "ca2bf9212707e83717934ec6c5d4cab42b39ca69",
+                        "git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
index 800a6099..ebc87273 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -5,7 +5,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     conda "bioconda::multiqc=1.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
+        'biocontainers/multiqc:1.14--pyhdfd78af_0' }"
 
     input:
     path versions
diff --git a/modules/nf-core/custom/sratoolsncbisettings/main.nf b/modules/nf-core/custom/sratoolsncbisettings/main.nf
index 36be10d3..5deb8892 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/main.nf
+++ b/modules/nf-core/custom/sratoolsncbisettings/main.nf
@@ -5,7 +5,7 @@ process CUSTOM_SRATOOLSNCBISETTINGS {
     conda "bioconda::sra-tools=2.11.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' :
-        'quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
+        'biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
 
     output:
     path('*.mkfg')     , emit: ncbi_settings
diff --git a/modules/nf-core/sratools/prefetch/main.nf b/modules/nf-core/sratools/prefetch/main.nf
index 57e8a3c9..91b8aec2 100644
--- a/modules/nf-core/sratools/prefetch/main.nf
+++ b/modules/nf-core/sratools/prefetch/main.nf
@@ -5,7 +5,7 @@ process SRATOOLS_PREFETCH {
     conda "bioconda::sra-tools=2.11.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' :
-        'quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
+        'biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
 
     input:
     tuple val(meta), val(id)
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml
index ed93a54a..4599bbd2 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: fastq_download_prefetch_fasterqdump_sratools
 description: Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
 keywords:

From e39a54ad3ab9cebf2b1686afa215e521d4aa397f Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 5 May 2023 10:01:44 +0100
Subject: [PATCH 260/852] Make CHANGELOG more templaty

---
 CHANGELOG.md | 26 +++++++++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 533488b3..d959887c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,12 +5,36 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-12
 
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Adam Talbot](https://github.com/adamrtalbot)
+- [Esha Joshi](https://github.com/ejseqera)
+- [Maxime Garcia](https://github.com/maxulysse)
+- [Moritz E. Beber](https://github.com/Midnighter)
+- [Rob Syme](https://github.com/robsyme)
+
+Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
+
+### Enhancements & fixes
+
 - [#144](https://github.com/nf-core/fetchngs/issues/144) - Add support to download 10X Genomics data
 - [#148](https://github.com/nf-core/fetchngs/pull/148) - Fix default metadata fields for ENA API v2.0
 - Bumped modules version to allow for sratools download of sralite format files.
 - Updated pipeline template to [nf-core/tools 2.8](https://github.com/nf-core/tools/releases/tag/2.8)
 
-### Enhancements & fixes
+### Software dependencies
+
+| Dependency      | Old version | New version |
+| --------------- | ----------- | ----------- |
+| `synapseclient` | 2.6.0       | 2.7.1       |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+>
+> **NB:** Dependency has been **added** if just the new version information is present.
+>
+> **NB:** Dependency has been **removed** if new version information isn't present.
 
 ## [[1.9](https://github.com/nf-core/fetchngs/releases/tag/1.9)] - 2022-12-21
 

From b9888eafb65469ed99ae3313e7fe8cfbb4d78f3e Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 5 May 2023 12:32:30 +0100
Subject: [PATCH 261/852] Use ubuntu image from quay.io nf-core account

---
 modules/local/sra_merge_samplesheet.nf     | 2 +-
 modules/local/synapse_merge_samplesheet.nf | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/sra_merge_samplesheet.nf b/modules/local/sra_merge_samplesheet.nf
index 66d697aa..1c2ee7df 100644
--- a/modules/local/sra_merge_samplesheet.nf
+++ b/modules/local/sra_merge_samplesheet.nf
@@ -3,7 +3,7 @@ process SRA_MERGE_SAMPLESHEET {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'docker.io/library/ubuntu:20.04' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     path ('samplesheets/*')
diff --git a/modules/local/synapse_merge_samplesheet.nf b/modules/local/synapse_merge_samplesheet.nf
index bfe89693..4cb2abc3 100644
--- a/modules/local/synapse_merge_samplesheet.nf
+++ b/modules/local/synapse_merge_samplesheet.nf
@@ -4,7 +4,7 @@ process SYNAPSE_MERGE_SAMPLESHEET {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'docker.io/library/ubuntu:20.04' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     path ('samplesheets/*')

From c0afa084e3d353bf6a315c14a54ecae983d6e0bc Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 6 May 2023 15:24:26 +0100
Subject: [PATCH 262/852] Add #85 to CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d959887c..b5b1a287 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,6 +19,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 
 ### Enhancements & fixes
 
+- [#85](https://github.com/nf-core/fetchngs/issues/85) - Not able to fetch metadata for ERR* ids associated with ArrayExpress
 - [#144](https://github.com/nf-core/fetchngs/issues/144) - Add support to download 10X Genomics data
 - [#148](https://github.com/nf-core/fetchngs/pull/148) - Fix default metadata fields for ENA API v2.0
 - Bumped modules version to allow for sratools download of sralite format files.

From 2aca881c5466590c74f8b36452ac788be10b5757 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 6 May 2023 16:12:00 +0100
Subject: [PATCH 263/852] Fix #129

---
 CHANGELOG.md              | 1 +
 bin/sra_ids_to_runinfo.py | 3 +--
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b5b1a287..1b3efa85 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,6 +20,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 ### Enhancements & fixes
 
 - [#85](https://github.com/nf-core/fetchngs/issues/85) - Not able to fetch metadata for ERR* ids associated with ArrayExpress
+- [#129](https://github.com/nf-core/fetchngs/issues/129) - Pipeline is working with SRA run IDs, but failing with corresponding Biosample IDs
 - [#144](https://github.com/nf-core/fetchngs/issues/144) - Add support to download 10X Genomics data
 - [#148](https://github.com/nf-core/fetchngs/pull/148) - Fix default metadata fields for ENA API v2.0
 - Bumped modules version to allow for sratools download of sralite format files.
diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index a0f6fcb3..6cf16800 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -191,7 +191,6 @@ class DatabaseResolver:
     _GEO_PREFIXES = {"GSE", "GSM"}
     _SRA_PREFIXES = {
         "PRJNA",
-        "SAMN",
         "DRA",
         "DRP",
         "DRS",
@@ -199,7 +198,7 @@ class DatabaseResolver:
         "PRJDB",
         "SAMD",
     }
-    _ENA_PREFIXES = {"ERR", "SRR", "DRR"}
+    _ENA_PREFIXES = {"ERR", "SRR", "SAMN", "DRR"}
 
     @classmethod
     def expand_identifier(cls, identifier):

From bc4edf654c7df6f2edaf8654870f6617e4f73c55 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 6 May 2023 16:18:47 +0100
Subject: [PATCH 264/852] Fix prettier

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1b3efa85..c1bf6a64 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,7 +19,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 
 ### Enhancements & fixes
 
-- [#85](https://github.com/nf-core/fetchngs/issues/85) - Not able to fetch metadata for ERR* ids associated with ArrayExpress
+- [#85](https://github.com/nf-core/fetchngs/issues/85) - Not able to fetch metadata for ERR\* ids associated with ArrayExpress
 - [#129](https://github.com/nf-core/fetchngs/issues/129) - Pipeline is working with SRA run IDs, but failing with corresponding Biosample IDs
 - [#144](https://github.com/nf-core/fetchngs/issues/144) - Add support to download 10X Genomics data
 - [#148](https://github.com/nf-core/fetchngs/pull/148) - Fix default metadata fields for ENA API v2.0

From b6b43947bee5f776090081b0ba1291bfc8b4603a Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 6 May 2023 20:20:19 +0100
Subject: [PATCH 265/852] Add multi-cloud CI for full-sized tests

---
 .github/workflows/cloud_tests_full.yml  | 81 +++++++++++++++++++++++++
 .github/workflows/cloud_tests_small.yml | 76 +++++++++++++++++++++++
 2 files changed, 157 insertions(+)
 create mode 100644 .github/workflows/cloud_tests_full.yml
 create mode 100644 .github/workflows/cloud_tests_small.yml

diff --git a/.github/workflows/cloud_tests_full.yml b/.github/workflows/cloud_tests_full.yml
new file mode 100644
index 00000000..d0ed0552
--- /dev/null
+++ b/.github/workflows/cloud_tests_full.yml
@@ -0,0 +1,81 @@
+name: full-sized tests on cloud providers
+run-name: Submitting workflow to all cloud providers using full sized data
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+    inputs:
+      platform:
+        description: "Platform to run test"
+        required: true
+        default: "all"
+        type: choice
+        options:
+          - all
+          - aws
+          - azure
+          - gcp
+jobs:
+  run-full-tests-on-aws:
+    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' || !github.event.inputs }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: seqeralabs/action-tower-launch@v1
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
+          workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/fetchngs/work-${{ github.sha }}"
+          run_name: "aws_fetchngs_full"
+          profiles: test_full
+          parameters: |
+            {
+                "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
+                "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/fetchngs/results-${{ github.sha }}"
+            }
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: tower_action_*.log
+  run-full-tests-on-gcp:
+    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' || !github.event.inputs }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: seqeralabs/action-tower-launch@v1
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_CE_GCP_CPU }}
+          workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/fetchngs/work-${{ github.sha }}"
+          run_name: "gcp_fetchngs_full"
+          profiles: test_full
+          parameters: |
+            {
+                "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
+                "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/fetchngs/results-${{ github.sha }}"
+            }
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: tower_action_*.log
+  run-full-tests-on-azure:
+    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' || !github.event.inputs }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: seqeralabs/action-tower-launch@v1
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }}
+          workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/fetchngs/work-${{ github.sha }}"
+          run_name: "azure_fetchngs_full"
+          profiles: test_full
+          parameters: |
+            {
+                "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
+                "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/fetchngs/results-${{ github.sha }}"
+            }
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: tower_action_*.log
diff --git a/.github/workflows/cloud_tests_small.yml b/.github/workflows/cloud_tests_small.yml
new file mode 100644
index 00000000..12b8daab
--- /dev/null
+++ b/.github/workflows/cloud_tests_small.yml
@@ -0,0 +1,76 @@
+name: small-sized tests on cloud providers
+run-name: Submitting workflow to all cloud providers using small sized data
+on:
+  workflow_dispatch:
+    inputs:
+      platform:
+        description: "Platform to run test"
+        required: true
+        default: "all"
+        type: choice
+        options:
+          - all
+          - aws
+          - azure
+          - gcp
+jobs:
+  run-small-tests-on-aws:
+    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: seqeralabs/action-tower-launch@v1
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
+          workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/fetchngs/work-${{ github.sha }}"
+          run_name: "aws_fetchngs_small"
+          profiles: test
+          parameters: |
+            {
+                "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/fetchngs/results-test-${{ github.sha }}"
+            }
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: tower_action_*.log
+  run-small-tests-on-gcp:
+    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: seqeralabs/action-tower-launch@v1
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_CE_GCP_CPU }}
+          workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/fetchngs/work-${{ github.sha }}"
+          run_name: "gcp_fetchngs_small"
+          profiles: test
+          parameters: |
+            {
+                "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/fetchngs/results-test-${{ github.sha }}"
+            }
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: tower_action_*.log
+  run-small-tests-on-azure:
+    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: seqeralabs/action-tower-launch@v1
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }}
+          workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/fetchngs/work-${{ github.sha }}"
+          run_name: "azure_fetchngs_small"
+          profiles: test
+          parameters: |
+            {
+                "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/fetchngs/results-test-${{ github.sha }}"
+            }
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: tower_action_*.log

From 9e112c1f3a761b2c39ef0151b937895ff2db92e8 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 6 May 2023 20:28:41 +0100
Subject: [PATCH 266/852] Remove old AWS CI tests

---
 .github/workflows/awsfulltest.yml | 31 -------------------------------
 .github/workflows/awstest.yml     | 29 -----------------------------
 2 files changed, 60 deletions(-)
 delete mode 100644 .github/workflows/awsfulltest.yml
 delete mode 100644 .github/workflows/awstest.yml

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
deleted file mode 100644
index 773c3a7e..00000000
--- a/.github/workflows/awsfulltest.yml
+++ /dev/null
@@ -1,31 +0,0 @@
-name: nf-core AWS full size tests
-# This workflow is triggered on published releases.
-# It can be additionally triggered manually with GitHub actions workflow dispatch button.
-# It runs the -profile 'test_full' on AWS batch
-
-on:
-  release:
-    types: [published]
-  workflow_dispatch:
-jobs:
-  run-tower:
-    name: Run AWS full tests
-    if: github.repository == 'nf-core/fetchngs'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v1
-        with:
-          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
-          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/fetchngs/work-${{ github.sha }}
-          parameters: |
-            {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/fetchngs/results-${{ github.sha }}"
-            }
-          profiles: test_full,aws_tower
-      - uses: actions/upload-artifact@v3
-        with:
-          name: Tower debug log file
-          path: tower_action_*.log
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
deleted file mode 100644
index cdfba2f0..00000000
--- a/.github/workflows/awstest.yml
+++ /dev/null
@@ -1,29 +0,0 @@
-name: nf-core AWS test
-# This workflow can be triggered manually with the GitHub actions workflow dispatch button.
-# It runs the -profile 'test' on AWS batch
-
-on:
-  workflow_dispatch:
-jobs:
-  run-tower:
-    name: Run AWS tests
-    if: github.repository == 'nf-core/fetchngs'
-    runs-on: ubuntu-latest
-    steps:
-      # Launch workflow using Tower CLI tool action
-      - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v1
-        with:
-          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
-          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/fetchngs/work-${{ github.sha }}
-          parameters: |
-            {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/fetchngs/results-test-${{ github.sha }}"
-            }
-          profiles: test,aws_tower
-      - uses: actions/upload-artifact@v3
-        with:
-          name: Tower debug log file
-          path: tower_action_*.log

From 7d858a3aed5800a743e13051069fab741987cd91 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 6 May 2023 20:36:41 +0100
Subject: [PATCH 267/852] Update CHANGELOG

---
 CHANGELOG.md | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c1bf6a64..4bb46ddb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,12 +19,13 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 
 ### Enhancements & fixes
 
-- [#85](https://github.com/nf-core/fetchngs/issues/85) - Not able to fetch metadata for ERR\* ids associated with ArrayExpress
-- [#129](https://github.com/nf-core/fetchngs/issues/129) - Pipeline is working with SRA run IDs, but failing with corresponding Biosample IDs
+- [#85](https://github.com/nf-core/fetchngs/issues/85) - Not able to fetch metadata for ERR ids associated with ArrayExpress
+- [#129](https://github.com/nf-core/fetchngs/issues/129) - Pipeline is working with SRA run ids but failing with corresponding Biosample ids
 - [#144](https://github.com/nf-core/fetchngs/issues/144) - Add support to download 10X Genomics data
-- [#148](https://github.com/nf-core/fetchngs/pull/148) - Fix default metadata fields for ENA API v2.0
-- Bumped modules version to allow for sratools download of sralite format files.
-- Updated pipeline template to [nf-core/tools 2.8](https://github.com/nf-core/tools/releases/tag/2.8)
+- [PR #140](https://github.com/nf-core/fetchngs/pull/140) - Bumped modules version to allow for sratools download of sralite format files
+- [PR #147](https://github.com/nf-core/fetchngs/pull/147) - Updated pipeline template to [nf-core/tools 2.8](https://github.com/nf-core/tools/releases/tag/2.8)
+- [PR #148](https://github.com/nf-core/fetchngs/pull/148) - Fix default metadata fields for ENA API v2.0
+- [PR #150](https://github.com/nf-core/fetchngs/pull/150) - Add infrastructure and CI for multi-cloud full-sized tests run via Nextflow Tower
 
 ### Software dependencies
 

From eaecac87ca7a50b3a74ee16d1ac03f1ecc46be92 Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Mon, 8 May 2023 02:02:48 -0400
Subject: [PATCH 268/852] feat: add support for jwt as input file

---
 modules/nf-core/sratools/fasterqdump/main.nf         |  3 +++
 modules/nf-core/sratools/prefetch/main.nf            |  2 ++
 nextflow.config                                      |  1 +
 .../main.nf                                          | 12 ++++++++++--
 4 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf
index 2336c318..4ed92814 100644
--- a/modules/nf-core/sratools/fasterqdump/main.nf
+++ b/modules/nf-core/sratools/fasterqdump/main.nf
@@ -10,6 +10,7 @@ process SRATOOLS_FASTERQDUMP {
     input:
     tuple val(meta), path(sra)
     path ncbi_settings
+    path certificate
 
     output:
     tuple val(meta), path('*.fastq.gz'), emit: reads
@@ -23,6 +24,7 @@ process SRATOOLS_FASTERQDUMP {
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def outfile = meta.single_end ? "${prefix}.fastq" : prefix
+    def key_file = certificate ? "--perm ${certificate}" : ''
     """
     export NCBI_SETTINGS="\$PWD/${ncbi_settings}"
 
@@ -30,6 +32,7 @@ process SRATOOLS_FASTERQDUMP {
         $args \\
         --threads $task.cpus \\
         --outfile $outfile \\
+        ${key_file} \\
         ${sra.name}
 
     pigz \\
diff --git a/modules/nf-core/sratools/prefetch/main.nf b/modules/nf-core/sratools/prefetch/main.nf
index 91b8aec2..5d894b88 100644
--- a/modules/nf-core/sratools/prefetch/main.nf
+++ b/modules/nf-core/sratools/prefetch/main.nf
@@ -10,6 +10,7 @@ process SRATOOLS_PREFETCH {
     input:
     tuple val(meta), val(id)
     path ncbi_settings
+    path certificate 
 
     output:
     tuple val(meta), path(id), emit: sra
@@ -20,6 +21,7 @@ process SRATOOLS_PREFETCH {
 
     shell:
     args = task.ext.args ?: ''
+    args += certificate ? " --perm ${certificate}" : ''
     args2 = task.ext.args2 ?: '5 1 100'  // <num retries> <base delay in seconds> <max delay in seconds>
     template 'retry_with_backoff.sh'
 }
diff --git a/nextflow.config b/nextflow.config
index 74ae84d6..61f89783 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -19,6 +19,7 @@ params {
     synapse_config              = null
     force_sratools_download     = false
     skip_fastq_download         = false
+    dbgap_key                   = null
 
     // Boilerplate options
     outdir                      = null
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf
index 1e1d0d7b..22b756ca 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf
@@ -23,13 +23,21 @@ workflow FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS {
     //
     // Prefetch sequencing reads in SRA format.
     //
-    SRATOOLS_PREFETCH ( ch_sra_ids, settings )
+    if (!params.dbgap_key) {
+        SRATOOLS_PREFETCH ( ch_sra_ids, settings, [] )
+    } else {
+        SRATOOLS_PREFETCH ( ch_sra_ids, settings, certificate = file(params.dbgap_key, checkIfExists: true) )
+    }
     ch_versions = ch_versions.mix(SRATOOLS_PREFETCH.out.versions.first())
 
     //
     // Convert the SRA format into one or more compressed FASTQ files.
     //
-    SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra, settings )
+    if (!params.dbgap_key) {
+       SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra, settings, [] ) 
+    } else {
+       SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra, settings, certificate = file(params.dbgap_key, checkIfExists: true) ) 
+    }
     ch_versions = ch_versions.mix(SRATOOLS_FASTERQDUMP.out.versions.first())
 
     emit:

From b71105020bfc4cef617ebb2c609fe52e756ca41e Mon Sep 17 00:00:00 2001
From: EC2 Default User <ec2-user@ip-172-31-58-117.ec2.internal>
Date: Mon, 8 May 2023 18:08:45 +0000
Subject: [PATCH 269/852] refactor: simplify logic for params.dbgap_key

---
 .../main.nf                                   | 27 ++++++++++---------
 1 file changed, 15 insertions(+), 12 deletions(-)

diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf
index 22b756ca..965d8779 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf
@@ -21,23 +21,26 @@ workflow FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS {
     ch_versions = ch_versions.mix(CUSTOM_SRATOOLSNCBISETTINGS.out.versions)
 
     //
-    // Prefetch sequencing reads in SRA format.
+    // Prefetch sequencing reads in SRA format and convert into one or more compressed FASTQ files.
+    // If specified in params, use the provided JWT file for pulling protected SRA runs, else provide 
+    // an empty list.
     //
+    
     if (!params.dbgap_key) {
-        SRATOOLS_PREFETCH ( ch_sra_ids, settings, [] )
-    } else {
-        SRATOOLS_PREFETCH ( ch_sra_ids, settings, certificate = file(params.dbgap_key, checkIfExists: true) )
-    }
-    ch_versions = ch_versions.mix(SRATOOLS_PREFETCH.out.versions.first())
+        
+        SRATOOLS_PREFETCH ( ch_sra_ids, settings, [] ) 
+        SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra, settings, [] )
 
-    //
-    // Convert the SRA format into one or more compressed FASTQ files.
-    //
-    if (!params.dbgap_key) {
-       SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra, settings, [] ) 
     } else {
-       SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra, settings, certificate = file(params.dbgap_key, checkIfExists: true) ) 
+        
+        certificate = file(params.dbgap_key, checkIfExists: true) // optional input channel for JWT
+
+        SRATOOLS_PREFETCH ( ch_sra_ids, settings, certificate ) 
+        SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra, settings, certificate ) 
+
     }
+
+    ch_versions = ch_versions.mix(SRATOOLS_PREFETCH.out.versions.first())
     ch_versions = ch_versions.mix(SRATOOLS_FASTERQDUMP.out.versions.first())
 
     emit:

From acf5ed960574e41de5f13e9cea1bda73a2d50b8b Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Mon, 8 May 2023 14:23:24 -0400
Subject: [PATCH 270/852] chore(nextflow_schema.json): update schema with
 dbgap_key param

---
 nextflow_schema.json | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 563c5e7b..487de1e6 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -64,6 +64,13 @@
                     "fa_icon": "fas fa-fast-forward",
                     "description": "Only download metadata for public data database ids and don't download the FastQ files."
                 },
+                "dbgap_key": {
+                    "type": "string",
+                    "default": null,
+                    "fa_icon": "fas fa-address-card",
+                    "help_text": "Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit. Users with granted access to controlled data can download the JWT cart file for the study from the SRA Run Selector upon logging in. The JWT file can only be used on cloud platforms and is valid for 1 hour upon creation.",
+                    "format": "file-path"
+                },
                 "outdir": {
                     "type": "string",
                     "format": "directory-path",

From a56363538ff1c1d901e8d88d5643bd531e8f204d Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Mon, 8 May 2023 14:39:03 -0400
Subject: [PATCH 271/852] docs(usage.md): add usage detail on providing jwt
 file

---
 docs/usage.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/usage.md b/docs/usage.md
index 55e47133..0f47198f 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -22,7 +22,7 @@ The pipeline has been set-up to automatically download and process the raw FastQ
 
 If `SRR`/`ERR`/`DRR` run ids are provided then these will be resolved back to their appropriate `SRX`/`ERX`/`DRX` ids to be able to merge multiple runs from the same experiment. This is conceptually the same as merging multiple libraries sequenced from the same sample.
 
-The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5 sums. If download links exist, the files will be downloaded in parallel by FTP. Otherwise they are downloaded using sra-tools.
+The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5 sums. If download links exist, the files will be downloaded in parallel by FTP. Otherwise they are downloaded using sra-tools. To download protected dbGAP data using sra-tools, a JWT cart file can be specified with `--dbgap_key /path/to/cart.jwt`. 
 
 All of the sample metadata obtained from the ENA will be appended as additional columns to help you manually curate the generated samplesheet before you run the pipeline. You can customise the metadata fields that are appended to the samplesheet via the `--ena_metadata_fields` parameter. The default list of fields used by the pipeline can be found at the top of the [`bin/sra_ids_to_runinfo.py`](https://github.com/nf-core/fetchngs/blob/master/bin/sra_ids_to_runinfo.py) script within the pipeline repo. However, this pipeline requires a minimal set of fields to download FastQ files i.e. `'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'`. A comprehensive list of accepted metadata fields can be obtained from the [ENA API](https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run).
 

From 87b2bd8ea3d0dd87113a2318f68f991dd22477bf Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Mon, 8 May 2023 21:45:19 -0400
Subject: [PATCH 272/852] chore: update changelog

---
 CHANGELOG.md | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c1bf6a64..066e3d71 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,12 +19,14 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 
 ### Enhancements & fixes
 
-- [#85](https://github.com/nf-core/fetchngs/issues/85) - Not able to fetch metadata for ERR\* ids associated with ArrayExpress
-- [#129](https://github.com/nf-core/fetchngs/issues/129) - Pipeline is working with SRA run IDs, but failing with corresponding Biosample IDs
+- [#85](https://github.com/nf-core/fetchngs/issues/85) - Not able to fetch metadata for ERR ids associated with ArrayExpress
+- [#129](https://github.com/nf-core/fetchngs/issues/129) - Pipeline is working with SRA run ids but failing with corresponding Biosample ids
 - [#144](https://github.com/nf-core/fetchngs/issues/144) - Add support to download 10X Genomics data
-- [#148](https://github.com/nf-core/fetchngs/pull/148) - Fix default metadata fields for ENA API v2.0
-- Bumped modules version to allow for sratools download of sralite format files.
-- Updated pipeline template to [nf-core/tools 2.8](https://github.com/nf-core/tools/releases/tag/2.8)
+- [PR #140](https://github.com/nf-core/fetchngs/pull/140) - Bumped modules version to allow for sratools download of sralite format files
+- [PR #147](https://github.com/nf-core/fetchngs/pull/147) - Updated pipeline template to [nf-core/tools 2.8](https://github.com/nf-core/tools/releases/tag/2.8)
+- [PR #148](https://github.com/nf-core/fetchngs/pull/148) - Fix default metadata fields for ENA API v2.0
+- [PR #150](https://github.com/nf-core/fetchngs/pull/150) - Add infrastructure and CI for multi-cloud full-sized tests run via Nextflow Tower
+- [PR #152](https://github.com/nf-core/fetchngs/pull/152) - Add support for downloading protected dbGAP data using a JWT file
 
 ### Software dependencies
 

From 1265a8fb9e55c6139bfb139205fb50b0ccd74356 Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Tue, 9 May 2023 23:38:12 -0400
Subject: [PATCH 273/852] fix: update gse resolver to use esearch api endpoint

---
 bin/sra_ids_to_runinfo.py | 15 ++++++---------
 1 file changed, 6 insertions(+), 9 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index 6cf16800..4297590f 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -14,7 +14,7 @@
 from urllib.error import HTTPError, URLError
 from urllib.parse import urlencode
 from urllib.request import urlopen
-
+import json
 
 logger = logging.getLogger()
 
@@ -240,16 +240,13 @@ def _id_to_srx(cls, identifier):
 
     @classmethod
     def _gse_to_srx(cls, identifier):
-        """Resolve the identifier to SRA experiments."""
+        """Resolve the GEO identifier to SRA experiments."""
         ids = []
-        params = {"id": identifier, "db": "gds", "rettype": "runinfo", "retmode": "text"}
-        response = fetch_url(f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?{urlencode(params)}")
+        params = {"term": identifier, "db": "sra", "retmode": "json"}
+        response = fetch_url(f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?{urlencode(params)}")
         cls._content_check(response, identifier)
-        gsm_ids = [
-            line.split("=")[1].strip()
-            for line in response.text().splitlines()
-            if line.split("=")[1].strip().startswith("GSM")
-        ]
+        r_json = json.loads(response.text())
+        gsm_ids = r_json['esearchresult']['idlist']
         for gsm_id in gsm_ids:
             ids += cls._id_to_srx(gsm_id)
         return ids

From 0bdeac4b44d311f03e095355ef4a57e83e758a8d Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Wed, 10 May 2023 01:29:04 -0400
Subject: [PATCH 274/852] feat: add support for GSE/GDS IDs and resolver to GSM
 then SRA

---
 bin/sra_ids_to_runinfo.py | 35 ++++++++++++++++++++++++++++++++---
 1 file changed, 32 insertions(+), 3 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index 4297590f..fc8942d1 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -188,7 +188,8 @@ def is_valid(cls, identifier):
 class DatabaseResolver:
     """Define a service class for resolving various identifiers to experiments."""
 
-    _GEO_PREFIXES = {"GSE", "GSM"}
+    _GEO_GSM_PREFIXES = {"GSM"}
+    _GEO_GSE_PREFIXES = {"GDS", "GSE"}
     _SRA_PREFIXES = {
         "PRJNA",
         "DRA",
@@ -214,7 +215,9 @@ def expand_identifier(cls, identifier):
 
         """
         prefix = ID_REGEX.match(identifier).group(1)
-        if prefix in cls._GEO_PREFIXES:
+        if prefix in cls._GEO_GSM_PREFIXES:
+            return cls._gsm_to_srx(identifier)
+        elif prefix in cls._GEO_GSE_PREFIXES:
             return cls._gse_to_srx(identifier)
         elif prefix in cls._SRA_PREFIXES:
             return cls._id_to_srx(identifier)
@@ -239,7 +242,7 @@ def _id_to_srx(cls, identifier):
         return [row["Experiment"] for row in open_table(response, delimiter=",")]
 
     @classmethod
-    def _gse_to_srx(cls, identifier):
+    def _gsm_to_srx(cls, identifier):
         """Resolve the GEO identifier to SRA experiments."""
         ids = []
         params = {"term": identifier, "db": "sra", "retmode": "json"}
@@ -250,6 +253,32 @@ def _gse_to_srx(cls, identifier):
         for gsm_id in gsm_ids:
             ids += cls._id_to_srx(gsm_id)
         return ids
+    
+    @classmethod
+    def _gds_to_gsm(cls, identifier):
+        """Resolve the GEO UIDs to GSM IDs to then resolve to SRA IDs."""
+        ids = []
+        params = {"id": identifier, "db": "gds", "retmode": "json", "retmax": 10}
+        response = fetch_url(f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?{urlencode(params)}")
+        cls._content_check(response, identifier)
+        r_json = json.loads(response.text())
+        
+        for each in r_json['result'][identifier]['samples'][0:]:
+            ids += cls._gsm_to_srx(each['accession'])
+        return ids
+
+    @classmethod
+    def _gse_to_srx(cls, identifier):
+        """Resolve the GSE identifier to GEO UIDs."""
+        ids = []
+        params = {"term": identifier, "db": "gds", "retmode": "json"}
+        response = fetch_url(f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?{urlencode(params)}")
+        cls._content_check(response, identifier)
+        r_json = json.loads(response.text())
+        gds_uids = r_json['esearchresult']['idlist']
+        for gds_uid in gds_uids:
+            ids += cls._gds_to_gsm(gds_uid)
+        return ids
 
     @classmethod
     def _id_to_erx(cls, identifier):

From 0c226d2aaf2a539ef428974f78c7585f98b797f6 Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Wed, 10 May 2023 01:29:53 -0400
Subject: [PATCH 275/852] fix: remove support for bioproject ID (doesn't work)

---
 bin/sra_ids_to_runinfo.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index fc8942d1..84a6623d 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -191,7 +191,6 @@ class DatabaseResolver:
     _GEO_GSM_PREFIXES = {"GSM"}
     _GEO_GSE_PREFIXES = {"GDS", "GSE"}
     _SRA_PREFIXES = {
-        "PRJNA",
         "DRA",
         "DRP",
         "DRS",

From bd540c0b1dd4f5cc2e3bc9a7cef19d92ecb52857 Mon Sep 17 00:00:00 2001
From: sirclockalot <l.c.stickley@gmail.com>
Date: Wed, 10 May 2023 13:59:37 +0200
Subject: [PATCH 276/852] Update nextflow_schema.json

Corrected the url for ena metadata
---
 nextflow_schema.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 696914e4..fc0e83ee 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -32,7 +32,7 @@
                     "type": "string",
                     "fa_icon": "fas fa-columns",
                     "description": "Comma-separated list of ENA metadata fields to fetch before downloading data.",
-                    "help_text": "The default list of fields used by the pipeline can be found at the top of the [`bin/sra_ids_to_runinfo.py`](https://github.com/nf-core/fetchngs/blob/master/bin/sra_ids_to_runinfo.py) script within the pipeline repo. This pipeline requires a minimal set of fields to download FastQ files i.e. `'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'`. Full list of accepted metadata fields can be obtained from the [ENA API](https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run])."
+                    "help_text": "The default list of fields used by the pipeline can be found at the top of the [`bin/sra_ids_to_runinfo.py`](https://github.com/nf-core/fetchngs/blob/master/bin/sra_ids_to_runinfo.py) script within the pipeline repo. This pipeline requires a minimal set of fields to download FastQ files i.e. `'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'`. Full list of accepted metadata fields can be obtained from the [ENA API](https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run)."
                 },
                 "sample_mapping_fields": {
                     "type": "string",

From a17861a2e04541b69ce4eda4e482a82ff7113aa6 Mon Sep 17 00:00:00 2001
From: Robert Syme <rob.syme@gmail.com>
Date: Wed, 10 May 2023 22:51:42 +0000
Subject: [PATCH 277/852] Set a default docker registry outside of profile
 scope.

The `docker.registry` configuration should always be set, as running
on cloud executors will need to pull docker images but will not
necessarily use the `docker` profile.
---
 nextflow.config | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 74ae84d6..3f336ca7 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -96,7 +96,6 @@ profiles {
     }
     docker {
         docker.enabled         = true
-        docker.registry        = 'quay.io'
         docker.userEmulation   = true
         conda.enabled          = false
         singularity.enabled    = false
@@ -179,6 +178,9 @@ env {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
+// Set default docker registry (will be unused unless pulling docker images)
+docker.registry = 'quay.io'
+
 def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true

From 3fdb87991fa6172bf444343c6022dd22ed251fbc Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Wed, 10 May 2023 19:03:57 -0400
Subject: [PATCH 278/852] chore: update docs to support GEO IDs, remove error
 handling for GEO

---
 README.md                | 15 ++-------------
 assets/schema_input.json |  4 ++--
 docs/output.md           |  6 +++---
 docs/usage.md            | 18 +++++++++---------
 lib/WorkflowMain.groovy  |  4 ++--
 lib/WorkflowSra.groovy   | 19 +------------------
 main.nf                  |  4 ++--
 nextflow_schema.json     |  2 +-
 workflows/sra.nf         |  7 -------
 9 files changed, 22 insertions(+), 57 deletions(-)

diff --git a/README.md b/README.md
index 94e6a5ba..a14f7fb1 100644
--- a/README.md
+++ b/README.md
@@ -12,7 +12,7 @@
 
 ## Introduction
 
-**nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from both public and private databases. At present, the pipeline supports SRA / ENA / DDBJ / Synapse ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)).
+**nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from both public and private databases. At present, the pipeline supports SRA / ENA / DDBJ / GEO /  Synapse ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)).
 
 ## Usage
 
@@ -56,7 +56,7 @@ For more details, please refer to the [usage documentation](https://nf-co.re/fet
 
 Via a single file of ids, provided one-per-line (see [example input file](https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv)) the pipeline performs the following steps:
 
-### SRA / ENA / DDBJ ids
+### SRA / ENA / DDBJ  / GEO ids
 
 1. Resolve database ids back to appropriate experiment-level ids and to be compatible with the [ENA API](https://ena-docs.readthedocs.io/en/latest/retrieval/programmatic-access.html)
 2. Fetch extensive id metadata via ENA API
@@ -65,17 +65,6 @@ Via a single file of ids, provided one-per-line (see [example input file](https:
    - Otherwise use [`sra-tools`](https://github.com/ncbi/sra-tools) to download `.sra` files and convert them to FastQ
 4. Collate id metadata and paths to FastQ files in a single samplesheet
 
-### GEO ids
-
-Support for GEO ids was dropped in [[v1.7](https://github.com/nf-core/fetchngs/releases/tag/1.7)] due to breaking changes introduced in the NCBI API. For more detailed information please see [this PR](https://github.com/nf-core/fetchngs/pull/102).
-
-As a workaround, if you have a GEO accession you can directly download a text file containing the appropriate SRA ids to pass to the pipeline instead:
-
-- Search for your GEO accession on [GEO](https://www.ncbi.nlm.nih.gov/geo)
-- Click `SRA Run Selector` at the bottom of the GEO accession page
-- Select the desired samples in the `SRA Run Selector` and then download the `Accession List`
-
-This downloads a text file called `SRR_Acc_List.txt` that can be directly provided to the pipeline once renamed with a .csv extension e.g. `--input SRR_Acc_List.csv`.
 
 ### Synapse ids
 
diff --git a/assets/schema_input.json b/assets/schema_input.json
index 71f0f976..9a800216 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -8,8 +8,8 @@
         "type": "array",
         "items": {
             "type": "string",
-            "pattern": "^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(syn))(\\d+)$",
-            "errorMessage": "Please provide a valid SRA, ENA, DDBJ identifier"
+            "pattern": "^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM])|(syn))(\\d+)$",
+            "errorMessage": "Please provide a valid SRA, ENA, DDBJ or GEO identifier"
         }
     }
 }
diff --git a/docs/output.md b/docs/output.md
index daaca914..7402976c 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -9,19 +9,19 @@ This document describes the output produced by the pipeline. The directories lis
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data depending on the type of ids provided:
 
 - Download FastQ files and create samplesheet from:
-  1. [SRA / ENA / DDBJ ids](#sra--ena--ddbj-ids)
+  1. [SRA / ENA / DDBJ / GEO ids](#sra--ena--ddbj--geo-ids)
   2. [Synapse ids](#synapse-ids)
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
 Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introduction) for a list of supported public repository identifiers and how to provide them to the pipeline.
 
-### SRA / ENA / DDBJ ids
+### SRA / ENA / DDBJ / GEO ids
 
 <details markdown="1">
 <summary>Output files</summary>
 
 - `fastq/`
-  - `*.fastq.gz`: Paired-end/single-end reads downloaded from the SRA / ENA / DDBJ.
+  - `*.fastq.gz`: Paired-end/single-end reads downloaded from the SRA / ENA / DDBJ / GEO.
 - `fastq/md5/`
   - `*.md5`: Files containing `md5` sum for FastQ files downloaded from the ENA.
 - `samplesheet/`
diff --git a/docs/usage.md b/docs/usage.md
index 55e47133..c2e32fa0 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -8,15 +8,15 @@
 
 The pipeline has been set-up to automatically download and process the raw FastQ files from both public and private repositories. Identifiers can be provided in a file, one-per-line via the `--input` parameter. Currently, the following types of example identifiers are supported:
 
-| `SRA`        | `ENA`        | `DDBJ`       | `Synapse`   |
-| ------------ | ------------ | ------------ | ----------- |
-| SRR11605097  | ERR4007730   | DRR171822    | syn26240435 |
-| SRX8171613   | ERX4009132   | DRX162434    |             |
-| SRS6531847   | ERS4399630   | DRS090921    |             |
-| SAMN14689442 | SAMEA6638373 | SAMD00114846 |             |
-| SRP256957    | ERP120836    | DRP004793    |             |
-| SRA1068758   | ERA2420837   | DRA008156    |             |
-| PRJNA625551  | PRJEB37513   | PRJDB4176    |             |
+| `SRA`        | `ENA`        | `DDBJ`       | `GEO`       | `Synapse`   |
+| ------------ | ------------ | ------------ | ----------- | ----------- |
+| SRR11605097  | ERR4007730   | DRR171822    | GSM4432381  | syn26240435 |
+| SRX8171613   | ERX4009132   | DRX162434    | GSE147507   |             |
+| SRS6531847   | ERS4399630   | DRS090921    |             |             |
+| SAMN14689442 | SAMEA6638373 | SAMD00114846 |             |             |
+| SRP256957    | ERP120836    | DRP004793    |             |             |
+| SRA1068758   | ERA2420837   | DRA008156    |             |             |
+| PRJNA625551  | PRJEB37513   | PRJDB4176    |             |             |
 
 ### SRR / ERR / DRR ids
 
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index 13fd6d82..99858d2a 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -111,7 +111,7 @@ class WorkflowMain {
             if (num_match == total_ids) {
                 is_sra = true
             } else {
-                Nextflow.error("Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / DDBJ or Synapse ids!")
+                Nextflow.error("Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / GEO / DDBJ or Synapse ids!")
             }
         }
         return is_sra
@@ -135,7 +135,7 @@ class WorkflowMain {
             if (num_match == total_ids) {
                 is_synapse = true
             } else {
-                Nextflow.error("Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / DDBJ or Synapse ids!")
+                Nextflow.error("Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / GEO / DDBJ or Synapse ids!")
             }
         }
         return is_synapse
diff --git a/lib/WorkflowSra.groovy b/lib/WorkflowSra.groovy
index 061f7ffb..2cd5ab75 100755
--- a/lib/WorkflowSra.groovy
+++ b/lib/WorkflowSra.groovy
@@ -30,21 +30,4 @@ class WorkflowSra {
             "  running nf-core/other pipelines.\n" +
             "==================================================================================="
     }
-
-    // Fail pipeline if input ids are from the GEO
-    public static void isGeoFail(ids) {
-        def pattern = /^(GS[EM])(\d+)$/
-        for (id in ids) {
-            if (id =~ pattern) {
-                def error_string = "===================================================================================\n" +
-                    "  GEO id detected: ${id}\n" +
-                    "  Support for GEO ids was dropped in v1.7 due to breaking changes in the NCBI API.\n" +
-                    "  Please remove any GEO ids from the input samplesheet.\n\n" +
-                    "  Please see:\n" +
-                    "  https://github.com/nf-core/fetchngs/pull/102\n" +
-                    "==================================================================================="
-                Nextflow.error(error_string)
-            }
-        }
-    }
-}
+}
\ No newline at end of file
diff --git a/main.nf b/main.nf
index e7d67165..6da732be 100644
--- a/main.nf
+++ b/main.nf
@@ -44,7 +44,7 @@ if (WorkflowMain.isSraId(ch_input)) {
 } else if (WorkflowMain.isSynapseId(ch_input)) {
     input_type = 'synapse'
 } else {
-    exit 1, 'Ids provided via --input not recognised please make sure they are either SRA / ENA / DDBJ or Synapse ids!'
+    exit 1, 'Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!'
 }
 
 if (params.input_type == input_type) {
@@ -63,7 +63,7 @@ if (params.input_type == input_type) {
 workflow NFCORE_FETCHNGS {
 
     //
-    // WORKFLOW: Download FastQ files for SRA / ENA / DDBJ ids
+    // WORKFLOW: Download FastQ files for SRA / ENA / GEO / DDBJ ids
     //
     if (params.input_type == 'sra') {
         SRA ( ch_ids )
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 563c5e7b..3f72c2f1 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -19,7 +19,7 @@
                     "pattern": "^\\S+\\.(csv|tsv|txt)$",
                     "schema": "assets/schema_input.json",
                     "fa_icon": "fas fa-file-excel",
-                    "description": "File containing SRA/ENA/DDBJ identifiers one per line to download their associated metadata and FastQ files."
+                    "description": "File containing SRA/ENA/GEO/DDBJ identifiers one per line to download their associated metadata and FastQ files."
                 },
                 "input_type": {
                     "type": "string",
diff --git a/workflows/sra.nf b/workflows/sra.nf
index e3ac447f..ae891aab 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -50,13 +50,6 @@ workflow SRA {
     main:
     ch_versions = Channel.empty()
 
-    //
-    // Fail the pipeline if GEO ids detected
-    //
-    ids
-        .collect()
-        .map { WorkflowSra.isGeoFail(it) }
-
     //
     // MODULE: Get SRA run information for public database ids
     //

From d19e7f41f6609d03d3814df65930d176a0a97e38 Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Wed, 10 May 2023 19:26:08 -0400
Subject: [PATCH 279/852] chore: update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4bb46ddb..5fe8e99a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -26,6 +26,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #147](https://github.com/nf-core/fetchngs/pull/147) - Updated pipeline template to [nf-core/tools 2.8](https://github.com/nf-core/tools/releases/tag/2.8)
 - [PR #148](https://github.com/nf-core/fetchngs/pull/148) - Fix default metadata fields for ENA API v2.0
 - [PR #150](https://github.com/nf-core/fetchngs/pull/150) - Add infrastructure and CI for multi-cloud full-sized tests run via Nextflow Tower
+- [PR #155](https://github.com/nf-core/fetchngs/pull/155) - Add support back in for [GEO IDs](https://www.ncbi.nlm.nih.gov/geo) (removed in v1.7)
 
 ### Software dependencies
 

From 2db65cc1e6f6fb09877888b341516d75181b79ed Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Wed, 10 May 2023 23:24:26 -0400
Subject: [PATCH 280/852] docs: update usage.md with dbGAP download details

---
 docs/usage.md | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/docs/usage.md b/docs/usage.md
index 0f47198f..231da022 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -22,7 +22,7 @@ The pipeline has been set-up to automatically download and process the raw FastQ
 
 If `SRR`/`ERR`/`DRR` run ids are provided then these will be resolved back to their appropriate `SRX`/`ERX`/`DRX` ids to be able to merge multiple runs from the same experiment. This is conceptually the same as merging multiple libraries sequenced from the same sample.
 
-The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5 sums. If download links exist, the files will be downloaded in parallel by FTP. Otherwise they are downloaded using sra-tools. To download protected dbGAP data using sra-tools, a JWT cart file can be specified with `--dbgap_key /path/to/cart.jwt`. 
+The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5 sums. If download links exist, the files will be downloaded in parallel by FTP. Otherwise they are downloaded using sra-tools. 
 
 All of the sample metadata obtained from the ENA will be appended as additional columns to help you manually curate the generated samplesheet before you run the pipeline. You can customise the metadata fields that are appended to the samplesheet via the `--ena_metadata_fields` parameter. The default list of fields used by the pipeline can be found at the top of the [`bin/sra_ids_to_runinfo.py`](https://github.com/nf-core/fetchngs/blob/master/bin/sra_ids_to_runinfo.py) script within the pipeline repo. However, this pipeline requires a minimal set of fields to download FastQ files i.e. `'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'`. A comprehensive list of accepted metadata fields can be obtained from the [ENA API](https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run).
 
@@ -70,6 +70,15 @@ From v1.9 of this pipeline the default `strandedness` in the output samplesheet
 
 If FTP connections are blocked on your network use the [`--force_sratools_download`](https://nf-co.re/fetchngs/parameters#force_sratools_download) parameter to force the pipeline to download data using sra-tools instead of the ENA FTP.
 
+### Downloading dbGAP data with JWT
+
+As of v1.10, the SRA Toolkit used in this pipeline can be configured to access protected data from dbGAP using a [JWT cart file](https://www.ncbi.nlm.nih.gov/sra/docs/sra-dbGAP-cloud-download/). The JWT cart file can be specified with `--dbgap_key /path/to/cart.jwt`. 
+ 
+
+Note that due to the way the pipeline resolves SRA IDs down to the experiment to be able to merge multiple runs, your JWT cart file must be generated for *all* runs in an experiment. Otherwise, upon running `prefetch` and `fasterq-dump`, the pipeline will return a `403 Error` when trying to download data for other runs under an experiment that are not authenticated for with the provided JWT cart file.
+
+Users can log into the [SRA Run Selector](https://www.ncbi.nlm.nih.gov/Traces/study/), search for the dbGAP study they have been granted access to using the phs identifier, and select all available runs to activate the `JWT Cart` button to download the file. 
+
 ## Running the pipeline
 
 The typical command for running the pipeline is as follows:

From b2c3d5ba69c43005fa285576b7d709904f5d219a Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Thu, 11 May 2023 08:25:47 +0100
Subject: [PATCH 281/852] Update nextflow.config

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 3f336ca7..fe374cae 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -178,7 +178,7 @@ env {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
-// Set default docker registry (will be unused unless pulling docker images)
+// Set default docker registry (will not be used unless pulling docker images)
 docker.registry = 'quay.io'
 
 def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')

From b80afbb4160b4c727f1337b13be4f33fa401220a Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Thu, 11 May 2023 11:07:39 +0200
Subject: [PATCH 282/852] Update nextflow.config

---
 nextflow.config | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index fe374cae..b554f445 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -119,7 +119,6 @@ profiles {
     }
     podman {
         podman.enabled         = true
-        podman.registry        = 'quay.io'
         conda.enabled          = false
         docker.enabled         = false
         singularity.enabled    = false
@@ -178,8 +177,11 @@ env {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
-// Set default docker registry (will not be used unless pulling docker images)
+// Set default registry for Docker and Podman independent of -profile
+// Will not be used unless Docker / Podman are enabled
+// Set to your registry if you have a mirror of containers
 docker.registry = 'quay.io'
+podman.registry = 'quay.io'
 
 def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {

From 37d0a033a7dd7a2175107af36aca5c577a778087 Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Thu, 11 May 2023 14:07:26 -0400
Subject: [PATCH 283/852] chore: apply linting for black and prettier

---
 bin/sra_ids_to_runinfo.py | 12 ++++++------
 lib/WorkflowSra.groovy    |  2 +-
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index 84a6623d..414d32a7 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -248,11 +248,11 @@ def _gsm_to_srx(cls, identifier):
         response = fetch_url(f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?{urlencode(params)}")
         cls._content_check(response, identifier)
         r_json = json.loads(response.text())
-        gsm_ids = r_json['esearchresult']['idlist']
+        gsm_ids = r_json["esearchresult"]["idlist"]
         for gsm_id in gsm_ids:
             ids += cls._id_to_srx(gsm_id)
         return ids
-    
+
     @classmethod
     def _gds_to_gsm(cls, identifier):
         """Resolve the GEO UIDs to GSM IDs to then resolve to SRA IDs."""
@@ -261,9 +261,9 @@ def _gds_to_gsm(cls, identifier):
         response = fetch_url(f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?{urlencode(params)}")
         cls._content_check(response, identifier)
         r_json = json.loads(response.text())
-        
-        for each in r_json['result'][identifier]['samples'][0:]:
-            ids += cls._gsm_to_srx(each['accession'])
+
+        for each in r_json["result"][identifier]["samples"][0:]:
+            ids += cls._gsm_to_srx(each["accession"])
         return ids
 
     @classmethod
@@ -274,7 +274,7 @@ def _gse_to_srx(cls, identifier):
         response = fetch_url(f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?{urlencode(params)}")
         cls._content_check(response, identifier)
         r_json = json.loads(response.text())
-        gds_uids = r_json['esearchresult']['idlist']
+        gds_uids = r_json["esearchresult"]["idlist"]
         for gds_uid in gds_uids:
             ids += cls._gds_to_gsm(gds_uid)
         return ids
diff --git a/lib/WorkflowSra.groovy b/lib/WorkflowSra.groovy
index 2cd5ab75..3c092a6f 100755
--- a/lib/WorkflowSra.groovy
+++ b/lib/WorkflowSra.groovy
@@ -30,4 +30,4 @@ class WorkflowSra {
             "  running nf-core/other pipelines.\n" +
             "==================================================================================="
     }
-}
\ No newline at end of file
+}

From 92af4687833ee77874bf3431b7236551a1356d58 Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Thu, 11 May 2023 14:13:48 -0400
Subject: [PATCH 284/852] chore: prettier linting

---
 docs/usage.md | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/docs/usage.md b/docs/usage.md
index 231da022..52eaf63d 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -22,7 +22,7 @@ The pipeline has been set-up to automatically download and process the raw FastQ
 
 If `SRR`/`ERR`/`DRR` run ids are provided then these will be resolved back to their appropriate `SRX`/`ERX`/`DRX` ids to be able to merge multiple runs from the same experiment. This is conceptually the same as merging multiple libraries sequenced from the same sample.
 
-The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5 sums. If download links exist, the files will be downloaded in parallel by FTP. Otherwise they are downloaded using sra-tools. 
+The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5 sums. If download links exist, the files will be downloaded in parallel by FTP. Otherwise they are downloaded using sra-tools.
 
 All of the sample metadata obtained from the ENA will be appended as additional columns to help you manually curate the generated samplesheet before you run the pipeline. You can customise the metadata fields that are appended to the samplesheet via the `--ena_metadata_fields` parameter. The default list of fields used by the pipeline can be found at the top of the [`bin/sra_ids_to_runinfo.py`](https://github.com/nf-core/fetchngs/blob/master/bin/sra_ids_to_runinfo.py) script within the pipeline repo. However, this pipeline requires a minimal set of fields to download FastQ files i.e. `'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'`. A comprehensive list of accepted metadata fields can be obtained from the [ENA API](https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run).
 
@@ -72,12 +72,11 @@ If FTP connections are blocked on your network use the [`--force_sratools_downlo
 
 ### Downloading dbGAP data with JWT
 
-As of v1.10, the SRA Toolkit used in this pipeline can be configured to access protected data from dbGAP using a [JWT cart file](https://www.ncbi.nlm.nih.gov/sra/docs/sra-dbGAP-cloud-download/). The JWT cart file can be specified with `--dbgap_key /path/to/cart.jwt`. 
- 
+As of v1.10, the SRA Toolkit used in this pipeline can be configured to access protected data from dbGAP using a [JWT cart file](https://www.ncbi.nlm.nih.gov/sra/docs/sra-dbGAP-cloud-download/). The JWT cart file can be specified with `--dbgap_key /path/to/cart.jwt`.
 
-Note that due to the way the pipeline resolves SRA IDs down to the experiment to be able to merge multiple runs, your JWT cart file must be generated for *all* runs in an experiment. Otherwise, upon running `prefetch` and `fasterq-dump`, the pipeline will return a `403 Error` when trying to download data for other runs under an experiment that are not authenticated for with the provided JWT cart file.
+Note that due to the way the pipeline resolves SRA IDs down to the experiment to be able to merge multiple runs, your JWT cart file must be generated for _all_ runs in an experiment. Otherwise, upon running `prefetch` and `fasterq-dump`, the pipeline will return a `403 Error` when trying to download data for other runs under an experiment that are not authenticated for with the provided JWT cart file.
 
-Users can log into the [SRA Run Selector](https://www.ncbi.nlm.nih.gov/Traces/study/), search for the dbGAP study they have been granted access to using the phs identifier, and select all available runs to activate the `JWT Cart` button to download the file. 
+Users can log into the [SRA Run Selector](https://www.ncbi.nlm.nih.gov/Traces/study/), search for the dbGAP study they have been granted access to using the phs identifier, and select all available runs to activate the `JWT Cart` button to download the file.
 
 ## Running the pipeline
 

From 21f37073e8f0041fb036905ddefc90e57cd5afad Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Thu, 11 May 2023 14:16:29 -0400
Subject: [PATCH 285/852] chore: lint docs and usage

---
 README.md     |  5 ++---
 docs/usage.md | 18 +++++++++---------
 2 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/README.md b/README.md
index a14f7fb1..4d6c2d35 100644
--- a/README.md
+++ b/README.md
@@ -12,7 +12,7 @@
 
 ## Introduction
 
-**nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from both public and private databases. At present, the pipeline supports SRA / ENA / DDBJ / GEO /  Synapse ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)).
+**nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from both public and private databases. At present, the pipeline supports SRA / ENA / DDBJ / GEO / Synapse ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)).
 
 ## Usage
 
@@ -56,7 +56,7 @@ For more details, please refer to the [usage documentation](https://nf-co.re/fet
 
 Via a single file of ids, provided one-per-line (see [example input file](https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv)) the pipeline performs the following steps:
 
-### SRA / ENA / DDBJ  / GEO ids
+### SRA / ENA / DDBJ / GEO ids
 
 1. Resolve database ids back to appropriate experiment-level ids and to be compatible with the [ENA API](https://ena-docs.readthedocs.io/en/latest/retrieval/programmatic-access.html)
 2. Fetch extensive id metadata via ENA API
@@ -65,7 +65,6 @@ Via a single file of ids, provided one-per-line (see [example input file](https:
    - Otherwise use [`sra-tools`](https://github.com/ncbi/sra-tools) to download `.sra` files and convert them to FastQ
 4. Collate id metadata and paths to FastQ files in a single samplesheet
 
-
 ### Synapse ids
 
 1. Resolve Synapse directory ids to their corresponding FastQ files ids via the `synapse list` command.
diff --git a/docs/usage.md b/docs/usage.md
index c2e32fa0..963d9229 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -8,15 +8,15 @@
 
 The pipeline has been set-up to automatically download and process the raw FastQ files from both public and private repositories. Identifiers can be provided in a file, one-per-line via the `--input` parameter. Currently, the following types of example identifiers are supported:
 
-| `SRA`        | `ENA`        | `DDBJ`       | `GEO`       | `Synapse`   |
-| ------------ | ------------ | ------------ | ----------- | ----------- |
-| SRR11605097  | ERR4007730   | DRR171822    | GSM4432381  | syn26240435 |
-| SRX8171613   | ERX4009132   | DRX162434    | GSE147507   |             |
-| SRS6531847   | ERS4399630   | DRS090921    |             |             |
-| SAMN14689442 | SAMEA6638373 | SAMD00114846 |             |             |
-| SRP256957    | ERP120836    | DRP004793    |             |             |
-| SRA1068758   | ERA2420837   | DRA008156    |             |             |
-| PRJNA625551  | PRJEB37513   | PRJDB4176    |             |             |
+| `SRA`        | `ENA`        | `DDBJ`       | `GEO`      | `Synapse`   |
+| ------------ | ------------ | ------------ | ---------- | ----------- |
+| SRR11605097  | ERR4007730   | DRR171822    | GSM4432381 | syn26240435 |
+| SRX8171613   | ERX4009132   | DRX162434    | GSE147507  |             |
+| SRS6531847   | ERS4399630   | DRS090921    |            |             |
+| SAMN14689442 | SAMEA6638373 | SAMD00114846 |            |             |
+| SRP256957    | ERP120836    | DRP004793    |            |             |
+| SRA1068758   | ERA2420837   | DRA008156    |            |             |
+| PRJNA625551  | PRJEB37513   | PRJDB4176    |            |             |
 
 ### SRR / ERR / DRR ids
 

From 0cb79229dc5d82bb4601ccfb8de87e5a22df3b7d Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 13 May 2023 20:27:31 +0100
Subject: [PATCH 286/852] Remove quay.io prefix from mulled containers

---
 modules/nf-core/sratools/fasterqdump/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf
index 2336c318..57a3dc9c 100644
--- a/modules/nf-core/sratools/fasterqdump/main.nf
+++ b/modules/nf-core/sratools/fasterqdump/main.nf
@@ -5,7 +5,7 @@ process SRATOOLS_FASTERQDUMP {
     conda "bioconda::sra-tools=2.11.0 conda-forge::pigz=2.6"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' :
-        'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' }"
+        'biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' }"
 
     input:
     tuple val(meta), path(sra)

From c5839cafa06732333faa7474397dacba6ba25d9d Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 13 May 2023 20:43:22 +0100
Subject: [PATCH 287/852] Add public_aws_ecr.config and use in CI tests

---
 .github/workflows/cloud_tests_full.yml  |  2 +-
 .github/workflows/cloud_tests_small.yml |  2 +-
 conf/public_aws_ecr.config              | 18 ++++++++++++++++++
 nextflow.config                         |  3 +++
 4 files changed, 23 insertions(+), 2 deletions(-)
 create mode 100644 conf/public_aws_ecr.config

diff --git a/.github/workflows/cloud_tests_full.yml b/.github/workflows/cloud_tests_full.yml
index d0ed0552..e25a97aa 100644
--- a/.github/workflows/cloud_tests_full.yml
+++ b/.github/workflows/cloud_tests_full.yml
@@ -27,7 +27,7 @@ jobs:
           compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
           workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/fetchngs/work-${{ github.sha }}"
           run_name: "aws_fetchngs_full"
-          profiles: test_full
+          profiles: test_full,public_aws_ecr
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
diff --git a/.github/workflows/cloud_tests_small.yml b/.github/workflows/cloud_tests_small.yml
index 12b8daab..e7636fdc 100644
--- a/.github/workflows/cloud_tests_small.yml
+++ b/.github/workflows/cloud_tests_small.yml
@@ -25,7 +25,7 @@ jobs:
           compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
           workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/fetchngs/work-${{ github.sha }}"
           run_name: "aws_fetchngs_small"
-          profiles: test
+          profiles: test,public_aws_ecr
           parameters: |
             {
                 "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/fetchngs/results-test-${{ github.sha }}"
diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config
new file mode 100644
index 00000000..59ac8c01
--- /dev/null
+++ b/conf/public_aws_ecr.config
@@ -0,0 +1,18 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    AWS ECR Config
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config to set public AWS ECR images wherever possible
+    This improves speed when running on AWS infrastructure.
+    Use this as an example template when using your own private registry.
+----------------------------------------------------------------------------------------
+*/
+
+docker.registry = 'public.ecr.aws'
+podman.registry = 'public.ecr.aws'
+
+process {
+    withName: '.*:SRATOOLS_FASTERQDUMP' {
+        container = 'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0'
+    }
+}
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index b554f445..18e065d0 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -158,6 +158,9 @@ profiles {
         executor.cpus          = 16
         executor.memory        = 60.GB
     }
+    public_aws_ecr {
+        includeConfig 'conf/public_aws_ecr.config'
+    }
     test         { includeConfig 'conf/test.config'         }
     test_synapse { includeConfig 'conf/test_synapse.config' }
     test_full    { includeConfig 'conf/test_full.config'    }

From 6a47ccd3c7e8e0e3450e52062fc159f7dbaf8687 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 13 May 2023 20:44:59 +0100
Subject: [PATCH 288/852] Update CHANGELOG

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4bb46ddb..297d1941 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@ Special thanks to the following for their contributions to the release:
 - [Maxime Garcia](https://github.com/maxulysse)
 - [Moritz E. Beber](https://github.com/Midnighter)
 - [Rob Syme](https://github.com/robsyme)
+- [sirclockalot](https://github.com/sirclockalot)
 
 Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
 
@@ -26,6 +27,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #147](https://github.com/nf-core/fetchngs/pull/147) - Updated pipeline template to [nf-core/tools 2.8](https://github.com/nf-core/tools/releases/tag/2.8)
 - [PR #148](https://github.com/nf-core/fetchngs/pull/148) - Fix default metadata fields for ENA API v2.0
 - [PR #150](https://github.com/nf-core/fetchngs/pull/150) - Add infrastructure and CI for multi-cloud full-sized tests run via Nextflow Tower
+- [PR #157](https://github.com/nf-core/fetchngs/pull/157) - Add `public_aws_ecr.config` to source mulled containers when using `public.ecr.aws` Docker Biocontainer registry
 
 ### Software dependencies
 

From 3e558a68195f4fccbe8c6af89caad3840e2d0211 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 13 May 2023 20:46:09 +0100
Subject: [PATCH 289/852] Run nf-core modules update to fix quay.io container
 definitions

---
 modules.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules.json b/modules.json
index dea81e71..ccf017da 100644
--- a/modules.json
+++ b/modules.json
@@ -17,7 +17,7 @@
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "10cb20f6a130d104fef335a8290f3ffce650f28d",
+                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/prefetch": {

From c9afc5cff2c80bd664e55420beb65e65540c2dc1 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 13 May 2023 20:47:37 +0100
Subject: [PATCH 290/852] Fix ECLint

---
 conf/public_aws_ecr.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config
index 59ac8c01..b9129571 100644
--- a/conf/public_aws_ecr.config
+++ b/conf/public_aws_ecr.config
@@ -15,4 +15,4 @@ process {
     withName: '.*:SRATOOLS_FASTERQDUMP' {
         container = 'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0'
     }
-}
\ No newline at end of file
+}

From 64a4971bea976940950d6cf24572d5ce3e730b19 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 14 May 2023 20:09:43 +0100
Subject: [PATCH 291/852] Update CHANGELOG

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 297d1941..d62cfdde 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-12
+## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-15
 
 ### Credits
 

From 740b2ce06d6e0b997432eac1c7d63f923436e2cc Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 14 May 2023 20:10:07 +0100
Subject: [PATCH 292/852] Bump pipeline version to 1.10.0

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 18e065d0..c1c66b07 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -211,7 +211,7 @@ manifest {
     description     = """Pipeline to fetch metadata and raw FastQ files from public databases"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '1.10.0dev'
+    version         = '1.10.0'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
 

From f510057968bc205cf5f8cccf488440da2a6d9365 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 14 May 2023 20:58:05 +0100
Subject: [PATCH 293/852] Add ubuntu containers to public_aws_ecr.config

---
 conf/public_aws_ecr.config | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config
index b9129571..abbe0fe4 100644
--- a/conf/public_aws_ecr.config
+++ b/conf/public_aws_ecr.config
@@ -15,4 +15,10 @@ process {
     withName: '.*:SRATOOLS_FASTERQDUMP' {
         container = 'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0'
     }
+    withName: '.*:SRA_MERGE_SAMPLESHEET' {
+        container = 'quay.io/nf-core/ubuntu:20.04'
+    }
+    withName: '.*:SYNAPSE_MERGE_SAMPLESHEET' {
+        container = 'quay.io/nf-core/ubuntu:20.04'
+    }
 }

From 3eb8afbdf39b6eaf299a866a0a6c3562fa970203 Mon Sep 17 00:00:00 2001
From: Esha Joshi <128735622+ejseqera@users.noreply.github.com>
Date: Mon, 15 May 2023 15:06:19 +0100
Subject: [PATCH 294/852] Update nextflow_schema.json

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 nextflow_schema.json | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 87d5024c..0abb1e39 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -66,7 +66,6 @@
                 },
                 "dbgap_key": {
                     "type": "string",
-                    "default": null,
                     "fa_icon": "fas fa-address-card",
                     "help_text": "Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit. Users with granted access to controlled data can download the JWT cart file for the study from the SRA Run Selector upon logging in. The JWT file can only be used on cloud platforms and is valid for 1 hour upon creation.",
                     "format": "file-path"

From fb7b6054c5c2d1a84fd553aa8df9c257fb07462e Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Mon, 15 May 2023 10:36:59 -0400
Subject: [PATCH 295/852] feat: move dbgap key param as input into parent
 workflow

---
 workflows/sra.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/workflows/sra.nf b/workflows/sra.nf
index e3ac447f..abf23dc3 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -113,7 +113,8 @@ workflow SRA {
         // SUBWORKFLOW: Download sequencing reads without FTP links using sra-tools.
         //
         FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS (
-            ch_sra_reads.sra.map { meta, reads -> [ meta, meta.run_accession ] }
+            ch_sra_reads.sra.map { meta, reads -> [ meta, meta.run_accession ] },
+            params.dbgap_key ?: []
         )
         ch_versions = ch_versions.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.versions.first())
 

From 43400b10746d79b5a502659358187dfbad294337 Mon Sep 17 00:00:00 2001
From: Esha Joshi <128735622+ejseqera@users.noreply.github.com>
Date: Mon, 15 May 2023 15:37:19 +0100
Subject: [PATCH 296/852] Update docs/usage.md

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 docs/usage.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/usage.md b/docs/usage.md
index 231da022..c9882467 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -22,7 +22,7 @@ The pipeline has been set-up to automatically download and process the raw FastQ
 
 If `SRR`/`ERR`/`DRR` run ids are provided then these will be resolved back to their appropriate `SRX`/`ERX`/`DRX` ids to be able to merge multiple runs from the same experiment. This is conceptually the same as merging multiple libraries sequenced from the same sample.
 
-The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5 sums. If download links exist, the files will be downloaded in parallel by FTP. Otherwise they are downloaded using sra-tools. 
+The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5 sums. If download links exist, the files will be downloaded in parallel by FTP. Otherwise they are downloaded using sra-tools.
 
 All of the sample metadata obtained from the ENA will be appended as additional columns to help you manually curate the generated samplesheet before you run the pipeline. You can customise the metadata fields that are appended to the samplesheet via the `--ena_metadata_fields` parameter. The default list of fields used by the pipeline can be found at the top of the [`bin/sra_ids_to_runinfo.py`](https://github.com/nf-core/fetchngs/blob/master/bin/sra_ids_to_runinfo.py) script within the pipeline repo. However, this pipeline requires a minimal set of fields to download FastQ files i.e. `'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'`. A comprehensive list of accepted metadata fields can be obtained from the [ENA API](https://www.ebi.ac.uk/ena/portal/api/returnFields?dataPortal=ena&format=tsv&result=read_run).
 

From d74d0561b4dd46c2f6d570a868245412d71c4c32 Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Mon, 15 May 2023 10:44:36 -0400
Subject: [PATCH 297/852] docs: update changelog to reference dbgap issue and
 not PR

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 066e3d71..73666bbe 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -26,7 +26,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #147](https://github.com/nf-core/fetchngs/pull/147) - Updated pipeline template to [nf-core/tools 2.8](https://github.com/nf-core/tools/releases/tag/2.8)
 - [PR #148](https://github.com/nf-core/fetchngs/pull/148) - Fix default metadata fields for ENA API v2.0
 - [PR #150](https://github.com/nf-core/fetchngs/pull/150) - Add infrastructure and CI for multi-cloud full-sized tests run via Nextflow Tower
-- [PR #152](https://github.com/nf-core/fetchngs/pull/152) - Add support for downloading protected dbGAP data using a JWT file
+- [#138](https://github.com/nf-core/fetchngs/issues/138) - Add support for downloading protected dbGAP data using a JWT file
 
 ### Software dependencies
 

From b07ca4290d6177e9c67c4fc0b444bd904072f72b Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Mon, 15 May 2023 11:50:06 -0400
Subject: [PATCH 298/852] refactor: fix changelog to reference geo issue

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5fe8e99a..1478af9f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -22,11 +22,11 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [#85](https://github.com/nf-core/fetchngs/issues/85) - Not able to fetch metadata for ERR ids associated with ArrayExpress
 - [#129](https://github.com/nf-core/fetchngs/issues/129) - Pipeline is working with SRA run ids but failing with corresponding Biosample ids
 - [#144](https://github.com/nf-core/fetchngs/issues/144) - Add support to download 10X Genomics data
+- [#104](https://github.com/nf-core/fetchngs/issues/104) - Add support back in for [GEO IDs](https://www.ncbi.nlm.nih.gov/geo) (removed in v1.7)
 - [PR #140](https://github.com/nf-core/fetchngs/pull/140) - Bumped modules version to allow for sratools download of sralite format files
 - [PR #147](https://github.com/nf-core/fetchngs/pull/147) - Updated pipeline template to [nf-core/tools 2.8](https://github.com/nf-core/tools/releases/tag/2.8)
 - [PR #148](https://github.com/nf-core/fetchngs/pull/148) - Fix default metadata fields for ENA API v2.0
 - [PR #150](https://github.com/nf-core/fetchngs/pull/150) - Add infrastructure and CI for multi-cloud full-sized tests run via Nextflow Tower
-- [PR #155](https://github.com/nf-core/fetchngs/pull/155) - Add support back in for [GEO IDs](https://www.ncbi.nlm.nih.gov/geo) (removed in v1.7)
 
 ### Software dependencies
 

From b3681617524b9cd4a4e6e8d4be792b4c1d02bd2b Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Mon, 15 May 2023 12:10:22 -0400
Subject: [PATCH 299/852] refactor: move up issue reference for dbgap

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 73666bbe..235f5c41 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -22,11 +22,11 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [#85](https://github.com/nf-core/fetchngs/issues/85) - Not able to fetch metadata for ERR ids associated with ArrayExpress
 - [#129](https://github.com/nf-core/fetchngs/issues/129) - Pipeline is working with SRA run ids but failing with corresponding Biosample ids
 - [#144](https://github.com/nf-core/fetchngs/issues/144) - Add support to download 10X Genomics data
+- [#138](https://github.com/nf-core/fetchngs/issues/138) - Add support for downloading protected dbGAP data using a JWT file
 - [PR #140](https://github.com/nf-core/fetchngs/pull/140) - Bumped modules version to allow for sratools download of sralite format files
 - [PR #147](https://github.com/nf-core/fetchngs/pull/147) - Updated pipeline template to [nf-core/tools 2.8](https://github.com/nf-core/tools/releases/tag/2.8)
 - [PR #148](https://github.com/nf-core/fetchngs/pull/148) - Fix default metadata fields for ENA API v2.0
 - [PR #150](https://github.com/nf-core/fetchngs/pull/150) - Add infrastructure and CI for multi-cloud full-sized tests run via Nextflow Tower
-- [#138](https://github.com/nf-core/fetchngs/issues/138) - Add support for downloading protected dbGAP data using a JWT file
 
 ### Software dependencies
 

From 32796feccc16b094411257b83e8fc78f5554f3b0 Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Mon, 15 May 2023 12:30:58 -0400
Subject: [PATCH 300/852] fix: modules update for sratools prefetch and
 fasterqdump

---
 CHANGELOG.md                                  |  1 +
 modules.json                                  |  6 ++--
 modules/nf-core/sratools/fasterqdump/main.nf  |  2 +-
 modules/nf-core/sratools/fasterqdump/meta.yml |  6 +++-
 modules/nf-core/sratools/prefetch/main.nf     |  2 +-
 modules/nf-core/sratools/prefetch/meta.yml    |  8 +++--
 .../main.nf                                   | 34 +++++++------------
 .../meta.yml                                  |  5 +++
 8 files changed, 34 insertions(+), 30 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 235f5c41..4b950fae 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -27,6 +27,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #147](https://github.com/nf-core/fetchngs/pull/147) - Updated pipeline template to [nf-core/tools 2.8](https://github.com/nf-core/tools/releases/tag/2.8)
 - [PR #148](https://github.com/nf-core/fetchngs/pull/148) - Fix default metadata fields for ENA API v2.0
 - [PR #150](https://github.com/nf-core/fetchngs/pull/150) - Add infrastructure and CI for multi-cloud full-sized tests run via Nextflow Tower
+- [nf-core/modules#3417](https://github.com/nf-core/modules/pull/3417) - Update sratools modules to optionally take a JWT file as input
 
 ### Software dependencies
 
diff --git a/modules.json b/modules.json
index dea81e71..3137b88b 100644
--- a/modules.json
+++ b/modules.json
@@ -17,12 +17,12 @@
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "10cb20f6a130d104fef335a8290f3ffce650f28d",
+                        "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/prefetch": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     }
                 }
@@ -31,7 +31,7 @@
                 "nf-core": {
                     "fastq_download_prefetch_fasterqdump_sratools": {
                         "branch": "master",
-                        "git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
+                        "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf
index 4ed92814..2d9090e2 100644
--- a/modules/nf-core/sratools/fasterqdump/main.nf
+++ b/modules/nf-core/sratools/fasterqdump/main.nf
@@ -5,7 +5,7 @@ process SRATOOLS_FASTERQDUMP {
     conda "bioconda::sra-tools=2.11.0 conda-forge::pigz=2.6"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' :
-        'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' }"
+        'biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' }"
 
     input:
     tuple val(meta), path(sra)
diff --git a/modules/nf-core/sratools/fasterqdump/meta.yml b/modules/nf-core/sratools/fasterqdump/meta.yml
index d6fbd444..629bdca5 100644
--- a/modules/nf-core/sratools/fasterqdump/meta.yml
+++ b/modules/nf-core/sratools/fasterqdump/meta.yml
@@ -27,7 +27,11 @@ input:
       description: >
         An NCBI user settings file.
       pattern: "*.mkfg"
-
+  - certificate:
+      type: file
+      description: >
+        Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit
+      pattern: "*.cart"
 output:
   - meta:
       type: map
diff --git a/modules/nf-core/sratools/prefetch/main.nf b/modules/nf-core/sratools/prefetch/main.nf
index 5d894b88..ba7be4bd 100644
--- a/modules/nf-core/sratools/prefetch/main.nf
+++ b/modules/nf-core/sratools/prefetch/main.nf
@@ -10,7 +10,7 @@ process SRATOOLS_PREFETCH {
     input:
     tuple val(meta), val(id)
     path ncbi_settings
-    path certificate 
+    path certificate
 
     output:
     tuple val(meta), path(id), emit: sra
diff --git a/modules/nf-core/sratools/prefetch/meta.yml b/modules/nf-core/sratools/prefetch/meta.yml
index a3a26522..9817b0b2 100644
--- a/modules/nf-core/sratools/prefetch/meta.yml
+++ b/modules/nf-core/sratools/prefetch/meta.yml
@@ -19,7 +19,7 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - id:
-      type: val
+      type: string
       description: >
         A string denoting an SRA id.
   - ncbi_settings:
@@ -27,7 +27,11 @@ input:
       description: >
         An NCBI user settings file.
       pattern: "*.mkfg"
-
+  - certificate:
+      type: file
+      description: >
+        Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit
+      pattern: "*.cart"
 output:
   - meta:
       type: map
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf
index 965d8779..de31637e 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf
@@ -7,7 +7,8 @@ include { SRATOOLS_FASTERQDUMP        } from '../../../modules/nf-core/sratools/
 //
 workflow FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS {
     take:
-    ch_sra_ids  // channel: [ val(meta), val(id) ]
+    ch_sra_ids   // channel: [ val(meta), val(id) ]
+    ch_dbgap_key // channel: [ path(dbgap_key) ]
 
     main:
 
@@ -17,33 +18,22 @@ workflow FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS {
     // Detect existing NCBI user settings or create new ones.
     //
     CUSTOM_SRATOOLSNCBISETTINGS()
-    def settings = CUSTOM_SRATOOLSNCBISETTINGS.out.ncbi_settings  // value channel: path(settings)
+    ch_ncbi_settings = CUSTOM_SRATOOLSNCBISETTINGS.out.ncbi_settings
     ch_versions = ch_versions.mix(CUSTOM_SRATOOLSNCBISETTINGS.out.versions)
 
     //
-    // Prefetch sequencing reads in SRA format and convert into one or more compressed FASTQ files.
-    // If specified in params, use the provided JWT file for pulling protected SRA runs, else provide 
-    // an empty list.
+    // Prefetch sequencing reads in SRA format.
     //
-    
-    if (!params.dbgap_key) {
-        
-        SRATOOLS_PREFETCH ( ch_sra_ids, settings, [] ) 
-        SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra, settings, [] )
-
-    } else {
-        
-        certificate = file(params.dbgap_key, checkIfExists: true) // optional input channel for JWT
-
-        SRATOOLS_PREFETCH ( ch_sra_ids, settings, certificate ) 
-        SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra, settings, certificate ) 
-
-    }
-
+    SRATOOLS_PREFETCH ( ch_sra_ids, ch_ncbi_settings, ch_dbgap_key )
     ch_versions = ch_versions.mix(SRATOOLS_PREFETCH.out.versions.first())
+
+    //
+    // Convert the SRA format into one or more compressed FASTQ files.
+    //
+    SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra, ch_ncbi_settings, ch_dbgap_key )
     ch_versions = ch_versions.mix(SRATOOLS_FASTERQDUMP.out.versions.first())
 
     emit:
-    reads    = SRATOOLS_FASTERQDUMP.out.reads  // channel: [ val(meta), [ reads ] ]
-    versions = ch_versions                     // channel: [ versions.yml ]
+    reads    = SRATOOLS_FASTERQDUMP.out.reads // channel: [ val(meta), [ reads ] ]
+    versions = ch_versions                    // channel: [ versions.yml ]
 }
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml
index 4599bbd2..6ff9442b 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml
@@ -22,6 +22,11 @@ input:
       type: string
       description: >
         SRA run identifier.
+  - certificate:
+      type: file
+      description: >
+        Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit
+      pattern: "*.cart"
 # TODO Update when we decide on a standard for subworkflow docs
 output:
   - meta:

From 1d75d1867c35411f0476b46c5c073a072303b617 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Mon, 15 May 2023 18:14:44 +0100
Subject: [PATCH 301/852] Apply suggestions from code review

---
 CHANGELOG.md  | 2 +-
 docs/usage.md | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c653e7d1..6eda7411 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -22,8 +22,8 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 
 - [#85](https://github.com/nf-core/fetchngs/issues/85) - Not able to fetch metadata for ERR ids associated with ArrayExpress
 - [#129](https://github.com/nf-core/fetchngs/issues/129) - Pipeline is working with SRA run ids but failing with corresponding Biosample ids
-- [#144](https://github.com/nf-core/fetchngs/issues/144) - Add support to download 10X Genomics data
 - [#138](https://github.com/nf-core/fetchngs/issues/138) - Add support for downloading protected dbGAP data using a JWT file
+- [#144](https://github.com/nf-core/fetchngs/issues/144) - Add support to download 10X Genomics data
 - [PR #140](https://github.com/nf-core/fetchngs/pull/140) - Bumped modules version to allow for sratools download of sralite format files
 - [PR #147](https://github.com/nf-core/fetchngs/pull/147) - Updated pipeline template to [nf-core/tools 2.8](https://github.com/nf-core/tools/releases/tag/2.8)
 - [PR #148](https://github.com/nf-core/fetchngs/pull/148) - Fix default metadata fields for ENA API v2.0
diff --git a/docs/usage.md b/docs/usage.md
index 52eaf63d..f0371eb3 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -72,7 +72,7 @@ If FTP connections are blocked on your network use the [`--force_sratools_downlo
 
 ### Downloading dbGAP data with JWT
 
-As of v1.10, the SRA Toolkit used in this pipeline can be configured to access protected data from dbGAP using a [JWT cart file](https://www.ncbi.nlm.nih.gov/sra/docs/sra-dbGAP-cloud-download/). The JWT cart file can be specified with `--dbgap_key /path/to/cart.jwt`.
+As of v1.10.0, the SRA Toolkit used in this pipeline can be configured to access protected data from dbGAP using a [JWT cart file](https://www.ncbi.nlm.nih.gov/sra/docs/sra-dbGAP-cloud-download/). The JWT cart file can be specified with `--dbgap_key /path/to/cart.jwt`.
 
 Note that due to the way the pipeline resolves SRA IDs down to the experiment to be able to merge multiple runs, your JWT cart file must be generated for _all_ runs in an experiment. Otherwise, upon running `prefetch` and `fasterq-dump`, the pipeline will return a `403 Error` when trying to download data for other runs under an experiment that are not authenticated for with the provided JWT cart file.
 

From b641a7adb80d1623ce6f58d67ee9fdd364ef2d36 Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Mon, 15 May 2023 14:56:55 -0400
Subject: [PATCH 302/852] docs: add SRA example for dbgap data download with
 jwt

---
 docs/usage.md | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/docs/usage.md b/docs/usage.md
index f0371eb3..e7a83805 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -72,12 +72,17 @@ If FTP connections are blocked on your network use the [`--force_sratools_downlo
 
 ### Downloading dbGAP data with JWT
 
-As of v1.10.0, the SRA Toolkit used in this pipeline can be configured to access protected data from dbGAP using a [JWT cart file](https://www.ncbi.nlm.nih.gov/sra/docs/sra-dbGAP-cloud-download/). The JWT cart file can be specified with `--dbgap_key /path/to/cart.jwt`.
+As of v1.10.0, the SRA Toolkit used in this pipeline can be configured to access protected data from dbGAP using a [JWT cart file](https://www.ncbi.nlm.nih.gov/sra/docs/sra-dbGAP-cloud-download/) on a supported cloud computing environment (Amazon Web Services or Google Cloud Platform). The JWT cart file can be specified with `--dbgap_key /path/to/cart.jwt`.
 
 Note that due to the way the pipeline resolves SRA IDs down to the experiment to be able to merge multiple runs, your JWT cart file must be generated for _all_ runs in an experiment. Otherwise, upon running `prefetch` and `fasterq-dump`, the pipeline will return a `403 Error` when trying to download data for other runs under an experiment that are not authenticated for with the provided JWT cart file.
 
 Users can log into the [SRA Run Selector](https://www.ncbi.nlm.nih.gov/Traces/study/), search for the dbGAP study they have been granted access to using the phs identifier, and select all available runs to activate the `JWT Cart` button to download the file.
 
+To test this functionality in your cloud computing environment, you can use the protected dbGAP cloud testing study with accession `SRR1219902`:
+
+- On the [SRA Run Selector page for `SRR1219902`](https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRR1219902&o=acc_s%3Aa&s=SRR1219902), select the available run and click on `JWT Cart` to download a key file called `jwt.cart` that can be directly provided to the pipeline with `--dbgap_key jwt.cart`
+- Click on `Accession List` to download a text file called `SRR_Acc_List.txt` that can be directly provided to the pipeline with `--input SRR_Acc_List.txt`
+
 ## Running the pipeline
 
 The typical command for running the pipeline is as follows:

From 76ad4b723ed7dd9a225b407c67a2d5695c55ebac Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Mon, 15 May 2023 15:30:45 -0400
Subject: [PATCH 303/852] docs: update test JWT sra accession ID to experiment
 ID

---
 docs/usage.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/usage.md b/docs/usage.md
index e7a83805..b3f215f3 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -78,10 +78,10 @@ Note that due to the way the pipeline resolves SRA IDs down to the experiment to
 
 Users can log into the [SRA Run Selector](https://www.ncbi.nlm.nih.gov/Traces/study/), search for the dbGAP study they have been granted access to using the phs identifier, and select all available runs to activate the `JWT Cart` button to download the file.
 
-To test this functionality in your cloud computing environment, you can use the protected dbGAP cloud testing study with accession `SRR1219902`:
+To test this functionality in your cloud computing environment, you can use the protected dbGAP cloud testing study with experiment accession `SRX512039`:
 
-- On the [SRA Run Selector page for `SRR1219902`](https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRR1219902&o=acc_s%3Aa&s=SRR1219902), select the available run and click on `JWT Cart` to download a key file called `jwt.cart` that can be directly provided to the pipeline with `--dbgap_key jwt.cart`
-- Click on `Accession List` to download a text file called `SRR_Acc_List.txt` that can be directly provided to the pipeline with `--input SRR_Acc_List.txt`
+- On the [SRA Run Selector page for `SRX512039`](https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRX512039&o=acc_s%3Aa), select the two available runs (`SRR1219865` and `SRR1219902`) and click on `JWT Cart` to download a key file called `cart.jwt` that can be directly provided to the pipeline with `--dbgap_key cart.jwt`
+- Click on `Accession List` to download a text file called `SRR_Acc_List.txt` with the SRR IDs that can be directly provided to the pipeline with `--input SRR_Acc_List.txt`
 
 ## Running the pipeline
 

From b0d32c2abc84a7cc508c16d69875f3a06b90601a Mon Sep 17 00:00:00 2001
From: Esha Joshi <128735622+ejseqera@users.noreply.github.com>
Date: Mon, 15 May 2023 20:34:22 +0100
Subject: [PATCH 304/852] Update workflows/sra.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 workflows/sra.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/sra.nf b/workflows/sra.nf
index abf23dc3..82120249 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -114,7 +114,7 @@ workflow SRA {
         //
         FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS (
             ch_sra_reads.sra.map { meta, reads -> [ meta, meta.run_accession ] },
-            params.dbgap_key ?: []
+            params.dbgap_key ? file(params.dbgap_key, checkIfExists: true) : []
         )
         ch_versions = ch_versions.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.versions.first())
 

From e84521daba5998e5307489e3b2bcc38a1e4fbd3b Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Mon, 15 May 2023 22:10:52 -0400
Subject: [PATCH 305/852] feat: add backoff strategy and handling for API
 responses

---
 bin/sra_ids_to_runinfo.py | 34 +++++++++++++++++++++++++++++++---
 1 file changed, 31 insertions(+), 3 deletions(-)

diff --git a/bin/sra_ids_to_runinfo.py b/bin/sra_ids_to_runinfo.py
index 414d32a7..0ffafba8 100755
--- a/bin/sra_ids_to_runinfo.py
+++ b/bin/sra_ids_to_runinfo.py
@@ -15,6 +15,7 @@
 from urllib.parse import urlencode
 from urllib.request import urlopen
 import json
+import time
 
 logger = logging.getLogger()
 
@@ -399,13 +400,40 @@ def validate_fields_parameter(param, valid_vals, param_desc):
 
 def fetch_url(url):
     """Return a response object for the given URL and handle errors appropriately."""
+    sleep_time = 5  # Hardcode sleep duration in seconds
+    max_num_attempts = 3  # Hardcode max number of request attempts
+    attempt = 0
+
     try:
         with urlopen(url) as response:
             return Response(response=response)
+
     except HTTPError as e:
-        logger.error("The server couldn't fulfill the request.")
-        logger.error(f"Status: {e.code} {e.reason}")
-        sys.exit(1)
+        if e.status == 429:
+            # If the response is 429, sleep and retry
+            if "Retry-After" in e.headers:
+                retry_after = int(e.headers["Retry-After"])
+                logging.warning(f"Received 429 response from server. Retrying after {retry_after} seconds...")
+                time.sleep(retry_after)
+            else:
+                logging.warning(f"Received 429 response from server. Retrying in {sleep_time} seconds...")
+                time.sleep(sleep_time)
+                sleep_time *= 2  # Increment sleep time
+            attempt += 1
+            return fetch_url(url)  # Recursive call to retry request
+
+        elif e.status == 500:
+            # If the response is 500, sleep and retry max 3 times
+            if attempt <= max_num_attempts:
+                logging.warning(f"Received 500 response from server. Retrying in {sleep_time} seconds...")
+                time.sleep(sleep_time)
+                sleep_time *= 2
+                attempt += 1
+                return fetch_url(url)
+            else:
+                logging.error("Exceeded max request attempts. Exiting.")
+                sys.exit(1)
+
     except URLError as e:
         logger.error("We failed to reach a server.")
         logger.error(f"Reason: {e.reason}")

From 945d87029a5acece603e22d6d66145a2675396ee Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Mon, 15 May 2023 22:14:39 -0400
Subject: [PATCH 306/852] docs: update changelog

---
 CHANGELOG.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1478af9f..0f936ef0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-12
+## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-16
 
 ### Credits
 
@@ -20,9 +20,9 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 ### Enhancements & fixes
 
 - [#85](https://github.com/nf-core/fetchngs/issues/85) - Not able to fetch metadata for ERR ids associated with ArrayExpress
+- [#104](https://github.com/nf-core/fetchngs/issues/104) - Add support back in for [GEO IDs](https://www.ncbi.nlm.nih.gov/geo) (removed in v1.7)
 - [#129](https://github.com/nf-core/fetchngs/issues/129) - Pipeline is working with SRA run ids but failing with corresponding Biosample ids
 - [#144](https://github.com/nf-core/fetchngs/issues/144) - Add support to download 10X Genomics data
-- [#104](https://github.com/nf-core/fetchngs/issues/104) - Add support back in for [GEO IDs](https://www.ncbi.nlm.nih.gov/geo) (removed in v1.7)
 - [PR #140](https://github.com/nf-core/fetchngs/pull/140) - Bumped modules version to allow for sratools download of sralite format files
 - [PR #147](https://github.com/nf-core/fetchngs/pull/147) - Updated pipeline template to [nf-core/tools 2.8](https://github.com/nf-core/tools/releases/tag/2.8)
 - [PR #148](https://github.com/nf-core/fetchngs/pull/148) - Fix default metadata fields for ENA API v2.0

From 6eeddaea28826db53f02853bfefa9cef62e7d4c8 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 16 May 2023 10:30:54 +0000
Subject: [PATCH 307/852] fix:

---
 conf/public_aws_ecr.config | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config
index abbe0fe4..b6711a54 100644
--- a/conf/public_aws_ecr.config
+++ b/conf/public_aws_ecr.config
@@ -12,6 +12,9 @@ docker.registry = 'public.ecr.aws'
 podman.registry = 'public.ecr.aws'
 
 process {
+    withName: 'SRA_IDS_TO_RUNINFO|SRA_RUNINFO_TO_FTP' {
+        container = 'quay.io/biocontainers/python:3.8.3'
+    }
     withName: '.*:SRATOOLS_FASTERQDUMP' {
         container = 'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0'
     }

From 751828548ff8d9eed7cb89ce75e321349e810b60 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 16 May 2023 10:35:47 +0000
Subject: [PATCH 308/852] Additional container image

---
 conf/public_aws_ecr.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config
index b6711a54..184d8c18 100644
--- a/conf/public_aws_ecr.config
+++ b/conf/public_aws_ecr.config
@@ -12,7 +12,7 @@ docker.registry = 'public.ecr.aws'
 podman.registry = 'public.ecr.aws'
 
 process {
-    withName: 'SRA_IDS_TO_RUNINFO|SRA_RUNINFO_TO_FTP' {
+    withName: 'SRA_IDS_TO_RUNINFO|SRA_RUNINFO_TO_FTP|MULTIQC_MAPPINGS_CONFIG' {
         container = 'quay.io/biocontainers/python:3.8.3'
     }
     withName: '.*:SRATOOLS_FASTERQDUMP' {

From c1bb2148a268e7947616247a644e651d425e917d Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 16 May 2023 10:50:20 +0000
Subject: [PATCH 309/852] Explicit container images per process

---
 conf/public_aws_ecr.config | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config
index 184d8c18..71180374 100644
--- a/conf/public_aws_ecr.config
+++ b/conf/public_aws_ecr.config
@@ -12,8 +12,14 @@ docker.registry = 'public.ecr.aws'
 podman.registry = 'public.ecr.aws'
 
 process {
-    withName: 'SRA_IDS_TO_RUNINFO|SRA_RUNINFO_TO_FTP|MULTIQC_MAPPINGS_CONFIG' {
-        container = 'quay.io/biocontainers/python:3.8.3'
+    withName: '.*:SRA_IDS_TO_RUNINFO' {
+        container = 'quay.io/biocontainers/python:3.9--1'
+    }
+    withName: '.*:SRA_RUNINFO_TO_FTP' {
+            container = 'quay.io/biocontainers/python:3.9--1'
+    }
+    withName: '.*:MULTIQC_MAPPINGS_CONFIG' {
+        container = 'quay.io/biocontainers/python:3.9--1'
     }
     withName: '.*:SRATOOLS_FASTERQDUMP' {
         container = 'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0'

From 255190ef0b634d09cf0bc92b7658986ed9f96031 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 16 May 2023 10:53:40 +0000
Subject: [PATCH 310/852] fixup

---
 conf/public_aws_ecr.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config
index 71180374..14b577d7 100644
--- a/conf/public_aws_ecr.config
+++ b/conf/public_aws_ecr.config
@@ -16,7 +16,7 @@ process {
         container = 'quay.io/biocontainers/python:3.9--1'
     }
     withName: '.*:SRA_RUNINFO_TO_FTP' {
-            container = 'quay.io/biocontainers/python:3.9--1'
+        container = 'quay.io/biocontainers/python:3.9--1'
     }
     withName: '.*:MULTIQC_MAPPINGS_CONFIG' {
         container = 'quay.io/biocontainers/python:3.9--1'

From e4efe564fc24aab09f4affe2f8d247c85b22d368 Mon Sep 17 00:00:00 2001
From: ejseqera <esha.joshi@seqera.io>
Date: Tue, 16 May 2023 13:00:31 -0400
Subject: [PATCH 311/852] Bump version to 1.11.0dev

---
 CHANGELOG.md    | 4 ++++
 nextflow.config | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 12ef2d50..2bd283e9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unpublished Version / DEV]
+
+### Enhancements & fixes
+
 ## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-16
 
 ### Credits
diff --git a/nextflow.config b/nextflow.config
index 1e9aaed0..0e0886e4 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -212,7 +212,7 @@ manifest {
     description     = """Pipeline to fetch metadata and raw FastQ files from public databases"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '1.10.0'
+    version         = '1.11.0dev'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
 

From ed05c7bc49f02317717b8811c7987fc57b6cca0e Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Mon, 8 May 2023 19:45:39 -0400
Subject: [PATCH 312/852] init-nf-tests

---
 nf-test.config                                |   8 +
 tests/config/tags.yml                         |  14 ++
 tests/modules/sra_ids_to_runinfo/main.nf.test |  43 +++++
 .../sra_ids_to_runinfo/main.nf.test.snap      |  28 ++++
 tests/nextflow.config                         |   5 +
 tests/pipeline/sra.nf.test                    |  28 ++++
 tests/pipeline/sra.nf.test.snap               |  60 +++++++
 tests/pipeline/sra_skip_fastq.nf.test         |  42 +++++
 tests/pipeline/sra_skip_fastq.nf.test.snap    |  30 ++++
 .../sra_with_nf_core_pipeline.nf.test         | 110 ++++++++++++
 .../sra_with_nf_core_pipeline.nf.test.snap    | 156 ++++++++++++++++++
 tests/pipeline/sra_with_sratools.nf.test      |  29 ++++
 tests/pipeline/sra_with_sratools.nf.test.snap |  49 ++++++
 tests/pipeline/synapse.test                   |  26 +++
 14 files changed, 628 insertions(+)
 create mode 100644 nf-test.config
 create mode 100644 tests/config/tags.yml
 create mode 100644 tests/modules/sra_ids_to_runinfo/main.nf.test
 create mode 100644 tests/modules/sra_ids_to_runinfo/main.nf.test.snap
 create mode 100644 tests/nextflow.config
 create mode 100644 tests/pipeline/sra.nf.test
 create mode 100644 tests/pipeline/sra.nf.test.snap
 create mode 100644 tests/pipeline/sra_skip_fastq.nf.test
 create mode 100644 tests/pipeline/sra_skip_fastq.nf.test.snap
 create mode 100644 tests/pipeline/sra_with_nf_core_pipeline.nf.test
 create mode 100644 tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
 create mode 100644 tests/pipeline/sra_with_sratools.nf.test
 create mode 100644 tests/pipeline/sra_with_sratools.nf.test.snap
 create mode 100644 tests/pipeline/synapse.test

diff --git a/nf-test.config b/nf-test.config
new file mode 100644
index 00000000..9d4198ff
--- /dev/null
+++ b/nf-test.config
@@ -0,0 +1,8 @@
+config {
+
+    testsDir "tests"
+    workDir ".nf-test"
+    configFile "nextflow.config"
+    profile ""
+
+}
diff --git a/tests/config/tags.yml b/tests/config/tags.yml
new file mode 100644
index 00000000..9214c834
--- /dev/null
+++ b/tests/config/tags.yml
@@ -0,0 +1,14 @@
+default:
+  - bin/**
+  - conf/**
+  - lib/**
+  - modules/**
+  - subworkflows/**
+  - tests/**
+  - workflows/**
+  - nextflow.config
+  - main.nf
+
+sra_ids_to_runinfo:
+  - modules/local/sra_ids_to_runinfo.nf
+  - tests/modules/sra_ids_to_runinfo/**
diff --git a/tests/modules/sra_ids_to_runinfo/main.nf.test b/tests/modules/sra_ids_to_runinfo/main.nf.test
new file mode 100644
index 00000000..f5467e75
--- /dev/null
+++ b/tests/modules/sra_ids_to_runinfo/main.nf.test
@@ -0,0 +1,43 @@
+nextflow_process {
+
+    name "Test Process SRA_IDS_TO_RUNINFO"
+    script "modules/local/sra_ids_to_runinfo.nf"
+    process "SRA_IDS_TO_RUNINFO"
+
+    test("Should run without failures without fields") {
+
+        when {
+            process {
+                """
+                input[0] = 'SRR9984183'
+                input[1] = ''
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+    test("Should run without failures with fields") {
+
+        when {
+            process {
+                """
+                input[0] = 'SRR9984183'
+                input[1] = 'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+}
diff --git a/tests/modules/sra_ids_to_runinfo/main.nf.test.snap b/tests/modules/sra_ids_to_runinfo/main.nf.test.snap
new file mode 100644
index 00000000..5a9ed62b
--- /dev/null
+++ b/tests/modules/sra_ids_to_runinfo/main.nf.test.snap
@@ -0,0 +1,28 @@
+{
+    "Should run without failures without fields": {
+        "content": [
+            {
+                "versions": [
+                    "versions.yml:md5,cd1056ca246a1ab3486fb6800f3012fb"
+                ],
+                "tsv": [
+                    "SRR9984183.runinfo.tsv:md5,a69083928f4b856d428a681c291b7ad6"
+                ]
+            }
+        ],
+        "timestamp": "2022-11-11T04:23:34+0000"
+    },
+    "Should run without failures with fields": {
+        "content": [
+            {
+                "versions": [
+                    "versions.yml:md5,cd1056ca246a1ab3486fb6800f3012fb"
+                ],
+                "tsv": [
+                    "SRR9984183.runinfo.tsv:md5,6419f18c29ab09634b3dd97a6b2acd06"
+                ]
+            }
+        ],
+        "timestamp": "2022-11-11T04:23:34+0000"
+    }
+}
diff --git a/tests/nextflow.config b/tests/nextflow.config
new file mode 100644
index 00000000..c19b1ad0
--- /dev/null
+++ b/tests/nextflow.config
@@ -0,0 +1,5 @@
+/*
+========================================================================================
+    Nextflow config file for running tests
+========================================================================================
+*/
diff --git a/tests/pipeline/sra.nf.test b/tests/pipeline/sra.nf.test
new file mode 100644
index 00000000..217eeaa1
--- /dev/null
+++ b/tests/pipeline/sra.nf.test
@@ -0,0 +1,28 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    options "-profile test,docker"
+    tag "pipeline"
+
+    test("SRA FASTQ & Metadata") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
+                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
+                { assert snapshot(path("$outputDir/metadata/").list()).match("metadata") },
+                { assert snapshot(path("$outputDir/samplesheet/").list()).match("samplesheet") }
+            )
+        }
+
+    }
+
+}
diff --git a/tests/pipeline/sra.nf.test.snap b/tests/pipeline/sra.nf.test.snap
new file mode 100644
index 00000000..8ed35844
--- /dev/null
+++ b/tests/pipeline/sra.nf.test.snap
@@ -0,0 +1,60 @@
+{
+    "metadata": {
+        "content": [
+            "DRR026872.runinfo_ftp.tsv:md5,5620768b65ecb4067b7547a49e07b67b",
+            "DRR028935.runinfo_ftp.tsv:md5,7f248072a55d5f729c4827937625a05b",
+            "ERR1109373.runinfo_ftp.tsv:md5,f7cd42805764f783388c2686fe2a3f95",
+            "ERR1160846.runinfo_ftp.tsv:md5,36257a2c851d10d61a97581f3496529d",
+            "SRR12848126.runinfo_ftp.tsv:md5,ce5380eceefba1210df0cefe321be62a",
+            "SRR13191702.runinfo_ftp.tsv:md5,37f87c5665e65cece1bc5e2b529e3b3b",
+            "SRR14593545.runinfo_ftp.tsv:md5,36a0fe8c5d3917f105e4cbbb7a720d7d",
+            "SRR14709033.runinfo_ftp.tsv:md5,8f06fa2e4708318dbe8e9505000ea919",
+            "SRR9984183.runinfo_ftp.tsv:md5,72047c09c02782932672862e8adf3fa5"
+        ],
+        "timestamp": "2023-04-27T17:03:41+0000"
+    },
+    "samplesheet": {
+        "content": [
+            "id_mappings.csv:md5,660db7a31a1c775cabad5f9b21addc06",
+            "multiqc_config.yml:md5,d01bd71fb5b9901c80166fba0637e430",
+            "samplesheet.csv:md5,90a48cdcc3773bd06586675a82571103"
+        ],
+        "timestamp": "2023-04-27T17:03:41+0000"
+    },
+    "software_versions": {
+        "content": [
+            "software_versions.yml:md5,015626dc3a0ea64e135bab19243e1586"
+        ],
+        "timestamp": "2023-04-27T17:03:41+0000"
+    },
+    "fastq": {
+        "content": [
+            "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791",
+            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
+            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30",
+            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
+            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
+            "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6",
+            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
+            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
+            "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
+            "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544",
+            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
+            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
+            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98",
+            [
+                "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d",
+                "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9",
+                "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f",
+                "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86",
+                "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499",
+                "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff",
+                "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4",
+                "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
+                "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
+            ]
+        ],
+        "timestamp": "2023-04-27T17:03:41+0000"
+    }
+}
\ No newline at end of file
diff --git a/tests/pipeline/sra_skip_fastq.nf.test b/tests/pipeline/sra_skip_fastq.nf.test
new file mode 100644
index 00000000..851099c3
--- /dev/null
+++ b/tests/pipeline/sra_skip_fastq.nf.test
@@ -0,0 +1,42 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    options "-profile test,docker"
+    tag "pipeline"
+
+    test("SRA Skip FASTQ") {
+
+        when {
+            params {
+                outdir              = "$outputDir"
+                skip_fastq_download = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
+                { assert snapshot(path("$outputDir/metadata/").list()).match("metadata") },
+                { assert snapshot(path("$outputDir/samplesheet/").list()).match("samplesheet") },
+                { assert !new File("$outputDir/fastq/DRX024467_DRR026872.fastq.gz").exists() },
+                { assert !new File("$outputDir/fastq/DRX026011_DRR028935_1.fastq.gz").exists() },
+                { assert !new File("$outputDir/fastq/DRX026011_DRR028935_2.fastq.gz").exists() },
+                { assert !new File("$outputDir/fastq/ERX1188904_ERR1109373_1.fastq.gz").exists() },
+                { assert !new File("$outputDir/fastq/ERX1188904_ERR1109373_2.fastq.gz").exists() },
+                { assert !new File("$outputDir/fastq/ERX1234253_ERR1160846.fastq.gz").exists() },
+                { assert !new File("$outputDir/fastq/SRX10940790_SRR14593545_1.fastq.gz").exists() },
+                { assert !new File("$outputDir/fastq/SRX10940790_SRR14593545_2.fastq.gz").exists() },
+                { assert !new File("$outputDir/fastq/SRX11047067_SRR14709033.fastq.gz").exists() },
+                { assert !new File("$outputDir/fastq/SRX6725035_SRR9984183.fastq.gz").exists() },
+                { assert !new File("$outputDir/fastq/SRX9315476_SRR12848126_1.fastq.gz").exists() },
+                { assert !new File("$outputDir/fastq/SRX9315476_SRR12848126_2.fastq.gz").exists() },
+                { assert !new File("$outputDir/fastq/SRX9626017_SRR13191702_1.fastq.gz").exists() },
+                { assert !new File("$outputDir/fastq/SRX9626017_SRR13191702_2.fastq.gz").exists() }
+            )
+        }
+
+    }
+
+}
diff --git a/tests/pipeline/sra_skip_fastq.nf.test.snap b/tests/pipeline/sra_skip_fastq.nf.test.snap
new file mode 100644
index 00000000..e04be0e0
--- /dev/null
+++ b/tests/pipeline/sra_skip_fastq.nf.test.snap
@@ -0,0 +1,30 @@
+{
+    "metadata": {
+        "content": [
+            "DRR026872.runinfo_ftp.tsv:md5,5620768b65ecb4067b7547a49e07b67b",
+            "DRR028935.runinfo_ftp.tsv:md5,7f248072a55d5f729c4827937625a05b",
+            "ERR1109373.runinfo_ftp.tsv:md5,f7cd42805764f783388c2686fe2a3f95",
+            "ERR1160846.runinfo_ftp.tsv:md5,36257a2c851d10d61a97581f3496529d",
+            "SRR12848126.runinfo_ftp.tsv:md5,ce5380eceefba1210df0cefe321be62a",
+            "SRR13191702.runinfo_ftp.tsv:md5,37f87c5665e65cece1bc5e2b529e3b3b",
+            "SRR14593545.runinfo_ftp.tsv:md5,36a0fe8c5d3917f105e4cbbb7a720d7d",
+            "SRR14709033.runinfo_ftp.tsv:md5,8f06fa2e4708318dbe8e9505000ea919",
+            "SRR9984183.runinfo_ftp.tsv:md5,72047c09c02782932672862e8adf3fa5"
+        ],
+        "timestamp": "2023-04-27T16:46:30+0000"
+    },
+    "samplesheet": {
+        "content": [
+            "id_mappings.csv:md5,660db7a31a1c775cabad5f9b21addc06",
+            "multiqc_config.yml:md5,d01bd71fb5b9901c80166fba0637e430",
+            "samplesheet.csv:md5,6b59e47a9fffdde864907419d0c4ad04"
+        ],
+        "timestamp": "2023-04-27T16:46:30+0000"
+    },
+    "software_versions": {
+        "content": [
+            "software_versions.yml:md5,d9a2185a464cbd9c0f576dad2ccea2cc"
+        ],
+        "timestamp": "2023-04-27T16:46:30+0000"
+    }
+}
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
new file mode 100644
index 00000000..a31c1fbb
--- /dev/null
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
@@ -0,0 +1,110 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    options "-profile test,docker"
+    tag "pipeline"
+
+    test("SRA NF-CORE/RNASEQ Samplesheet") {
+
+        when {
+            params {
+                outdir           = "$outputDir"
+                nf_core_pipeline = "rnaseq"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
+                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
+                { assert snapshot(path("$outputDir/metadata/").list()).match("rnaseq_metadata") },
+                { assert snapshot(path("$outputDir/samplesheet/").list()).match("rnaseq_samplesheet") }
+            )
+        }
+    }
+
+    test("SRA NF-CORE/RNASEQ Samplesheet With ENA metadata") {
+
+        when {
+            params {
+                outdir                = "$outputDir"
+                nf_core_pipeline      = "rnaseq"
+                ena_metadata_fields   = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5"
+                sample_mapping_fields = "run_accession,library_layout"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
+                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
+                { assert snapshot(path("$outputDir/metadata/").list()).match("rnaseq_ena_metadata") },
+                { assert snapshot(path("$outputDir/samplesheet/").list()).match("rnaseq_specific_ena_samplesheet") }
+            )
+        }
+    }
+
+    test("SRA NF-CORE/ATACSEQ Samplesheet") {
+
+        when {
+            params {
+                outdir           = "$outputDir"
+                nf_core_pipeline = "atacseq"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
+                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
+                { assert snapshot(path("$outputDir/metadata/").list()).match("atacseq_metadata") },
+                { assert snapshot(path("$outputDir/samplesheet/").list()).match("atacseq_samplesheet") }
+            )
+        }
+    }
+
+    test("SRA NF-CORE/VIRALRECON Samplesheet") {
+
+        when {
+            params {
+                outdir           = "$outputDir"
+                nf_core_pipeline = "viralrecon"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
+                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
+                { assert snapshot(path("$outputDir/metadata/").list()).match("viralrecon_metadata") },
+                { assert snapshot(path("$outputDir/samplesheet/").list()).match("viralrecon_samplesheet") }
+            )
+        }
+    }
+
+    test("SRA NF-CORE/TAXPROFILER Samplesheet") {
+
+        when {
+            params {
+                outdir           = "$outputDir"
+                nf_core_pipeline = "taxprofiler"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
+                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
+                { assert snapshot(path("$outputDir/metadata/").list()).match("taxprofiler_metadata") },
+                { assert snapshot(path("$outputDir/samplesheet/").list()).match("taxprofiler_samplesheet") }
+            )
+        }
+    }
+
+}
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
new file mode 100644
index 00000000..75d6ae55
--- /dev/null
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
@@ -0,0 +1,156 @@
+{
+    "taxprofiler_metadata": {
+        "content": [
+            "DRR026872.runinfo_ftp.tsv:md5,5620768b65ecb4067b7547a49e07b67b",
+            "DRR028935.runinfo_ftp.tsv:md5,7f248072a55d5f729c4827937625a05b",
+            "ERR1109373.runinfo_ftp.tsv:md5,f7cd42805764f783388c2686fe2a3f95",
+            "ERR1160846.runinfo_ftp.tsv:md5,36257a2c851d10d61a97581f3496529d",
+            "SRR12848126.runinfo_ftp.tsv:md5,ce5380eceefba1210df0cefe321be62a",
+            "SRR13191702.runinfo_ftp.tsv:md5,37f87c5665e65cece1bc5e2b529e3b3b",
+            "SRR14593545.runinfo_ftp.tsv:md5,36a0fe8c5d3917f105e4cbbb7a720d7d",
+            "SRR14709033.runinfo_ftp.tsv:md5,8f06fa2e4708318dbe8e9505000ea919",
+            "SRR9984183.runinfo_ftp.tsv:md5,72047c09c02782932672862e8adf3fa5"
+        ],
+        "timestamp": "2023-04-27T16:34:28+0000"
+    },
+    "software_versions": {
+        "content": [
+            "software_versions.yml:md5,015626dc3a0ea64e135bab19243e1586"
+        ],
+        "timestamp": "2023-04-27T16:34:28+0000"
+    },
+    "viralrecon_metadata": {
+        "content": [
+            "DRR026872.runinfo_ftp.tsv:md5,5620768b65ecb4067b7547a49e07b67b",
+            "DRR028935.runinfo_ftp.tsv:md5,7f248072a55d5f729c4827937625a05b",
+            "ERR1109373.runinfo_ftp.tsv:md5,f7cd42805764f783388c2686fe2a3f95",
+            "ERR1160846.runinfo_ftp.tsv:md5,36257a2c851d10d61a97581f3496529d",
+            "SRR12848126.runinfo_ftp.tsv:md5,ce5380eceefba1210df0cefe321be62a",
+            "SRR13191702.runinfo_ftp.tsv:md5,37f87c5665e65cece1bc5e2b529e3b3b",
+            "SRR14593545.runinfo_ftp.tsv:md5,36a0fe8c5d3917f105e4cbbb7a720d7d",
+            "SRR14709033.runinfo_ftp.tsv:md5,8f06fa2e4708318dbe8e9505000ea919",
+            "SRR9984183.runinfo_ftp.tsv:md5,72047c09c02782932672862e8adf3fa5"
+        ],
+        "timestamp": "2023-04-27T16:34:28+0000"
+    },
+    "viralrecon_samplesheet": {
+        "content": [
+            "id_mappings.csv:md5,660db7a31a1c775cabad5f9b21addc06",
+            "multiqc_config.yml:md5,d01bd71fb5b9901c80166fba0637e430",
+            "samplesheet.csv:md5,68c882e413afec7fec5aaa3f83aa7d22"
+        ],
+        "timestamp": "2023-04-27T16:34:28+0000"
+    },
+    "atacseq_metadata": {
+        "content": [
+            "DRR026872.runinfo_ftp.tsv:md5,5620768b65ecb4067b7547a49e07b67b",
+            "DRR028935.runinfo_ftp.tsv:md5,7f248072a55d5f729c4827937625a05b",
+            "ERR1109373.runinfo_ftp.tsv:md5,f7cd42805764f783388c2686fe2a3f95",
+            "ERR1160846.runinfo_ftp.tsv:md5,36257a2c851d10d61a97581f3496529d",
+            "SRR12848126.runinfo_ftp.tsv:md5,ce5380eceefba1210df0cefe321be62a",
+            "SRR13191702.runinfo_ftp.tsv:md5,37f87c5665e65cece1bc5e2b529e3b3b",
+            "SRR14593545.runinfo_ftp.tsv:md5,36a0fe8c5d3917f105e4cbbb7a720d7d",
+            "SRR14709033.runinfo_ftp.tsv:md5,8f06fa2e4708318dbe8e9505000ea919",
+            "SRR9984183.runinfo_ftp.tsv:md5,72047c09c02782932672862e8adf3fa5"
+        ],
+        "timestamp": "2023-04-27T16:34:28+0000"
+    },
+    "rnaseq_ena_metadata": {
+        "content": [
+            "DRR026872.runinfo_ftp.tsv:md5,74a5f7058f27a565ce59db481355ca54",
+            "DRR028935.runinfo_ftp.tsv:md5,07a98fdcec207686a4ea2c9a3997edf3",
+            "ERR1109373.runinfo_ftp.tsv:md5,868897310855c50b1d5fc77d1195a1f9",
+            "ERR1160846.runinfo_ftp.tsv:md5,146d7f2ec778b32b7da7ad040e554114",
+            "SRR12848126.runinfo_ftp.tsv:md5,cf8827612a76645824e83418d7d76cbf",
+            "SRR13191702.runinfo_ftp.tsv:md5,2031ca9b7ab736dbde37d05b10cdb0ad",
+            "SRR14593545.runinfo_ftp.tsv:md5,3a1ac14d71744224a61ab542f869e180",
+            "SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1",
+            "SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236"
+        ],
+        "timestamp": "2023-04-27T16:34:28+0000"
+    },
+    "rnaseq_samplesheet": {
+        "content": [
+            "id_mappings.csv:md5,660db7a31a1c775cabad5f9b21addc06",
+            "multiqc_config.yml:md5,d01bd71fb5b9901c80166fba0637e430",
+            "samplesheet.csv:md5,83a47dad4e4a78390d8ed5492c20f2a1"
+        ],
+        "timestamp": "2023-04-27T16:34:28+0000"
+    },
+    "rnaseq_samplesheet_specific_ena": {
+        "content": [
+            "id_mappings.csv:md5,0efde324e1818c0827390a17449a6e8a",
+            "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd",
+            "samplesheet.csv:md5,dc7371849e112d0e95646ef1c34339d0"
+        ],
+        "timestamp": "2023-04-27T16:34:28+0000"
+    },
+    "rnaseq_metadata": {
+        "content": [
+            "DRR026872.runinfo_ftp.tsv:md5,5620768b65ecb4067b7547a49e07b67b",
+            "DRR028935.runinfo_ftp.tsv:md5,7f248072a55d5f729c4827937625a05b",
+            "ERR1109373.runinfo_ftp.tsv:md5,f7cd42805764f783388c2686fe2a3f95",
+            "ERR1160846.runinfo_ftp.tsv:md5,36257a2c851d10d61a97581f3496529d",
+            "SRR12848126.runinfo_ftp.tsv:md5,ce5380eceefba1210df0cefe321be62a",
+            "SRR13191702.runinfo_ftp.tsv:md5,37f87c5665e65cece1bc5e2b529e3b3b",
+            "SRR14593545.runinfo_ftp.tsv:md5,36a0fe8c5d3917f105e4cbbb7a720d7d",
+            "SRR14709033.runinfo_ftp.tsv:md5,8f06fa2e4708318dbe8e9505000ea919",
+            "SRR9984183.runinfo_ftp.tsv:md5,72047c09c02782932672862e8adf3fa5"
+        ],
+        "timestamp": "2023-04-27T16:34:28+0000"
+    },
+    "rnaseq_specific_ena_samplesheet": {
+        "content": [
+            "id_mappings.csv:md5,0efde324e1818c0827390a17449a6e8a",
+            "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd",
+            "samplesheet.csv:md5,dc7371849e112d0e95646ef1c34339d0"
+        ],
+        "timestamp": "2023-04-27T16:34:28+0000"
+    },
+    "atacseq_samplesheet": {
+        "content": [
+            "id_mappings.csv:md5,660db7a31a1c775cabad5f9b21addc06",
+            "multiqc_config.yml:md5,d01bd71fb5b9901c80166fba0637e430",
+            "samplesheet.csv:md5,0c5df4b98006b33257d444eacbdcbfbe"
+        ],
+        "timestamp": "2023-04-27T16:34:28+0000"
+    },
+    "taxprofiler_samplesheet": {
+        "content": [
+            "id_mappings.csv:md5,660db7a31a1c775cabad5f9b21addc06",
+            "multiqc_config.yml:md5,d01bd71fb5b9901c80166fba0637e430",
+            "samplesheet.csv:md5,56f9b2713f8923a4bca194ca4fbbf245"
+        ],
+        "timestamp": "2023-04-27T16:34:28+0000"
+    },
+    "fastq": {
+        "content": [
+            "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791",
+            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
+            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30",
+            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
+            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
+            "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6",
+            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
+            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
+            "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
+            "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544",
+            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
+            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
+            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98",
+            [
+                "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d",
+                "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9",
+                "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f",
+                "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86",
+                "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499",
+                "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff",
+                "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4",
+                "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
+                "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
+            ]
+        ],
+        "timestamp": "2023-04-27T16:34:28+0000"
+    }
+}
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_sratools.nf.test b/tests/pipeline/sra_with_sratools.nf.test
new file mode 100644
index 00000000..97602440
--- /dev/null
+++ b/tests/pipeline/sra_with_sratools.nf.test
@@ -0,0 +1,29 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    options "-profile test,docker"
+    tag "pipeline"
+
+    test("SRA Force SRAtools Download") {
+
+        when {
+            params {
+                outdir                  = "$outputDir"
+                force_sratools_download = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
+                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
+                { assert snapshot(path("$outputDir/metadata/").list()).match("metadata") },
+                { assert snapshot(path("$outputDir/samplesheet/").list()).match("samplesheet") }
+            )
+        }
+
+    }
+
+}
diff --git a/tests/pipeline/sra_with_sratools.nf.test.snap b/tests/pipeline/sra_with_sratools.nf.test.snap
new file mode 100644
index 00000000..87af9987
--- /dev/null
+++ b/tests/pipeline/sra_with_sratools.nf.test.snap
@@ -0,0 +1,49 @@
+{
+    "metadata": {
+        "content": [
+            "DRR026872.runinfo_ftp.tsv:md5,5620768b65ecb4067b7547a49e07b67b",
+            "DRR028935.runinfo_ftp.tsv:md5,7f248072a55d5f729c4827937625a05b",
+            "ERR1109373.runinfo_ftp.tsv:md5,f7cd42805764f783388c2686fe2a3f95",
+            "ERR1160846.runinfo_ftp.tsv:md5,36257a2c851d10d61a97581f3496529d",
+            "SRR12848126.runinfo_ftp.tsv:md5,ce5380eceefba1210df0cefe321be62a",
+            "SRR13191702.runinfo_ftp.tsv:md5,37f87c5665e65cece1bc5e2b529e3b3b",
+            "SRR14593545.runinfo_ftp.tsv:md5,36a0fe8c5d3917f105e4cbbb7a720d7d",
+            "SRR14709033.runinfo_ftp.tsv:md5,8f06fa2e4708318dbe8e9505000ea919",
+            "SRR9984183.runinfo_ftp.tsv:md5,72047c09c02782932672862e8adf3fa5"
+        ],
+        "timestamp": "2023-04-27T16:51:33+0000"
+    },
+    "samplesheet": {
+        "content": [
+            "id_mappings.csv:md5,660db7a31a1c775cabad5f9b21addc06",
+            "multiqc_config.yml:md5,d01bd71fb5b9901c80166fba0637e430",
+            "samplesheet.csv:md5,2087763d7cdce58c331ae379b2e1dc27"
+        ],
+        "timestamp": "2023-04-27T16:51:33+0000"
+    },
+    "software_versions": {
+        "content": [
+            "software_versions.yml:md5,029defc466fd9a709cf95d2d903e1324"
+        ],
+        "timestamp": "2023-04-27T16:51:33+0000"
+    },
+    "fastq": {
+        "content": [
+            "DRX024467_DRR026872.fastq.gz:md5,bd3f113c3b06cf4499fa0e00c634ec85",
+            "DRX026011_DRR028935_1.fastq.gz:md5,0f96fb60e903c8cbd55a6977e66f7c93",
+            "DRX026011_DRR028935_2.fastq.gz:md5,b97b1e0e806bcae10a7443e2f22d6ca2",
+            "ERX1188904_ERR1109373_1.fastq.gz:md5,e7edae2715dfaf4c318d37959fd9ae22",
+            "ERX1188904_ERR1109373_2.fastq.gz:md5,34ab048c92201a5ec4ab36d8dc1c5732",
+            "ERX1234253_ERR1160846.fastq.gz:md5,22683b24b2467494e430643423f1e275",
+            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
+            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
+            "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
+            "SRX6725035_SRR9984183.fastq.gz:md5,7a70e678c400366869601c8be41fe74b",
+            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
+            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
+            "SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7",
+            "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af"
+        ],
+        "timestamp": "2023-04-27T16:51:33+0000"
+    }
+}
\ No newline at end of file
diff --git a/tests/pipeline/synapse.test b/tests/pipeline/synapse.test
new file mode 100644
index 00000000..91f865dc
--- /dev/null
+++ b/tests/pipeline/synapse.test
@@ -0,0 +1,26 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    options "-profile test_synapse,docker"
+    tag "pipeline"
+
+    test("Synapse Input Type") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
+                { assert snapshot(path("$outputDir/samplesheet/").list()).match("samplesheet") }
+            )
+        }
+
+    }
+
+}

From 028584dca40ea3c14073a82402e588c902ccd2d0 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Mon, 8 May 2023 19:46:02 -0400
Subject: [PATCH 313/852] update-ci-for-nf-tests

---
 .github/workflows/ci.yml | 80 +++++++++++++++++++++++++---------------
 .nf-core.yml             |  1 +
 2 files changed, 51 insertions(+), 30 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 5bef3edd..1b1f6b73 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,63 +1,83 @@
+# This is the nf-core CI workflow configuration for GitHub Actions
 name: nf-core CI
-# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+
+# This workflow is triggered when a pull request is made to the 'dev' branch or when a new release is published
 on:
-  push:
+  pull_request:
     branches:
       - dev
-  pull_request:
   release:
     types: [published]
 
+# Setting environment variable for Nextflow logs
 env:
   NXF_ANSI_LOG: false
 
+# Cancel if a newer run is started
 concurrency:
-  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
+  # Define the jobs to be run in parallel
 jobs:
   test:
-    name: Run pipeline with test data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}"
+    # Name the job with the corresponding profile, Nextflow version and aligner
+    name: Run ${{ matrix.profile }}-${{ matrix.NXF_VER }} pipeline test
+
+    # Set the condition for running the job
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}"
+
+    # Specify the runner for the job
     runs-on: ubuntu-latest
+
+    # Define the matrix for different Nextflow versions, profiles and aligners
     strategy:
       matrix:
         NXF_VER:
-          - "22.10.1"
           - "latest-everything"
+        profile: ["docker"]
+
+    # Define the steps for the job
     steps:
+      # Checkout the pipeline code from the repository
       - name: Check out pipeline code
         uses: actions/checkout@v3
 
+      # Cache Test Data
+      - name: Cache test data
+        uses: actions/cache@v2
+        with:
+          path: /usr/local/bin/nextflow
+          key: ${{ runner.os }}
+          restore-keys: |
+            ${{ runner.os }}-nextflow-
+
+      # Install the specified version of Nextflow
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Run pipeline with test data
+      # Install nf-test
+      - name: Install nf-test
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
 
-  parameters:
-    name: Test workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        parameters:
-          - "--nf_core_pipeline rnaseq"
-          - "--ena_metadata_fields run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5 --sample_mapping_fields run_accession,library_layout"
-          - "--skip_fastq_download"
-          - "--force_sratools_download"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Install Nextflow
+      # Run nf-test with the specified aligner and output test results in TAP format
+      - name: Run nf-test
         run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-      - name: Run pipeline with various parameters
+          nf-test test tests/pipeline/ --tap=test.tap
+
+      # If the test fails, output the software_versions.yml using the 'batcat' utility
+      - name: Output log on failure
+        if: failure()
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always /home/runner/work/fetchngs/fetchngs/.nf-test/tests/*/output/pipeline_info/software_versions.yml
+
+      # Use TAP summary to display test results
+      - uses: pcolby/tap-summary@v1
+        with:
+          path: >-
+            test.tap
diff --git a/.nf-core.yml b/.nf-core.yml
index cafd671c..0d8fc46d 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -3,3 +3,4 @@ lint:
   files_unchanged:
     - assets/sendmail_template.txt
     - lib/NfcoreTemplate.groovy
+  actions_ci: False
\ No newline at end of file

From e5ed5a53555eb652535d40241b3506bfde89a9a5 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Mon, 8 May 2023 19:47:36 -0400
Subject: [PATCH 314/852] prettier-fix-nf-core-yml

---
 .nf-core.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index 0d8fc46d..402025a7 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -3,4 +3,4 @@ lint:
   files_unchanged:
     - assets/sendmail_template.txt
     - lib/NfcoreTemplate.groovy
-  actions_ci: False
\ No newline at end of file
+  actions_ci: False

From 0136187a1105985cfa612b5ed90e3af7b60202fe Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Mon, 8 May 2023 20:41:06 -0400
Subject: [PATCH 315/852] rebase-and-update-snapshots

---
 .gitignore                                    |   2 +
 tests/pipeline/sra.nf.test.snap               |  34 ++---
 tests/pipeline/sra_skip_fastq.nf.test.snap    |  32 ++---
 .../sra_with_nf_core_pipeline.nf.test.snap    | 126 +++++++++---------
 tests/pipeline/sra_with_sratools.nf.test.snap |  34 ++---
 5 files changed, 115 insertions(+), 113 deletions(-)

diff --git a/.gitignore b/.gitignore
index 5124c9ac..935326a7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,5 @@ results/
 testing/
 testing*
 *.pyc
+.nf-test/
+nf-test
diff --git a/tests/pipeline/sra.nf.test.snap b/tests/pipeline/sra.nf.test.snap
index 8ed35844..3ce84e64 100644
--- a/tests/pipeline/sra.nf.test.snap
+++ b/tests/pipeline/sra.nf.test.snap
@@ -1,31 +1,31 @@
 {
     "metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,5620768b65ecb4067b7547a49e07b67b",
-            "DRR028935.runinfo_ftp.tsv:md5,7f248072a55d5f729c4827937625a05b",
-            "ERR1109373.runinfo_ftp.tsv:md5,f7cd42805764f783388c2686fe2a3f95",
-            "ERR1160846.runinfo_ftp.tsv:md5,36257a2c851d10d61a97581f3496529d",
-            "SRR12848126.runinfo_ftp.tsv:md5,ce5380eceefba1210df0cefe321be62a",
-            "SRR13191702.runinfo_ftp.tsv:md5,37f87c5665e65cece1bc5e2b529e3b3b",
-            "SRR14593545.runinfo_ftp.tsv:md5,36a0fe8c5d3917f105e4cbbb7a720d7d",
-            "SRR14709033.runinfo_ftp.tsv:md5,8f06fa2e4708318dbe8e9505000ea919",
-            "SRR9984183.runinfo_ftp.tsv:md5,72047c09c02782932672862e8adf3fa5"
+            "DRR026872.runinfo_ftp.tsv:md5,f46819ed848d0d28dff80fd0f5a4cd34",
+            "DRR028935.runinfo_ftp.tsv:md5,ef08c3756034e6705b0e13d1f37bfea5",
+            "ERR1109373.runinfo_ftp.tsv:md5,6e7960f43046c6080435a024e9c426c9",
+            "ERR1160846.runinfo_ftp.tsv:md5,db8b7bc5877a62b90e719d7cf3c0d25f",
+            "SRR12848126.runinfo_ftp.tsv:md5,b8ac151eb85a001e9aa3d7319156c016",
+            "SRR13191702.runinfo_ftp.tsv:md5,7188ac3b1d73ec297a900450e73bf751",
+            "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
+            "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
+            "SRR9984183.runinfo_ftp.tsv:md5,827751e211294eeecbb7239f70ead9a5"
         ],
-        "timestamp": "2023-04-27T17:03:41+0000"
+        "timestamp": "2023-05-09T00:33:33+0000"
     },
     "samplesheet": {
         "content": [
-            "id_mappings.csv:md5,660db7a31a1c775cabad5f9b21addc06",
-            "multiqc_config.yml:md5,d01bd71fb5b9901c80166fba0637e430",
-            "samplesheet.csv:md5,90a48cdcc3773bd06586675a82571103"
+            "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
+            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
+            "samplesheet.csv:md5,a12fd27d7741f1aa687049eb6ce9ed9a"
         ],
-        "timestamp": "2023-04-27T17:03:41+0000"
+        "timestamp": "2023-05-09T00:33:33+0000"
     },
     "software_versions": {
         "content": [
-            "software_versions.yml:md5,015626dc3a0ea64e135bab19243e1586"
+            "software_versions.yml:md5,c8ccda032b4de8e103eace767442fcf4"
         ],
-        "timestamp": "2023-04-27T17:03:41+0000"
+        "timestamp": "2023-05-09T00:33:33+0000"
     },
     "fastq": {
         "content": [
@@ -55,6 +55,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-04-27T17:03:41+0000"
+        "timestamp": "2023-05-09T00:33:33+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_skip_fastq.nf.test.snap b/tests/pipeline/sra_skip_fastq.nf.test.snap
index e04be0e0..4c208a29 100644
--- a/tests/pipeline/sra_skip_fastq.nf.test.snap
+++ b/tests/pipeline/sra_skip_fastq.nf.test.snap
@@ -1,30 +1,30 @@
 {
     "metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,5620768b65ecb4067b7547a49e07b67b",
-            "DRR028935.runinfo_ftp.tsv:md5,7f248072a55d5f729c4827937625a05b",
-            "ERR1109373.runinfo_ftp.tsv:md5,f7cd42805764f783388c2686fe2a3f95",
-            "ERR1160846.runinfo_ftp.tsv:md5,36257a2c851d10d61a97581f3496529d",
-            "SRR12848126.runinfo_ftp.tsv:md5,ce5380eceefba1210df0cefe321be62a",
-            "SRR13191702.runinfo_ftp.tsv:md5,37f87c5665e65cece1bc5e2b529e3b3b",
-            "SRR14593545.runinfo_ftp.tsv:md5,36a0fe8c5d3917f105e4cbbb7a720d7d",
-            "SRR14709033.runinfo_ftp.tsv:md5,8f06fa2e4708318dbe8e9505000ea919",
-            "SRR9984183.runinfo_ftp.tsv:md5,72047c09c02782932672862e8adf3fa5"
+            "DRR026872.runinfo_ftp.tsv:md5,f46819ed848d0d28dff80fd0f5a4cd34",
+            "DRR028935.runinfo_ftp.tsv:md5,ef08c3756034e6705b0e13d1f37bfea5",
+            "ERR1109373.runinfo_ftp.tsv:md5,6e7960f43046c6080435a024e9c426c9",
+            "ERR1160846.runinfo_ftp.tsv:md5,db8b7bc5877a62b90e719d7cf3c0d25f",
+            "SRR12848126.runinfo_ftp.tsv:md5,b8ac151eb85a001e9aa3d7319156c016",
+            "SRR13191702.runinfo_ftp.tsv:md5,7188ac3b1d73ec297a900450e73bf751",
+            "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
+            "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
+            "SRR9984183.runinfo_ftp.tsv:md5,827751e211294eeecbb7239f70ead9a5"
         ],
-        "timestamp": "2023-04-27T16:46:30+0000"
+        "timestamp": "2023-05-09T00:28:56+0000"
     },
     "samplesheet": {
         "content": [
-            "id_mappings.csv:md5,660db7a31a1c775cabad5f9b21addc06",
-            "multiqc_config.yml:md5,d01bd71fb5b9901c80166fba0637e430",
-            "samplesheet.csv:md5,6b59e47a9fffdde864907419d0c4ad04"
+            "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
+            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
+            "samplesheet.csv:md5,2006cc16ca44e947b5244528310c03e0"
         ],
-        "timestamp": "2023-04-27T16:46:30+0000"
+        "timestamp": "2023-05-09T00:28:56+0000"
     },
     "software_versions": {
         "content": [
-            "software_versions.yml:md5,d9a2185a464cbd9c0f576dad2ccea2cc"
+            "software_versions.yml:md5,8b5ec8d90481271f6584ceff4d990caa"
         ],
-        "timestamp": "2023-04-27T16:46:30+0000"
+        "timestamp": "2023-05-09T00:28:56+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
index 75d6ae55..df54719e 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
@@ -1,59 +1,59 @@
 {
     "taxprofiler_metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,5620768b65ecb4067b7547a49e07b67b",
-            "DRR028935.runinfo_ftp.tsv:md5,7f248072a55d5f729c4827937625a05b",
-            "ERR1109373.runinfo_ftp.tsv:md5,f7cd42805764f783388c2686fe2a3f95",
-            "ERR1160846.runinfo_ftp.tsv:md5,36257a2c851d10d61a97581f3496529d",
-            "SRR12848126.runinfo_ftp.tsv:md5,ce5380eceefba1210df0cefe321be62a",
-            "SRR13191702.runinfo_ftp.tsv:md5,37f87c5665e65cece1bc5e2b529e3b3b",
-            "SRR14593545.runinfo_ftp.tsv:md5,36a0fe8c5d3917f105e4cbbb7a720d7d",
-            "SRR14709033.runinfo_ftp.tsv:md5,8f06fa2e4708318dbe8e9505000ea919",
-            "SRR9984183.runinfo_ftp.tsv:md5,72047c09c02782932672862e8adf3fa5"
+            "DRR026872.runinfo_ftp.tsv:md5,f46819ed848d0d28dff80fd0f5a4cd34",
+            "DRR028935.runinfo_ftp.tsv:md5,ef08c3756034e6705b0e13d1f37bfea5",
+            "ERR1109373.runinfo_ftp.tsv:md5,6e7960f43046c6080435a024e9c426c9",
+            "ERR1160846.runinfo_ftp.tsv:md5,db8b7bc5877a62b90e719d7cf3c0d25f",
+            "SRR12848126.runinfo_ftp.tsv:md5,b8ac151eb85a001e9aa3d7319156c016",
+            "SRR13191702.runinfo_ftp.tsv:md5,7188ac3b1d73ec297a900450e73bf751",
+            "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
+            "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
+            "SRR9984183.runinfo_ftp.tsv:md5,827751e211294eeecbb7239f70ead9a5"
         ],
-        "timestamp": "2023-04-27T16:34:28+0000"
+        "timestamp": "2023-05-09T00:32:47+0000"
     },
     "software_versions": {
         "content": [
-            "software_versions.yml:md5,015626dc3a0ea64e135bab19243e1586"
+            "software_versions.yml:md5,c8ccda032b4de8e103eace767442fcf4"
         ],
-        "timestamp": "2023-04-27T16:34:28+0000"
+        "timestamp": "2023-05-09T00:32:47+0000"
     },
     "viralrecon_metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,5620768b65ecb4067b7547a49e07b67b",
-            "DRR028935.runinfo_ftp.tsv:md5,7f248072a55d5f729c4827937625a05b",
-            "ERR1109373.runinfo_ftp.tsv:md5,f7cd42805764f783388c2686fe2a3f95",
-            "ERR1160846.runinfo_ftp.tsv:md5,36257a2c851d10d61a97581f3496529d",
-            "SRR12848126.runinfo_ftp.tsv:md5,ce5380eceefba1210df0cefe321be62a",
-            "SRR13191702.runinfo_ftp.tsv:md5,37f87c5665e65cece1bc5e2b529e3b3b",
-            "SRR14593545.runinfo_ftp.tsv:md5,36a0fe8c5d3917f105e4cbbb7a720d7d",
-            "SRR14709033.runinfo_ftp.tsv:md5,8f06fa2e4708318dbe8e9505000ea919",
-            "SRR9984183.runinfo_ftp.tsv:md5,72047c09c02782932672862e8adf3fa5"
+            "DRR026872.runinfo_ftp.tsv:md5,f46819ed848d0d28dff80fd0f5a4cd34",
+            "DRR028935.runinfo_ftp.tsv:md5,ef08c3756034e6705b0e13d1f37bfea5",
+            "ERR1109373.runinfo_ftp.tsv:md5,6e7960f43046c6080435a024e9c426c9",
+            "ERR1160846.runinfo_ftp.tsv:md5,db8b7bc5877a62b90e719d7cf3c0d25f",
+            "SRR12848126.runinfo_ftp.tsv:md5,b8ac151eb85a001e9aa3d7319156c016",
+            "SRR13191702.runinfo_ftp.tsv:md5,7188ac3b1d73ec297a900450e73bf751",
+            "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
+            "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
+            "SRR9984183.runinfo_ftp.tsv:md5,827751e211294eeecbb7239f70ead9a5"
         ],
-        "timestamp": "2023-04-27T16:34:28+0000"
+        "timestamp": "2023-05-09T00:32:47+0000"
     },
     "viralrecon_samplesheet": {
         "content": [
-            "id_mappings.csv:md5,660db7a31a1c775cabad5f9b21addc06",
-            "multiqc_config.yml:md5,d01bd71fb5b9901c80166fba0637e430",
-            "samplesheet.csv:md5,68c882e413afec7fec5aaa3f83aa7d22"
+            "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
+            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
+            "samplesheet.csv:md5,b3063b7ccd5713c903f20c61ca59db00"
         ],
-        "timestamp": "2023-04-27T16:34:28+0000"
+        "timestamp": "2023-05-09T00:32:47+0000"
     },
     "atacseq_metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,5620768b65ecb4067b7547a49e07b67b",
-            "DRR028935.runinfo_ftp.tsv:md5,7f248072a55d5f729c4827937625a05b",
-            "ERR1109373.runinfo_ftp.tsv:md5,f7cd42805764f783388c2686fe2a3f95",
-            "ERR1160846.runinfo_ftp.tsv:md5,36257a2c851d10d61a97581f3496529d",
-            "SRR12848126.runinfo_ftp.tsv:md5,ce5380eceefba1210df0cefe321be62a",
-            "SRR13191702.runinfo_ftp.tsv:md5,37f87c5665e65cece1bc5e2b529e3b3b",
-            "SRR14593545.runinfo_ftp.tsv:md5,36a0fe8c5d3917f105e4cbbb7a720d7d",
-            "SRR14709033.runinfo_ftp.tsv:md5,8f06fa2e4708318dbe8e9505000ea919",
-            "SRR9984183.runinfo_ftp.tsv:md5,72047c09c02782932672862e8adf3fa5"
+            "DRR026872.runinfo_ftp.tsv:md5,f46819ed848d0d28dff80fd0f5a4cd34",
+            "DRR028935.runinfo_ftp.tsv:md5,ef08c3756034e6705b0e13d1f37bfea5",
+            "ERR1109373.runinfo_ftp.tsv:md5,6e7960f43046c6080435a024e9c426c9",
+            "ERR1160846.runinfo_ftp.tsv:md5,db8b7bc5877a62b90e719d7cf3c0d25f",
+            "SRR12848126.runinfo_ftp.tsv:md5,b8ac151eb85a001e9aa3d7319156c016",
+            "SRR13191702.runinfo_ftp.tsv:md5,7188ac3b1d73ec297a900450e73bf751",
+            "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
+            "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
+            "SRR9984183.runinfo_ftp.tsv:md5,827751e211294eeecbb7239f70ead9a5"
         ],
-        "timestamp": "2023-04-27T16:34:28+0000"
+        "timestamp": "2023-05-09T00:32:47+0000"
     },
     "rnaseq_ena_metadata": {
         "content": [
@@ -67,15 +67,15 @@
             "SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1",
             "SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236"
         ],
-        "timestamp": "2023-04-27T16:34:28+0000"
+        "timestamp": "2023-05-09T00:32:47+0000"
     },
     "rnaseq_samplesheet": {
         "content": [
-            "id_mappings.csv:md5,660db7a31a1c775cabad5f9b21addc06",
-            "multiqc_config.yml:md5,d01bd71fb5b9901c80166fba0637e430",
-            "samplesheet.csv:md5,83a47dad4e4a78390d8ed5492c20f2a1"
+            "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
+            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
+            "samplesheet.csv:md5,f0c8636a26f811f9f0e4aa8046496148"
         ],
-        "timestamp": "2023-04-27T16:34:28+0000"
+        "timestamp": "2023-05-09T00:32:47+0000"
     },
     "rnaseq_samplesheet_specific_ena": {
         "content": [
@@ -83,45 +83,45 @@
             "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd",
             "samplesheet.csv:md5,dc7371849e112d0e95646ef1c34339d0"
         ],
-        "timestamp": "2023-04-27T16:34:28+0000"
+        "timestamp": "2023-05-09T00:32:47+0000"
     },
     "rnaseq_metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,5620768b65ecb4067b7547a49e07b67b",
-            "DRR028935.runinfo_ftp.tsv:md5,7f248072a55d5f729c4827937625a05b",
-            "ERR1109373.runinfo_ftp.tsv:md5,f7cd42805764f783388c2686fe2a3f95",
-            "ERR1160846.runinfo_ftp.tsv:md5,36257a2c851d10d61a97581f3496529d",
-            "SRR12848126.runinfo_ftp.tsv:md5,ce5380eceefba1210df0cefe321be62a",
-            "SRR13191702.runinfo_ftp.tsv:md5,37f87c5665e65cece1bc5e2b529e3b3b",
-            "SRR14593545.runinfo_ftp.tsv:md5,36a0fe8c5d3917f105e4cbbb7a720d7d",
-            "SRR14709033.runinfo_ftp.tsv:md5,8f06fa2e4708318dbe8e9505000ea919",
-            "SRR9984183.runinfo_ftp.tsv:md5,72047c09c02782932672862e8adf3fa5"
+            "DRR026872.runinfo_ftp.tsv:md5,f46819ed848d0d28dff80fd0f5a4cd34",
+            "DRR028935.runinfo_ftp.tsv:md5,ef08c3756034e6705b0e13d1f37bfea5",
+            "ERR1109373.runinfo_ftp.tsv:md5,6e7960f43046c6080435a024e9c426c9",
+            "ERR1160846.runinfo_ftp.tsv:md5,db8b7bc5877a62b90e719d7cf3c0d25f",
+            "SRR12848126.runinfo_ftp.tsv:md5,b8ac151eb85a001e9aa3d7319156c016",
+            "SRR13191702.runinfo_ftp.tsv:md5,7188ac3b1d73ec297a900450e73bf751",
+            "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
+            "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
+            "SRR9984183.runinfo_ftp.tsv:md5,827751e211294eeecbb7239f70ead9a5"
         ],
-        "timestamp": "2023-04-27T16:34:28+0000"
+        "timestamp": "2023-05-09T00:32:47+0000"
     },
     "rnaseq_specific_ena_samplesheet": {
         "content": [
             "id_mappings.csv:md5,0efde324e1818c0827390a17449a6e8a",
             "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd",
-            "samplesheet.csv:md5,dc7371849e112d0e95646ef1c34339d0"
+            "samplesheet.csv:md5,f6348f24c001ab15872ca73b493cbd79"
         ],
-        "timestamp": "2023-04-27T16:34:28+0000"
+        "timestamp": "2023-05-09T00:32:47+0000"
     },
     "atacseq_samplesheet": {
         "content": [
-            "id_mappings.csv:md5,660db7a31a1c775cabad5f9b21addc06",
-            "multiqc_config.yml:md5,d01bd71fb5b9901c80166fba0637e430",
-            "samplesheet.csv:md5,0c5df4b98006b33257d444eacbdcbfbe"
+            "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
+            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
+            "samplesheet.csv:md5,522e4a3fed3f69cee16bae0709bf4e61"
         ],
-        "timestamp": "2023-04-27T16:34:28+0000"
+        "timestamp": "2023-05-09T00:32:47+0000"
     },
     "taxprofiler_samplesheet": {
         "content": [
-            "id_mappings.csv:md5,660db7a31a1c775cabad5f9b21addc06",
-            "multiqc_config.yml:md5,d01bd71fb5b9901c80166fba0637e430",
-            "samplesheet.csv:md5,56f9b2713f8923a4bca194ca4fbbf245"
+            "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
+            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
+            "samplesheet.csv:md5,3f1776eed364e1568fb47e37435db20b"
         ],
-        "timestamp": "2023-04-27T16:34:28+0000"
+        "timestamp": "2023-05-09T00:32:47+0000"
     },
     "fastq": {
         "content": [
@@ -151,6 +151,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-04-27T16:34:28+0000"
+        "timestamp": "2023-05-09T00:32:47+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_sratools.nf.test.snap b/tests/pipeline/sra_with_sratools.nf.test.snap
index 87af9987..ad2ebaf0 100644
--- a/tests/pipeline/sra_with_sratools.nf.test.snap
+++ b/tests/pipeline/sra_with_sratools.nf.test.snap
@@ -1,31 +1,31 @@
 {
     "metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,5620768b65ecb4067b7547a49e07b67b",
-            "DRR028935.runinfo_ftp.tsv:md5,7f248072a55d5f729c4827937625a05b",
-            "ERR1109373.runinfo_ftp.tsv:md5,f7cd42805764f783388c2686fe2a3f95",
-            "ERR1160846.runinfo_ftp.tsv:md5,36257a2c851d10d61a97581f3496529d",
-            "SRR12848126.runinfo_ftp.tsv:md5,ce5380eceefba1210df0cefe321be62a",
-            "SRR13191702.runinfo_ftp.tsv:md5,37f87c5665e65cece1bc5e2b529e3b3b",
-            "SRR14593545.runinfo_ftp.tsv:md5,36a0fe8c5d3917f105e4cbbb7a720d7d",
-            "SRR14709033.runinfo_ftp.tsv:md5,8f06fa2e4708318dbe8e9505000ea919",
-            "SRR9984183.runinfo_ftp.tsv:md5,72047c09c02782932672862e8adf3fa5"
+            "DRR026872.runinfo_ftp.tsv:md5,f46819ed848d0d28dff80fd0f5a4cd34",
+            "DRR028935.runinfo_ftp.tsv:md5,ef08c3756034e6705b0e13d1f37bfea5",
+            "ERR1109373.runinfo_ftp.tsv:md5,6e7960f43046c6080435a024e9c426c9",
+            "ERR1160846.runinfo_ftp.tsv:md5,db8b7bc5877a62b90e719d7cf3c0d25f",
+            "SRR12848126.runinfo_ftp.tsv:md5,b8ac151eb85a001e9aa3d7319156c016",
+            "SRR13191702.runinfo_ftp.tsv:md5,7188ac3b1d73ec297a900450e73bf751",
+            "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
+            "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
+            "SRR9984183.runinfo_ftp.tsv:md5,827751e211294eeecbb7239f70ead9a5"
         ],
-        "timestamp": "2023-04-27T16:51:33+0000"
+        "timestamp": "2023-05-09T00:28:30+0000"
     },
     "samplesheet": {
         "content": [
-            "id_mappings.csv:md5,660db7a31a1c775cabad5f9b21addc06",
-            "multiqc_config.yml:md5,d01bd71fb5b9901c80166fba0637e430",
-            "samplesheet.csv:md5,2087763d7cdce58c331ae379b2e1dc27"
+            "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
+            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
+            "samplesheet.csv:md5,f8c7dff22f06a380e987049d7f04f096"
         ],
-        "timestamp": "2023-04-27T16:51:33+0000"
+        "timestamp": "2023-05-09T00:28:30+0000"
     },
     "software_versions": {
         "content": [
-            "software_versions.yml:md5,029defc466fd9a709cf95d2d903e1324"
+            "software_versions.yml:md5,ec1f5ee8c99879c3b8f04e7e683f540f"
         ],
-        "timestamp": "2023-04-27T16:51:33+0000"
+        "timestamp": "2023-05-09T00:28:30+0000"
     },
     "fastq": {
         "content": [
@@ -44,6 +44,6 @@
             "SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7",
             "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af"
         ],
-        "timestamp": "2023-04-27T16:51:33+0000"
+        "timestamp": "2023-05-09T00:28:30+0000"
     }
 }
\ No newline at end of file

From a58f46f6986df04fbf382e54b669407ddd305569 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Mon, 8 May 2023 20:58:18 -0400
Subject: [PATCH 316/852] update-ci-yml

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1b1f6b73..22e8274e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -25,7 +25,7 @@ jobs:
     name: Run ${{ matrix.profile }}-${{ matrix.NXF_VER }} pipeline test
 
     # Set the condition for running the job
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}"
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}"
 
     # Specify the runner for the job
     runs-on: ubuntu-latest

From 7a6af979623d8575782f712a730ec9345ebb817b Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Mon, 8 May 2023 22:27:20 -0400
Subject: [PATCH 317/852] update-snapshots

---
 .../sra_ids_to_runinfo/main.nf.test.snap      | 28 ++++++++++-----
 tests/pipeline/sra.nf.test.snap               | 10 +++---
 .../sra_with_nf_core_pipeline.nf.test.snap    | 36 +++++++++----------
 tests/pipeline/sra_with_sratools.nf.test.snap | 10 +++---
 4 files changed, 48 insertions(+), 36 deletions(-)

diff --git a/tests/modules/sra_ids_to_runinfo/main.nf.test.snap b/tests/modules/sra_ids_to_runinfo/main.nf.test.snap
index 5a9ed62b..e13c470f 100644
--- a/tests/modules/sra_ids_to_runinfo/main.nf.test.snap
+++ b/tests/modules/sra_ids_to_runinfo/main.nf.test.snap
@@ -2,27 +2,39 @@
     "Should run without failures without fields": {
         "content": [
             {
-                "versions": [
-                    "versions.yml:md5,cd1056ca246a1ab3486fb6800f3012fb"
+                "0": [
+                    "SRR9984183.runinfo.tsv:md5,6bc8bfb7058412e5a54b83e08d3d1673"
+                ],
+                "1": [
+                    "versions.yml:md5,61ebf47bc00075513ff16295beddb197"
                 ],
                 "tsv": [
-                    "SRR9984183.runinfo.tsv:md5,a69083928f4b856d428a681c291b7ad6"
+                    "SRR9984183.runinfo.tsv:md5,6bc8bfb7058412e5a54b83e08d3d1673"
+                ],
+                "versions": [
+                    "versions.yml:md5,61ebf47bc00075513ff16295beddb197"
                 ]
             }
         ],
-        "timestamp": "2022-11-11T04:23:34+0000"
+        "timestamp": "2023-05-09T02:22:52+0000"
     },
     "Should run without failures with fields": {
         "content": [
             {
-                "versions": [
-                    "versions.yml:md5,cd1056ca246a1ab3486fb6800f3012fb"
+                "0": [
+                    "SRR9984183.runinfo.tsv:md5,6419f18c29ab09634b3dd97a6b2acd06"
+                ],
+                "1": [
+                    "versions.yml:md5,61ebf47bc00075513ff16295beddb197"
                 ],
                 "tsv": [
                     "SRR9984183.runinfo.tsv:md5,6419f18c29ab09634b3dd97a6b2acd06"
+                ],
+                "versions": [
+                    "versions.yml:md5,61ebf47bc00075513ff16295beddb197"
                 ]
             }
         ],
-        "timestamp": "2022-11-11T04:23:34+0000"
+        "timestamp": "2023-05-09T02:22:52+0000"
     }
-}
+}
\ No newline at end of file
diff --git a/tests/pipeline/sra.nf.test.snap b/tests/pipeline/sra.nf.test.snap
index 3ce84e64..3e53c207 100644
--- a/tests/pipeline/sra.nf.test.snap
+++ b/tests/pipeline/sra.nf.test.snap
@@ -11,21 +11,21 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,827751e211294eeecbb7239f70ead9a5"
         ],
-        "timestamp": "2023-05-09T00:33:33+0000"
+        "timestamp": "2023-05-09T02:22:08+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
             "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
-            "samplesheet.csv:md5,a12fd27d7741f1aa687049eb6ce9ed9a"
+            "samplesheet.csv:md5,22cd8487e80f23686f54779a0b55c54d"
         ],
-        "timestamp": "2023-05-09T00:33:33+0000"
+        "timestamp": "2023-05-09T02:22:08+0000"
     },
     "software_versions": {
         "content": [
             "software_versions.yml:md5,c8ccda032b4de8e103eace767442fcf4"
         ],
-        "timestamp": "2023-05-09T00:33:33+0000"
+        "timestamp": "2023-05-09T02:22:08+0000"
     },
     "fastq": {
         "content": [
@@ -55,6 +55,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-05-09T00:33:33+0000"
+        "timestamp": "2023-05-09T02:22:08+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
index df54719e..8cbf7bfa 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
@@ -11,13 +11,13 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,827751e211294eeecbb7239f70ead9a5"
         ],
-        "timestamp": "2023-05-09T00:32:47+0000"
+        "timestamp": "2023-05-09T02:19:58+0000"
     },
     "software_versions": {
         "content": [
             "software_versions.yml:md5,c8ccda032b4de8e103eace767442fcf4"
         ],
-        "timestamp": "2023-05-09T00:32:47+0000"
+        "timestamp": "2023-05-09T02:19:58+0000"
     },
     "viralrecon_metadata": {
         "content": [
@@ -31,15 +31,15 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,827751e211294eeecbb7239f70ead9a5"
         ],
-        "timestamp": "2023-05-09T00:32:47+0000"
+        "timestamp": "2023-05-09T02:19:58+0000"
     },
     "viralrecon_samplesheet": {
         "content": [
             "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
             "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
-            "samplesheet.csv:md5,b3063b7ccd5713c903f20c61ca59db00"
+            "samplesheet.csv:md5,9bdd606909eb08fcb6a4b10a5c1fea7a"
         ],
-        "timestamp": "2023-05-09T00:32:47+0000"
+        "timestamp": "2023-05-09T02:19:58+0000"
     },
     "atacseq_metadata": {
         "content": [
@@ -53,7 +53,7 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,827751e211294eeecbb7239f70ead9a5"
         ],
-        "timestamp": "2023-05-09T00:32:47+0000"
+        "timestamp": "2023-05-09T02:19:58+0000"
     },
     "rnaseq_ena_metadata": {
         "content": [
@@ -67,15 +67,15 @@
             "SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1",
             "SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236"
         ],
-        "timestamp": "2023-05-09T00:32:47+0000"
+        "timestamp": "2023-05-09T02:19:58+0000"
     },
     "rnaseq_samplesheet": {
         "content": [
             "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
             "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
-            "samplesheet.csv:md5,f0c8636a26f811f9f0e4aa8046496148"
+            "samplesheet.csv:md5,d6f1c7e9cc6f8e531fc92a9a4ae9993f"
         ],
-        "timestamp": "2023-05-09T00:32:47+0000"
+        "timestamp": "2023-05-09T02:19:58+0000"
     },
     "rnaseq_samplesheet_specific_ena": {
         "content": [
@@ -83,7 +83,7 @@
             "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd",
             "samplesheet.csv:md5,dc7371849e112d0e95646ef1c34339d0"
         ],
-        "timestamp": "2023-05-09T00:32:47+0000"
+        "timestamp": "2023-05-09T02:19:58+0000"
     },
     "rnaseq_metadata": {
         "content": [
@@ -97,31 +97,31 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,827751e211294eeecbb7239f70ead9a5"
         ],
-        "timestamp": "2023-05-09T00:32:47+0000"
+        "timestamp": "2023-05-09T02:19:58+0000"
     },
     "rnaseq_specific_ena_samplesheet": {
         "content": [
             "id_mappings.csv:md5,0efde324e1818c0827390a17449a6e8a",
             "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd",
-            "samplesheet.csv:md5,f6348f24c001ab15872ca73b493cbd79"
+            "samplesheet.csv:md5,6a08c28af1ed2629e18f0014f4d72ed6"
         ],
-        "timestamp": "2023-05-09T00:32:47+0000"
+        "timestamp": "2023-05-09T02:19:58+0000"
     },
     "atacseq_samplesheet": {
         "content": [
             "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
             "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
-            "samplesheet.csv:md5,522e4a3fed3f69cee16bae0709bf4e61"
+            "samplesheet.csv:md5,65e8d7f0f4174271205e777689fe8491"
         ],
-        "timestamp": "2023-05-09T00:32:47+0000"
+        "timestamp": "2023-05-09T02:19:58+0000"
     },
     "taxprofiler_samplesheet": {
         "content": [
             "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
             "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
-            "samplesheet.csv:md5,3f1776eed364e1568fb47e37435db20b"
+            "samplesheet.csv:md5,c00d9e0b7c6222a8f31cd22a265c33fe"
         ],
-        "timestamp": "2023-05-09T00:32:47+0000"
+        "timestamp": "2023-05-09T02:19:58+0000"
     },
     "fastq": {
         "content": [
@@ -151,6 +151,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-05-09T00:32:47+0000"
+        "timestamp": "2023-05-09T02:19:58+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_sratools.nf.test.snap b/tests/pipeline/sra_with_sratools.nf.test.snap
index ad2ebaf0..5bc9b9bf 100644
--- a/tests/pipeline/sra_with_sratools.nf.test.snap
+++ b/tests/pipeline/sra_with_sratools.nf.test.snap
@@ -11,21 +11,21 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,827751e211294eeecbb7239f70ead9a5"
         ],
-        "timestamp": "2023-05-09T00:28:30+0000"
+        "timestamp": "2023-05-09T02:12:04+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
             "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
-            "samplesheet.csv:md5,f8c7dff22f06a380e987049d7f04f096"
+            "samplesheet.csv:md5,24d51c3c83f25902d1841096b12e2d67"
         ],
-        "timestamp": "2023-05-09T00:28:30+0000"
+        "timestamp": "2023-05-09T02:12:04+0000"
     },
     "software_versions": {
         "content": [
             "software_versions.yml:md5,ec1f5ee8c99879c3b8f04e7e683f540f"
         ],
-        "timestamp": "2023-05-09T00:28:30+0000"
+        "timestamp": "2023-05-09T02:12:04+0000"
     },
     "fastq": {
         "content": [
@@ -44,6 +44,6 @@
             "SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7",
             "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af"
         ],
-        "timestamp": "2023-05-09T00:28:30+0000"
+        "timestamp": "2023-05-09T02:12:04+0000"
     }
 }
\ No newline at end of file

From 5a160bdc5e8994b44a1a87dc8849dbb25f8d8a9d Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Tue, 9 May 2023 10:17:49 -0400
Subject: [PATCH 318/852] update-snapshots

---
 tests/pipeline/sra.nf.test.snap               | 24 ++---
 tests/pipeline/sra_skip_fastq.nf.test.snap    | 22 ++---
 .../sra_with_nf_core_pipeline.nf.test         |  2 +-
 .../sra_with_nf_core_pipeline.nf.test.snap    | 90 +++++++++----------
 tests/pipeline/sra_with_sratools.nf.test      |  2 +-
 tests/pipeline/sra_with_sratools.nf.test.snap | 24 ++---
 6 files changed, 82 insertions(+), 82 deletions(-)

diff --git a/tests/pipeline/sra.nf.test.snap b/tests/pipeline/sra.nf.test.snap
index 3e53c207..26e56065 100644
--- a/tests/pipeline/sra.nf.test.snap
+++ b/tests/pipeline/sra.nf.test.snap
@@ -1,31 +1,31 @@
 {
     "metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,f46819ed848d0d28dff80fd0f5a4cd34",
-            "DRR028935.runinfo_ftp.tsv:md5,ef08c3756034e6705b0e13d1f37bfea5",
-            "ERR1109373.runinfo_ftp.tsv:md5,6e7960f43046c6080435a024e9c426c9",
-            "ERR1160846.runinfo_ftp.tsv:md5,db8b7bc5877a62b90e719d7cf3c0d25f",
-            "SRR12848126.runinfo_ftp.tsv:md5,b8ac151eb85a001e9aa3d7319156c016",
-            "SRR13191702.runinfo_ftp.tsv:md5,7188ac3b1d73ec297a900450e73bf751",
+            "DRR026872.runinfo_ftp.tsv:md5,c5ab92f6f50717b8163580b642b37aec",
+            "DRR028935.runinfo_ftp.tsv:md5,9db5d6cba5ce2cccd9b2cc3faaa092e2",
+            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
+            "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
+            "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
+            "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
-            "SRR9984183.runinfo_ftp.tsv:md5,827751e211294eeecbb7239f70ead9a5"
+            "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-09T02:22:08+0000"
+        "timestamp": "2023-05-09T14:15:30+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
             "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
-            "samplesheet.csv:md5,22cd8487e80f23686f54779a0b55c54d"
+            "samplesheet.csv:md5,254be0ca1de8071d22c7e6d6e67fc95e"
         ],
-        "timestamp": "2023-05-09T02:22:08+0000"
+        "timestamp": "2023-05-09T14:15:30+0000"
     },
     "software_versions": {
         "content": [
             "software_versions.yml:md5,c8ccda032b4de8e103eace767442fcf4"
         ],
-        "timestamp": "2023-05-09T02:22:08+0000"
+        "timestamp": "2023-05-09T14:15:30+0000"
     },
     "fastq": {
         "content": [
@@ -55,6 +55,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-05-09T02:22:08+0000"
+        "timestamp": "2023-05-09T14:15:30+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_skip_fastq.nf.test.snap b/tests/pipeline/sra_skip_fastq.nf.test.snap
index 4c208a29..4116e888 100644
--- a/tests/pipeline/sra_skip_fastq.nf.test.snap
+++ b/tests/pipeline/sra_skip_fastq.nf.test.snap
@@ -1,30 +1,30 @@
 {
     "metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,f46819ed848d0d28dff80fd0f5a4cd34",
-            "DRR028935.runinfo_ftp.tsv:md5,ef08c3756034e6705b0e13d1f37bfea5",
-            "ERR1109373.runinfo_ftp.tsv:md5,6e7960f43046c6080435a024e9c426c9",
-            "ERR1160846.runinfo_ftp.tsv:md5,db8b7bc5877a62b90e719d7cf3c0d25f",
-            "SRR12848126.runinfo_ftp.tsv:md5,b8ac151eb85a001e9aa3d7319156c016",
-            "SRR13191702.runinfo_ftp.tsv:md5,7188ac3b1d73ec297a900450e73bf751",
+            "DRR026872.runinfo_ftp.tsv:md5,c5ab92f6f50717b8163580b642b37aec",
+            "DRR028935.runinfo_ftp.tsv:md5,9db5d6cba5ce2cccd9b2cc3faaa092e2",
+            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
+            "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
+            "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
+            "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
-            "SRR9984183.runinfo_ftp.tsv:md5,827751e211294eeecbb7239f70ead9a5"
+            "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-09T00:28:56+0000"
+        "timestamp": "2023-05-09T14:08:13+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
             "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
-            "samplesheet.csv:md5,2006cc16ca44e947b5244528310c03e0"
+            "samplesheet.csv:md5,c5cadf299f1c842cd9063200fb640445"
         ],
-        "timestamp": "2023-05-09T00:28:56+0000"
+        "timestamp": "2023-05-09T14:08:13+0000"
     },
     "software_versions": {
         "content": [
             "software_versions.yml:md5,8b5ec8d90481271f6584ceff4d990caa"
         ],
-        "timestamp": "2023-05-09T00:28:56+0000"
+        "timestamp": "2023-05-09T14:08:13+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
index a31c1fbb..9034910c 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
@@ -25,7 +25,7 @@ nextflow_pipeline {
         }
     }
 
-    test("SRA NF-CORE/RNASEQ Samplesheet With ENA metadata") {
+    test("SRA NF-CORE/RNASEQ Samplesheet With Specific ENA metadata") {
 
         when {
             params {
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
index 8cbf7bfa..77c9c730 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
@@ -1,59 +1,59 @@
 {
     "taxprofiler_metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,f46819ed848d0d28dff80fd0f5a4cd34",
-            "DRR028935.runinfo_ftp.tsv:md5,ef08c3756034e6705b0e13d1f37bfea5",
-            "ERR1109373.runinfo_ftp.tsv:md5,6e7960f43046c6080435a024e9c426c9",
-            "ERR1160846.runinfo_ftp.tsv:md5,db8b7bc5877a62b90e719d7cf3c0d25f",
-            "SRR12848126.runinfo_ftp.tsv:md5,b8ac151eb85a001e9aa3d7319156c016",
-            "SRR13191702.runinfo_ftp.tsv:md5,7188ac3b1d73ec297a900450e73bf751",
+            "DRR026872.runinfo_ftp.tsv:md5,c5ab92f6f50717b8163580b642b37aec",
+            "DRR028935.runinfo_ftp.tsv:md5,9db5d6cba5ce2cccd9b2cc3faaa092e2",
+            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
+            "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
+            "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
+            "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
-            "SRR9984183.runinfo_ftp.tsv:md5,827751e211294eeecbb7239f70ead9a5"
+            "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-09T02:19:58+0000"
+        "timestamp": "2023-05-09T14:11:58+0000"
     },
     "software_versions": {
         "content": [
             "software_versions.yml:md5,c8ccda032b4de8e103eace767442fcf4"
         ],
-        "timestamp": "2023-05-09T02:19:58+0000"
+        "timestamp": "2023-05-09T14:11:58+0000"
     },
     "viralrecon_metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,f46819ed848d0d28dff80fd0f5a4cd34",
-            "DRR028935.runinfo_ftp.tsv:md5,ef08c3756034e6705b0e13d1f37bfea5",
-            "ERR1109373.runinfo_ftp.tsv:md5,6e7960f43046c6080435a024e9c426c9",
-            "ERR1160846.runinfo_ftp.tsv:md5,db8b7bc5877a62b90e719d7cf3c0d25f",
-            "SRR12848126.runinfo_ftp.tsv:md5,b8ac151eb85a001e9aa3d7319156c016",
-            "SRR13191702.runinfo_ftp.tsv:md5,7188ac3b1d73ec297a900450e73bf751",
+            "DRR026872.runinfo_ftp.tsv:md5,c5ab92f6f50717b8163580b642b37aec",
+            "DRR028935.runinfo_ftp.tsv:md5,9db5d6cba5ce2cccd9b2cc3faaa092e2",
+            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
+            "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
+            "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
+            "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
-            "SRR9984183.runinfo_ftp.tsv:md5,827751e211294eeecbb7239f70ead9a5"
+            "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-09T02:19:58+0000"
+        "timestamp": "2023-05-09T14:11:58+0000"
     },
     "viralrecon_samplesheet": {
         "content": [
             "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
             "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
-            "samplesheet.csv:md5,9bdd606909eb08fcb6a4b10a5c1fea7a"
+            "samplesheet.csv:md5,da9e9eca2c1c05e4da526806316faa5f"
         ],
-        "timestamp": "2023-05-09T02:19:58+0000"
+        "timestamp": "2023-05-09T14:11:58+0000"
     },
     "atacseq_metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,f46819ed848d0d28dff80fd0f5a4cd34",
-            "DRR028935.runinfo_ftp.tsv:md5,ef08c3756034e6705b0e13d1f37bfea5",
-            "ERR1109373.runinfo_ftp.tsv:md5,6e7960f43046c6080435a024e9c426c9",
-            "ERR1160846.runinfo_ftp.tsv:md5,db8b7bc5877a62b90e719d7cf3c0d25f",
-            "SRR12848126.runinfo_ftp.tsv:md5,b8ac151eb85a001e9aa3d7319156c016",
-            "SRR13191702.runinfo_ftp.tsv:md5,7188ac3b1d73ec297a900450e73bf751",
+            "DRR026872.runinfo_ftp.tsv:md5,c5ab92f6f50717b8163580b642b37aec",
+            "DRR028935.runinfo_ftp.tsv:md5,9db5d6cba5ce2cccd9b2cc3faaa092e2",
+            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
+            "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
+            "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
+            "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
-            "SRR9984183.runinfo_ftp.tsv:md5,827751e211294eeecbb7239f70ead9a5"
+            "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-09T02:19:58+0000"
+        "timestamp": "2023-05-09T14:11:58+0000"
     },
     "rnaseq_ena_metadata": {
         "content": [
@@ -67,15 +67,15 @@
             "SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1",
             "SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236"
         ],
-        "timestamp": "2023-05-09T02:19:58+0000"
+        "timestamp": "2023-05-09T14:11:58+0000"
     },
     "rnaseq_samplesheet": {
         "content": [
             "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
             "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
-            "samplesheet.csv:md5,d6f1c7e9cc6f8e531fc92a9a4ae9993f"
+            "samplesheet.csv:md5,9fa43672fb5ffcf0dec423a4627dc028"
         ],
-        "timestamp": "2023-05-09T02:19:58+0000"
+        "timestamp": "2023-05-09T14:11:58+0000"
     },
     "rnaseq_samplesheet_specific_ena": {
         "content": [
@@ -83,21 +83,21 @@
             "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd",
             "samplesheet.csv:md5,dc7371849e112d0e95646ef1c34339d0"
         ],
-        "timestamp": "2023-05-09T02:19:58+0000"
+        "timestamp": "2023-05-09T14:11:58+0000"
     },
     "rnaseq_metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,f46819ed848d0d28dff80fd0f5a4cd34",
-            "DRR028935.runinfo_ftp.tsv:md5,ef08c3756034e6705b0e13d1f37bfea5",
-            "ERR1109373.runinfo_ftp.tsv:md5,6e7960f43046c6080435a024e9c426c9",
-            "ERR1160846.runinfo_ftp.tsv:md5,db8b7bc5877a62b90e719d7cf3c0d25f",
-            "SRR12848126.runinfo_ftp.tsv:md5,b8ac151eb85a001e9aa3d7319156c016",
-            "SRR13191702.runinfo_ftp.tsv:md5,7188ac3b1d73ec297a900450e73bf751",
+            "DRR026872.runinfo_ftp.tsv:md5,c5ab92f6f50717b8163580b642b37aec",
+            "DRR028935.runinfo_ftp.tsv:md5,9db5d6cba5ce2cccd9b2cc3faaa092e2",
+            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
+            "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
+            "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
+            "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
-            "SRR9984183.runinfo_ftp.tsv:md5,827751e211294eeecbb7239f70ead9a5"
+            "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-09T02:19:58+0000"
+        "timestamp": "2023-05-09T14:11:58+0000"
     },
     "rnaseq_specific_ena_samplesheet": {
         "content": [
@@ -105,23 +105,23 @@
             "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd",
             "samplesheet.csv:md5,6a08c28af1ed2629e18f0014f4d72ed6"
         ],
-        "timestamp": "2023-05-09T02:19:58+0000"
+        "timestamp": "2023-05-09T14:11:58+0000"
     },
     "atacseq_samplesheet": {
         "content": [
             "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
             "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
-            "samplesheet.csv:md5,65e8d7f0f4174271205e777689fe8491"
+            "samplesheet.csv:md5,236f64ee8d40b3b658aecc0298cccfb2"
         ],
-        "timestamp": "2023-05-09T02:19:58+0000"
+        "timestamp": "2023-05-09T14:11:58+0000"
     },
     "taxprofiler_samplesheet": {
         "content": [
             "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
             "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
-            "samplesheet.csv:md5,c00d9e0b7c6222a8f31cd22a265c33fe"
+            "samplesheet.csv:md5,336e53f72cc538a58911880ec7c9b5da"
         ],
-        "timestamp": "2023-05-09T02:19:58+0000"
+        "timestamp": "2023-05-09T14:11:58+0000"
     },
     "fastq": {
         "content": [
@@ -151,6 +151,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-05-09T02:19:58+0000"
+        "timestamp": "2023-05-09T14:11:58+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_sratools.nf.test b/tests/pipeline/sra_with_sratools.nf.test
index 97602440..c86ed056 100644
--- a/tests/pipeline/sra_with_sratools.nf.test
+++ b/tests/pipeline/sra_with_sratools.nf.test
@@ -5,7 +5,7 @@ nextflow_pipeline {
     options "-profile test,docker"
     tag "pipeline"
 
-    test("SRA Force SRAtools Download") {
+    test("Force SRA-Tools Download") {
 
         when {
             params {
diff --git a/tests/pipeline/sra_with_sratools.nf.test.snap b/tests/pipeline/sra_with_sratools.nf.test.snap
index 5bc9b9bf..fb5ab805 100644
--- a/tests/pipeline/sra_with_sratools.nf.test.snap
+++ b/tests/pipeline/sra_with_sratools.nf.test.snap
@@ -1,31 +1,31 @@
 {
     "metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,f46819ed848d0d28dff80fd0f5a4cd34",
-            "DRR028935.runinfo_ftp.tsv:md5,ef08c3756034e6705b0e13d1f37bfea5",
-            "ERR1109373.runinfo_ftp.tsv:md5,6e7960f43046c6080435a024e9c426c9",
-            "ERR1160846.runinfo_ftp.tsv:md5,db8b7bc5877a62b90e719d7cf3c0d25f",
-            "SRR12848126.runinfo_ftp.tsv:md5,b8ac151eb85a001e9aa3d7319156c016",
-            "SRR13191702.runinfo_ftp.tsv:md5,7188ac3b1d73ec297a900450e73bf751",
+            "DRR026872.runinfo_ftp.tsv:md5,c5ab92f6f50717b8163580b642b37aec",
+            "DRR028935.runinfo_ftp.tsv:md5,9db5d6cba5ce2cccd9b2cc3faaa092e2",
+            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
+            "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
+            "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
+            "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
-            "SRR9984183.runinfo_ftp.tsv:md5,827751e211294eeecbb7239f70ead9a5"
+            "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-09T02:12:04+0000"
+        "timestamp": "2023-05-09T14:07:50+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
             "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
-            "samplesheet.csv:md5,24d51c3c83f25902d1841096b12e2d67"
+            "samplesheet.csv:md5,03ae9aa2cd8b3fc60a123c00e15e7b9a"
         ],
-        "timestamp": "2023-05-09T02:12:04+0000"
+        "timestamp": "2023-05-09T14:07:50+0000"
     },
     "software_versions": {
         "content": [
             "software_versions.yml:md5,ec1f5ee8c99879c3b8f04e7e683f540f"
         ],
-        "timestamp": "2023-05-09T02:12:04+0000"
+        "timestamp": "2023-05-09T14:07:50+0000"
     },
     "fastq": {
         "content": [
@@ -44,6 +44,6 @@
             "SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7",
             "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af"
         ],
-        "timestamp": "2023-05-09T02:12:04+0000"
+        "timestamp": "2023-05-09T14:07:50+0000"
     }
 }
\ No newline at end of file

From 9b6ec394a8df647f17970c742f6c801314f8f684 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Tue, 9 May 2023 10:54:34 -0400
Subject: [PATCH 319/852] remove-samplesheet-with-paths-snapshots

---
 tests/pipeline/sra.nf.test                            | 4 +++-
 tests/pipeline/sra.nf.test.snap                       | 3 +--
 tests/pipeline/sra_skip_fastq.nf.test                 | 4 +++-
 tests/pipeline/sra_skip_fastq.nf.test.snap            | 3 +--
 tests/pipeline/sra_with_nf_core_pipeline.nf.test      | 4 +++-
 tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap | 3 +--
 tests/pipeline/sra_with_sratools.nf.test              | 4 +++-
 tests/pipeline/sra_with_sratools.nf.test.snap         | 3 +--
 8 files changed, 16 insertions(+), 12 deletions(-)

diff --git a/tests/pipeline/sra.nf.test b/tests/pipeline/sra.nf.test
index 217eeaa1..00d8ad0f 100644
--- a/tests/pipeline/sra.nf.test
+++ b/tests/pipeline/sra.nf.test
@@ -19,7 +19,9 @@ nextflow_pipeline {
                 { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/").list()).match("metadata") },
-                { assert snapshot(path("$outputDir/samplesheet/").list()).match("samplesheet") }
+                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
+                                path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
+                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
             )
         }
 
diff --git a/tests/pipeline/sra.nf.test.snap b/tests/pipeline/sra.nf.test.snap
index 26e56065..d16a31ec 100644
--- a/tests/pipeline/sra.nf.test.snap
+++ b/tests/pipeline/sra.nf.test.snap
@@ -16,8 +16,7 @@
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
-            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
-            "samplesheet.csv:md5,254be0ca1de8071d22c7e6d6e67fc95e"
+            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d"
         ],
         "timestamp": "2023-05-09T14:15:30+0000"
     },
diff --git a/tests/pipeline/sra_skip_fastq.nf.test b/tests/pipeline/sra_skip_fastq.nf.test
index 851099c3..0d6849b9 100644
--- a/tests/pipeline/sra_skip_fastq.nf.test
+++ b/tests/pipeline/sra_skip_fastq.nf.test
@@ -19,7 +19,9 @@ nextflow_pipeline {
                 { assert workflow.success },
                 { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
                 { assert snapshot(path("$outputDir/metadata/").list()).match("metadata") },
-                { assert snapshot(path("$outputDir/samplesheet/").list()).match("samplesheet") },
+                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
+                                path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
+                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() },
                 { assert !new File("$outputDir/fastq/DRX024467_DRR026872.fastq.gz").exists() },
                 { assert !new File("$outputDir/fastq/DRX026011_DRR028935_1.fastq.gz").exists() },
                 { assert !new File("$outputDir/fastq/DRX026011_DRR028935_2.fastq.gz").exists() },
diff --git a/tests/pipeline/sra_skip_fastq.nf.test.snap b/tests/pipeline/sra_skip_fastq.nf.test.snap
index 4116e888..a4b5fa9f 100644
--- a/tests/pipeline/sra_skip_fastq.nf.test.snap
+++ b/tests/pipeline/sra_skip_fastq.nf.test.snap
@@ -16,8 +16,7 @@
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
-            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
-            "samplesheet.csv:md5,c5cadf299f1c842cd9063200fb640445"
+            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d"
         ],
         "timestamp": "2023-05-09T14:08:13+0000"
     },
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
index 9034910c..0618eb81 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
@@ -20,7 +20,9 @@ nextflow_pipeline {
                 { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/").list()).match("rnaseq_metadata") },
-                { assert snapshot(path("$outputDir/samplesheet/").list()).match("rnaseq_samplesheet") }
+                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
+                                path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
+                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
             )
         }
     }
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
index 77c9c730..fda160f4 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
@@ -36,8 +36,7 @@
     "viralrecon_samplesheet": {
         "content": [
             "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
-            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
-            "samplesheet.csv:md5,da9e9eca2c1c05e4da526806316faa5f"
+            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d"
         ],
         "timestamp": "2023-05-09T14:11:58+0000"
     },
diff --git a/tests/pipeline/sra_with_sratools.nf.test b/tests/pipeline/sra_with_sratools.nf.test
index c86ed056..dd85131c 100644
--- a/tests/pipeline/sra_with_sratools.nf.test
+++ b/tests/pipeline/sra_with_sratools.nf.test
@@ -20,7 +20,9 @@ nextflow_pipeline {
                 { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/").list()).match("metadata") },
-                { assert snapshot(path("$outputDir/samplesheet/").list()).match("samplesheet") }
+                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
+                                path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
+                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
             )
         }
 
diff --git a/tests/pipeline/sra_with_sratools.nf.test.snap b/tests/pipeline/sra_with_sratools.nf.test.snap
index fb5ab805..44daeaa0 100644
--- a/tests/pipeline/sra_with_sratools.nf.test.snap
+++ b/tests/pipeline/sra_with_sratools.nf.test.snap
@@ -16,8 +16,7 @@
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
-            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
-            "samplesheet.csv:md5,03ae9aa2cd8b3fc60a123c00e15e7b9a"
+            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d"
         ],
         "timestamp": "2023-05-09T14:07:50+0000"
     },

From aec2794c85b6e7f50113097c7783da9d166b9b81 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Tue, 9 May 2023 11:11:54 -0400
Subject: [PATCH 320/852] remove-samplesheet-md5-snapshot

---
 .../sra_with_nf_core_pipeline.nf.test.snap        | 15 +++++----------
 1 file changed, 5 insertions(+), 10 deletions(-)

diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
index fda160f4..cd236ca2 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
@@ -71,16 +71,14 @@
     "rnaseq_samplesheet": {
         "content": [
             "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
-            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
-            "samplesheet.csv:md5,9fa43672fb5ffcf0dec423a4627dc028"
+            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d"
         ],
         "timestamp": "2023-05-09T14:11:58+0000"
     },
     "rnaseq_samplesheet_specific_ena": {
         "content": [
             "id_mappings.csv:md5,0efde324e1818c0827390a17449a6e8a",
-            "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd",
-            "samplesheet.csv:md5,dc7371849e112d0e95646ef1c34339d0"
+            "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd"
         ],
         "timestamp": "2023-05-09T14:11:58+0000"
     },
@@ -101,24 +99,21 @@
     "rnaseq_specific_ena_samplesheet": {
         "content": [
             "id_mappings.csv:md5,0efde324e1818c0827390a17449a6e8a",
-            "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd",
-            "samplesheet.csv:md5,6a08c28af1ed2629e18f0014f4d72ed6"
+            "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd"
         ],
         "timestamp": "2023-05-09T14:11:58+0000"
     },
     "atacseq_samplesheet": {
         "content": [
             "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
-            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
-            "samplesheet.csv:md5,236f64ee8d40b3b658aecc0298cccfb2"
+            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d"
         ],
         "timestamp": "2023-05-09T14:11:58+0000"
     },
     "taxprofiler_samplesheet": {
         "content": [
             "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
-            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d",
-            "samplesheet.csv:md5,336e53f72cc538a58911880ec7c9b5da"
+            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d"
         ],
         "timestamp": "2023-05-09T14:11:58+0000"
     },

From 5fd4dde3a66e4aa19e5652780b92db0cccb4404e Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Tue, 9 May 2023 11:20:02 -0400
Subject: [PATCH 321/852] update-samplesheet-nf-test

---
 .../pipeline/sra_with_nf_core_pipeline.nf.test | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
index 0618eb81..a12c678a 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
@@ -21,7 +21,7 @@ nextflow_pipeline {
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/").list()).match("rnaseq_metadata") },
                 { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
-                                path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
+                                path("$outputDir/samplesheet/multiqc_config.yml")).match("rnaseq_samplesheet") },
                 { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
             )
         }
@@ -44,7 +44,9 @@ nextflow_pipeline {
                 { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/").list()).match("rnaseq_ena_metadata") },
-                { assert snapshot(path("$outputDir/samplesheet/").list()).match("rnaseq_specific_ena_samplesheet") }
+                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
+                                path("$outputDir/samplesheet/multiqc_config.yml")).match("rnaseq_ena_samplesheet") },
+                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
             )
         }
     }
@@ -64,7 +66,9 @@ nextflow_pipeline {
                 { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/").list()).match("atacseq_metadata") },
-                { assert snapshot(path("$outputDir/samplesheet/").list()).match("atacseq_samplesheet") }
+                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
+                                path("$outputDir/samplesheet/multiqc_config.yml")).match("atacseq_samplesheet") },
+                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
             )
         }
     }
@@ -84,7 +88,9 @@ nextflow_pipeline {
                 { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/").list()).match("viralrecon_metadata") },
-                { assert snapshot(path("$outputDir/samplesheet/").list()).match("viralrecon_samplesheet") }
+                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
+                                path("$outputDir/samplesheet/multiqc_config.yml")).match("viralrecon_samplesheet") },
+                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
             )
         }
     }
@@ -104,7 +110,9 @@ nextflow_pipeline {
                 { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/").list()).match("taxprofiler_metadata") },
-                { assert snapshot(path("$outputDir/samplesheet/").list()).match("taxprofiler_samplesheet") }
+                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
+                                path("$outputDir/samplesheet/multiqc_config.yml")).match("taxprofiler_samplesheet") },
+                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
             )
         }
     }

From 7c0ca3e7a78c6387c9f6ced5f1641fd5c45800ea Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Thu, 11 May 2023 17:19:35 -0500
Subject: [PATCH 322/852] chore: Add snaps to generated files

---
 .gitattributes | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitattributes b/.gitattributes
index 7a2dabc2..c1c17000 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1,4 +1,5 @@
 *.config linguist-language=nextflow
 *.nf.test linguist-language=nextflow
+tests/**/*nf.test.snap linguist-generated
 modules/nf-core/** linguist-generated
 subworkflows/nf-core/** linguist-generated

From 0b64654f88f684c4c15bb1f31547bc9a4012efea Mon Sep 17 00:00:00 2001
From: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
Date: Thu, 11 May 2023 22:13:56 -0400
Subject: [PATCH 323/852] Update tests/pipeline/sra_skip_fastq.nf.test

Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
---
 tests/pipeline/sra_skip_fastq.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/pipeline/sra_skip_fastq.nf.test b/tests/pipeline/sra_skip_fastq.nf.test
index 0d6849b9..bdf992ef 100644
--- a/tests/pipeline/sra_skip_fastq.nf.test
+++ b/tests/pipeline/sra_skip_fastq.nf.test
@@ -2,7 +2,7 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
-    options "-profile test,docker"
+    profile "test,docker"
     tag "pipeline"
 
     test("SRA Skip FASTQ") {

From 7dbb311d63460d56e0dafd3e55e750659c11cf6c Mon Sep 17 00:00:00 2001
From: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
Date: Thu, 11 May 2023 22:14:08 -0400
Subject: [PATCH 324/852] Update
 tests/pipeline/sra_with_nf_core_pipeline.nf.test

Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
---
 tests/pipeline/sra_with_nf_core_pipeline.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
index a12c678a..813c25da 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
@@ -2,7 +2,7 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
-    options "-profile test,docker"
+    profile "test,docker"
     tag "pipeline"
 
     test("SRA NF-CORE/RNASEQ Samplesheet") {

From 6779785dd561562f7ccf34dc71a49f6cd6d32f7c Mon Sep 17 00:00:00 2001
From: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
Date: Thu, 11 May 2023 22:14:16 -0400
Subject: [PATCH 325/852] Update tests/pipeline/sra_with_sratools.nf.test

Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
---
 tests/pipeline/sra_with_sratools.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/pipeline/sra_with_sratools.nf.test b/tests/pipeline/sra_with_sratools.nf.test
index dd85131c..5bc903ac 100644
--- a/tests/pipeline/sra_with_sratools.nf.test
+++ b/tests/pipeline/sra_with_sratools.nf.test
@@ -2,7 +2,7 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
-    options "-profile test,docker"
+    profile "test,docker"
     tag "pipeline"
 
     test("Force SRA-Tools Download") {

From 0d03bcb6389e8f7cdabff67edb518d3480ddbc85 Mon Sep 17 00:00:00 2001
From: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
Date: Thu, 11 May 2023 22:14:28 -0400
Subject: [PATCH 326/852] Update tests/pipeline/synapse.test

Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
---
 tests/pipeline/synapse.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/pipeline/synapse.test b/tests/pipeline/synapse.test
index 91f865dc..a59ebf0b 100644
--- a/tests/pipeline/synapse.test
+++ b/tests/pipeline/synapse.test
@@ -2,7 +2,7 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
-    options "-profile test_synapse,docker"
+    profile "test_synapse,docker"
     tag "pipeline"
 
     test("Synapse Input Type") {

From a42c998ea446d63f2da822884bdd3302aed02bed Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Tue, 16 May 2023 12:21:20 -0400
Subject: [PATCH 327/852] update-snapshots-1.10.0

---
 tests/nextflow.config                         |  5 --
 tests/pipeline/sra.nf.test.snap               | 36 +++++++--
 tests/pipeline/sra_skip_fastq.nf.test.snap    | 14 ++--
 .../sra_with_nf_core_pipeline.nf.test.snap    | 81 ++++++++++++++-----
 tests/pipeline/sra_with_sratools.nf.test.snap | 26 ++++--
 5 files changed, 115 insertions(+), 47 deletions(-)
 delete mode 100644 tests/nextflow.config

diff --git a/tests/nextflow.config b/tests/nextflow.config
deleted file mode 100644
index c19b1ad0..00000000
--- a/tests/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-/*
-========================================================================================
-    Nextflow config file for running tests
-========================================================================================
-*/
diff --git a/tests/pipeline/sra.nf.test.snap b/tests/pipeline/sra.nf.test.snap
index d16a31ec..c1fe0af7 100644
--- a/tests/pipeline/sra.nf.test.snap
+++ b/tests/pipeline/sra.nf.test.snap
@@ -5,26 +5,28 @@
             "DRR028935.runinfo_ftp.tsv:md5,9db5d6cba5ce2cccd9b2cc3faaa092e2",
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
+            "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
+            "GSM4907283.runinfo_ftp.tsv:md5,3d2c2395ee6690338f56fca84acb54ba",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-09T14:15:30+0000"
+        "timestamp": "2023-05-16T16:13:55+0000"
     },
     "samplesheet": {
         "content": [
-            "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
-            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d"
+            "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
+            "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-09T14:15:30+0000"
+        "timestamp": "2023-05-16T16:13:55+0000"
     },
     "software_versions": {
         "content": [
-            "software_versions.yml:md5,c8ccda032b4de8e103eace767442fcf4"
+            "software_versions.yml:md5,7837dd6b0454c15b69cc8d2e6a0e9f83"
         ],
-        "timestamp": "2023-05-09T14:15:30+0000"
+        "timestamp": "2023-05-16T16:13:55+0000"
     },
     "fastq": {
         "content": [
@@ -37,9 +39,19 @@
             "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
             "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
             "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
+            "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64",
+            "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83",
             "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544",
             "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
             "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
+            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
+            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962",
+            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
+            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76",
+            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
+            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88",
+            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
+            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04",
             "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
             "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98",
             [
@@ -49,11 +61,21 @@
                 "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86",
                 "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499",
                 "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff",
+                "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75",
+                "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85",
                 "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4",
+                "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc",
+                "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0",
+                "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368",
+                "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8",
+                "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f",
+                "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3",
+                "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8",
+                "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882",
                 "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-05-09T14:15:30+0000"
+        "timestamp": "2023-05-16T16:13:55+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_skip_fastq.nf.test.snap b/tests/pipeline/sra_skip_fastq.nf.test.snap
index a4b5fa9f..7b65f527 100644
--- a/tests/pipeline/sra_skip_fastq.nf.test.snap
+++ b/tests/pipeline/sra_skip_fastq.nf.test.snap
@@ -5,25 +5,27 @@
             "DRR028935.runinfo_ftp.tsv:md5,9db5d6cba5ce2cccd9b2cc3faaa092e2",
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
+            "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
+            "GSM4907283.runinfo_ftp.tsv:md5,3d2c2395ee6690338f56fca84acb54ba",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-09T14:08:13+0000"
+        "timestamp": "2023-05-16T16:01:52+0000"
     },
     "samplesheet": {
         "content": [
-            "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
-            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d"
+            "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
+            "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-09T14:08:13+0000"
+        "timestamp": "2023-05-16T16:01:52+0000"
     },
     "software_versions": {
         "content": [
-            "software_versions.yml:md5,8b5ec8d90481271f6584ceff4d990caa"
+            "software_versions.yml:md5,fc7829c56a38a69722534e223ad9d818"
         ],
-        "timestamp": "2023-05-09T14:08:13+0000"
+        "timestamp": "2023-05-16T16:01:52+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
index cd236ca2..54312645 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
@@ -5,19 +5,21 @@
             "DRR028935.runinfo_ftp.tsv:md5,9db5d6cba5ce2cccd9b2cc3faaa092e2",
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
+            "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
+            "GSM4907283.runinfo_ftp.tsv:md5,3d2c2395ee6690338f56fca84acb54ba",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-09T14:11:58+0000"
+        "timestamp": "2023-05-16T16:11:36+0000"
     },
     "software_versions": {
         "content": [
-            "software_versions.yml:md5,c8ccda032b4de8e103eace767442fcf4"
+            "software_versions.yml:md5,7837dd6b0454c15b69cc8d2e6a0e9f83"
         ],
-        "timestamp": "2023-05-09T14:11:58+0000"
+        "timestamp": "2023-05-16T16:11:36+0000"
     },
     "viralrecon_metadata": {
         "content": [
@@ -25,20 +27,22 @@
             "DRR028935.runinfo_ftp.tsv:md5,9db5d6cba5ce2cccd9b2cc3faaa092e2",
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
+            "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
+            "GSM4907283.runinfo_ftp.tsv:md5,3d2c2395ee6690338f56fca84acb54ba",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-09T14:11:58+0000"
+        "timestamp": "2023-05-16T16:11:36+0000"
     },
     "viralrecon_samplesheet": {
         "content": [
-            "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
-            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d"
+            "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
+            "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-09T14:11:58+0000"
+        "timestamp": "2023-05-16T16:11:36+0000"
     },
     "atacseq_metadata": {
         "content": [
@@ -46,13 +50,15 @@
             "DRR028935.runinfo_ftp.tsv:md5,9db5d6cba5ce2cccd9b2cc3faaa092e2",
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
+            "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
+            "GSM4907283.runinfo_ftp.tsv:md5,3d2c2395ee6690338f56fca84acb54ba",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-09T14:11:58+0000"
+        "timestamp": "2023-05-16T16:11:36+0000"
     },
     "rnaseq_ena_metadata": {
         "content": [
@@ -60,27 +66,29 @@
             "DRR028935.runinfo_ftp.tsv:md5,07a98fdcec207686a4ea2c9a3997edf3",
             "ERR1109373.runinfo_ftp.tsv:md5,868897310855c50b1d5fc77d1195a1f9",
             "ERR1160846.runinfo_ftp.tsv:md5,146d7f2ec778b32b7da7ad040e554114",
+            "GSE214215.runinfo_ftp.tsv:md5,adf62affe371dc9bad8e271450bdc2fe",
+            "GSM4907283.runinfo_ftp.tsv:md5,5758453402e82490c4841c8e85a6aa53",
             "SRR12848126.runinfo_ftp.tsv:md5,cf8827612a76645824e83418d7d76cbf",
             "SRR13191702.runinfo_ftp.tsv:md5,2031ca9b7ab736dbde37d05b10cdb0ad",
             "SRR14593545.runinfo_ftp.tsv:md5,3a1ac14d71744224a61ab542f869e180",
             "SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1",
             "SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236"
         ],
-        "timestamp": "2023-05-09T14:11:58+0000"
+        "timestamp": "2023-05-16T16:11:36+0000"
     },
     "rnaseq_samplesheet": {
         "content": [
-            "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
-            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d"
+            "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
+            "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-09T14:11:58+0000"
+        "timestamp": "2023-05-16T16:11:36+0000"
     },
     "rnaseq_samplesheet_specific_ena": {
         "content": [
             "id_mappings.csv:md5,0efde324e1818c0827390a17449a6e8a",
             "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd"
         ],
-        "timestamp": "2023-05-09T14:11:58+0000"
+        "timestamp": "2023-05-16T16:11:36+0000"
     },
     "rnaseq_metadata": {
         "content": [
@@ -88,34 +96,43 @@
             "DRR028935.runinfo_ftp.tsv:md5,9db5d6cba5ce2cccd9b2cc3faaa092e2",
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
+            "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
+            "GSM4907283.runinfo_ftp.tsv:md5,3d2c2395ee6690338f56fca84acb54ba",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-09T14:11:58+0000"
+        "timestamp": "2023-05-16T16:11:36+0000"
     },
     "rnaseq_specific_ena_samplesheet": {
         "content": [
             "id_mappings.csv:md5,0efde324e1818c0827390a17449a6e8a",
             "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd"
         ],
-        "timestamp": "2023-05-09T14:11:58+0000"
+        "timestamp": "2023-05-16T16:11:36+0000"
     },
     "atacseq_samplesheet": {
         "content": [
-            "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
-            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d"
+            "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
+            "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-09T14:11:58+0000"
+        "timestamp": "2023-05-16T16:11:36+0000"
+    },
+    "rnaseq_ena_samplesheet": {
+        "content": [
+            "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f",
+            "multiqc_config.yml:md5,6f6189ee58855de81eaf82ad86e21040"
+        ],
+        "timestamp": "2023-05-16T16:11:36+0000"
     },
     "taxprofiler_samplesheet": {
         "content": [
-            "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
-            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d"
+            "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
+            "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-09T14:11:58+0000"
+        "timestamp": "2023-05-16T16:11:36+0000"
     },
     "fastq": {
         "content": [
@@ -128,9 +145,19 @@
             "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
             "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
             "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
+            "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64",
+            "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83",
             "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544",
             "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
             "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
+            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
+            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962",
+            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
+            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76",
+            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
+            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88",
+            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
+            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04",
             "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
             "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98",
             [
@@ -140,11 +167,21 @@
                 "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86",
                 "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499",
                 "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff",
+                "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75",
+                "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85",
                 "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4",
+                "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc",
+                "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0",
+                "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368",
+                "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8",
+                "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f",
+                "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3",
+                "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8",
+                "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882",
                 "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-05-09T14:11:58+0000"
+        "timestamp": "2023-05-16T16:11:36+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_sratools.nf.test.snap b/tests/pipeline/sra_with_sratools.nf.test.snap
index 44daeaa0..040113af 100644
--- a/tests/pipeline/sra_with_sratools.nf.test.snap
+++ b/tests/pipeline/sra_with_sratools.nf.test.snap
@@ -5,26 +5,28 @@
             "DRR028935.runinfo_ftp.tsv:md5,9db5d6cba5ce2cccd9b2cc3faaa092e2",
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
+            "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
+            "GSM4907283.runinfo_ftp.tsv:md5,3d2c2395ee6690338f56fca84acb54ba",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-09T14:07:50+0000"
+        "timestamp": "2023-05-16T16:01:21+0000"
     },
     "samplesheet": {
         "content": [
-            "id_mappings.csv:md5,40c6daa8d668b4930bfd9045248e16ec",
-            "multiqc_config.yml:md5,a6370add94bbe60c6bbe1bb48a038e8d"
+            "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
+            "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-09T14:07:50+0000"
+        "timestamp": "2023-05-16T16:01:21+0000"
     },
     "software_versions": {
         "content": [
-            "software_versions.yml:md5,ec1f5ee8c99879c3b8f04e7e683f540f"
+            "software_versions.yml:md5,703fe5063c179f27f5df05252c29b82b"
         ],
-        "timestamp": "2023-05-09T14:07:50+0000"
+        "timestamp": "2023-05-16T16:01:21+0000"
     },
     "fastq": {
         "content": [
@@ -37,12 +39,22 @@
             "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
             "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
             "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
+            "SRX17709227_SRR21711856.fastq.gz:md5,eae43f1368d4568f415581394dc9726e",
+            "SRX17709228_SRR21711855.fastq.gz:md5,5194f8009b74552595c4ec5b7605d231",
             "SRX6725035_SRR9984183.fastq.gz:md5,7a70e678c400366869601c8be41fe74b",
             "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
             "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
+            "SRX9504942_SRR13055517_1.fastq.gz:md5,b6d912a73466c8f27b1d8021f80ec2bb",
+            "SRX9504942_SRR13055517_2.fastq.gz:md5,7c6e220694fa5d6d9124c739aa70ea92",
+            "SRX9504942_SRR13055518_1.fastq.gz:md5,ed29278c21a1bb2d8907a74be0dd4bc4",
+            "SRX9504942_SRR13055518_2.fastq.gz:md5,83785b728312deb81483fc1fd5b14264",
+            "SRX9504942_SRR13055519_1.fastq.gz:md5,28babc59a625b5161d97392efd4d0018",
+            "SRX9504942_SRR13055519_2.fastq.gz:md5,cf1eb4c61ab3522f4d473c86b2f696e1",
+            "SRX9504942_SRR13055520_1.fastq.gz:md5,cc75af896ec8a7cececb37851b0c6fcd",
+            "SRX9504942_SRR13055520_2.fastq.gz:md5,fe3e2bf9f738e4959243fad59e879eae",
             "SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7",
             "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af"
         ],
-        "timestamp": "2023-05-09T14:07:50+0000"
+        "timestamp": "2023-05-16T16:01:21+0000"
     }
 }
\ No newline at end of file

From bc1dca9c5fb2da51193329dca74e042150d15b35 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Tue, 16 May 2023 15:30:24 -0400
Subject: [PATCH 328/852] update-ci-testing-min-nxf-ver

---
 .github/workflows/ci.yml | 33 +++++++++++++++++++++++----------
 1 file changed, 23 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 22e8274e..c54b696c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -18,31 +18,44 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
-  # Define the jobs to be run in parallel
+# Define the jobs to be run in parallel
 jobs:
+  get_version:
+    runs-on: ubuntu-latest
+    outputs:
+      version: ${{ steps.get_version.outputs.version }}
+
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v3
+
+      - name: Get Minimum supported Nextflow version
+        id: get_version
+        run: |
+          VERSION=$(grep 'nextflowVersion' nextflow.config | awk -F'= ' '{print $2}' | tr -d '!>=" ')
+          echo "::set-output name=version::$VERSION"
+
   test:
-    # Name the job with the corresponding profile, Nextflow version and aligner
-    name: Run ${{ matrix.profile }}-${{ matrix.NXF_VER }} pipeline test
+    name: Run ${{ matrix.profile }} pipeline test
+    needs: get_version
 
-    # Set the condition for running the job
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}"
 
-    # Specify the runner for the job
     runs-on: ubuntu-latest
+    env:
+      NXF_VER: ${{ needs.get_version.outputs.version }}
 
-    # Define the matrix for different Nextflow versions, profiles and aligners
     strategy:
       matrix:
-        NXF_VER:
-          - "latest-everything"
         profile: ["docker"]
 
-    # Define the steps for the job
     steps:
-      # Checkout the pipeline code from the repository
       - name: Check out pipeline code
         uses: actions/checkout@v3
 
+      - name: Use Nextflow version
+        run: echo "Using Nextflow version $NXF_VER"
+
       # Cache Test Data
       - name: Cache test data
         uses: actions/cache@v2

From 6d0aab77f7d756fdb475dab0cbc2f0c5aa94ccd7 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Tue, 16 May 2023 15:54:28 -0400
Subject: [PATCH 329/852] update-snapshots-22.10.1

---
 tests/pipeline/sra.nf.test.snap               | 10 +++----
 tests/pipeline/sra_skip_fastq.nf.test.snap    |  8 ++---
 .../sra_with_nf_core_pipeline.nf.test.snap    | 30 +++++++++----------
 tests/pipeline/sra_with_sratools.nf.test.snap | 10 +++----
 4 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/tests/pipeline/sra.nf.test.snap b/tests/pipeline/sra.nf.test.snap
index c1fe0af7..01c60787 100644
--- a/tests/pipeline/sra.nf.test.snap
+++ b/tests/pipeline/sra.nf.test.snap
@@ -13,20 +13,20 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-16T16:13:55+0000"
+        "timestamp": "2023-05-16T19:53:51+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-16T16:13:55+0000"
+        "timestamp": "2023-05-16T19:53:51+0000"
     },
     "software_versions": {
         "content": [
-            "software_versions.yml:md5,7837dd6b0454c15b69cc8d2e6a0e9f83"
+            "software_versions.yml:md5,a1fb45ebb6c1d809de31398b910942dc"
         ],
-        "timestamp": "2023-05-16T16:13:55+0000"
+        "timestamp": "2023-05-16T19:53:51+0000"
     },
     "fastq": {
         "content": [
@@ -76,6 +76,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-05-16T16:13:55+0000"
+        "timestamp": "2023-05-16T19:53:51+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_skip_fastq.nf.test.snap b/tests/pipeline/sra_skip_fastq.nf.test.snap
index 7b65f527..f3067391 100644
--- a/tests/pipeline/sra_skip_fastq.nf.test.snap
+++ b/tests/pipeline/sra_skip_fastq.nf.test.snap
@@ -13,19 +13,19 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-16T16:01:52+0000"
+        "timestamp": "2023-05-16T19:38:26+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-16T16:01:52+0000"
+        "timestamp": "2023-05-16T19:38:26+0000"
     },
     "software_versions": {
         "content": [
-            "software_versions.yml:md5,fc7829c56a38a69722534e223ad9d818"
+            "software_versions.yml:md5,6615486e6d186ded463ec1dea7c5012f"
         ],
-        "timestamp": "2023-05-16T16:01:52+0000"
+        "timestamp": "2023-05-16T19:38:26+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
index 54312645..958a361e 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
@@ -13,13 +13,13 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-16T16:11:36+0000"
+        "timestamp": "2023-05-16T19:40:34+0000"
     },
     "software_versions": {
         "content": [
-            "software_versions.yml:md5,7837dd6b0454c15b69cc8d2e6a0e9f83"
+            "software_versions.yml:md5,a1fb45ebb6c1d809de31398b910942dc"
         ],
-        "timestamp": "2023-05-16T16:11:36+0000"
+        "timestamp": "2023-05-16T19:40:34+0000"
     },
     "viralrecon_metadata": {
         "content": [
@@ -35,14 +35,14 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-16T16:11:36+0000"
+        "timestamp": "2023-05-16T19:40:34+0000"
     },
     "viralrecon_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-16T16:11:36+0000"
+        "timestamp": "2023-05-16T19:40:34+0000"
     },
     "atacseq_metadata": {
         "content": [
@@ -58,7 +58,7 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-16T16:11:36+0000"
+        "timestamp": "2023-05-16T19:40:34+0000"
     },
     "rnaseq_ena_metadata": {
         "content": [
@@ -74,21 +74,21 @@
             "SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1",
             "SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236"
         ],
-        "timestamp": "2023-05-16T16:11:36+0000"
+        "timestamp": "2023-05-16T19:40:34+0000"
     },
     "rnaseq_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-16T16:11:36+0000"
+        "timestamp": "2023-05-16T19:40:34+0000"
     },
     "rnaseq_samplesheet_specific_ena": {
         "content": [
             "id_mappings.csv:md5,0efde324e1818c0827390a17449a6e8a",
             "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd"
         ],
-        "timestamp": "2023-05-16T16:11:36+0000"
+        "timestamp": "2023-05-16T19:40:34+0000"
     },
     "rnaseq_metadata": {
         "content": [
@@ -104,35 +104,35 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-16T16:11:36+0000"
+        "timestamp": "2023-05-16T19:40:34+0000"
     },
     "rnaseq_specific_ena_samplesheet": {
         "content": [
             "id_mappings.csv:md5,0efde324e1818c0827390a17449a6e8a",
             "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd"
         ],
-        "timestamp": "2023-05-16T16:11:36+0000"
+        "timestamp": "2023-05-16T19:40:34+0000"
     },
     "atacseq_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-16T16:11:36+0000"
+        "timestamp": "2023-05-16T19:40:34+0000"
     },
     "rnaseq_ena_samplesheet": {
         "content": [
             "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f",
             "multiqc_config.yml:md5,6f6189ee58855de81eaf82ad86e21040"
         ],
-        "timestamp": "2023-05-16T16:11:36+0000"
+        "timestamp": "2023-05-16T19:40:34+0000"
     },
     "taxprofiler_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-16T16:11:36+0000"
+        "timestamp": "2023-05-16T19:40:34+0000"
     },
     "fastq": {
         "content": [
@@ -182,6 +182,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-05-16T16:11:36+0000"
+        "timestamp": "2023-05-16T19:40:34+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_sratools.nf.test.snap b/tests/pipeline/sra_with_sratools.nf.test.snap
index 040113af..13e1b5f6 100644
--- a/tests/pipeline/sra_with_sratools.nf.test.snap
+++ b/tests/pipeline/sra_with_sratools.nf.test.snap
@@ -13,20 +13,20 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-16T16:01:21+0000"
+        "timestamp": "2023-05-16T19:37:55+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-16T16:01:21+0000"
+        "timestamp": "2023-05-16T19:37:55+0000"
     },
     "software_versions": {
         "content": [
-            "software_versions.yml:md5,703fe5063c179f27f5df05252c29b82b"
+            "software_versions.yml:md5,ece325a9469ecf48050340b577e252a1"
         ],
-        "timestamp": "2023-05-16T16:01:21+0000"
+        "timestamp": "2023-05-16T19:37:55+0000"
     },
     "fastq": {
         "content": [
@@ -55,6 +55,6 @@
             "SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7",
             "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af"
         ],
-        "timestamp": "2023-05-16T16:01:21+0000"
+        "timestamp": "2023-05-16T19:37:55+0000"
     }
 }
\ No newline at end of file

From 04ac6584548954a46395d595b5d598be39a10558 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Tue, 16 May 2023 17:39:25 -0400
Subject: [PATCH 330/852] update-snaps-1.11.0

---
 tests/pipeline/sra.nf.test.snap               | 10 +++----
 tests/pipeline/sra_skip_fastq.nf.test.snap    |  8 ++---
 .../sra_with_nf_core_pipeline.nf.test.snap    | 30 +++++++++----------
 tests/pipeline/sra_with_sratools.nf.test.snap | 10 +++----
 4 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/tests/pipeline/sra.nf.test.snap b/tests/pipeline/sra.nf.test.snap
index 01c60787..be0a6829 100644
--- a/tests/pipeline/sra.nf.test.snap
+++ b/tests/pipeline/sra.nf.test.snap
@@ -13,20 +13,20 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-16T19:53:51+0000"
+        "timestamp": "2023-05-16T21:05:23+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-16T19:53:51+0000"
+        "timestamp": "2023-05-16T21:05:23+0000"
     },
     "software_versions": {
         "content": [
-            "software_versions.yml:md5,a1fb45ebb6c1d809de31398b910942dc"
+            "software_versions.yml:md5,9f477f11e8db6ac81cda776d0375fbb3"
         ],
-        "timestamp": "2023-05-16T19:53:51+0000"
+        "timestamp": "2023-05-16T21:05:23+0000"
     },
     "fastq": {
         "content": [
@@ -76,6 +76,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-05-16T19:53:51+0000"
+        "timestamp": "2023-05-16T21:05:23+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_skip_fastq.nf.test.snap b/tests/pipeline/sra_skip_fastq.nf.test.snap
index f3067391..116af376 100644
--- a/tests/pipeline/sra_skip_fastq.nf.test.snap
+++ b/tests/pipeline/sra_skip_fastq.nf.test.snap
@@ -13,19 +13,19 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-16T19:38:26+0000"
+        "timestamp": "2023-05-16T20:52:16+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-16T19:38:26+0000"
+        "timestamp": "2023-05-16T20:52:16+0000"
     },
     "software_versions": {
         "content": [
-            "software_versions.yml:md5,6615486e6d186ded463ec1dea7c5012f"
+            "software_versions.yml:md5,5a1fd397bea2323067ca0a6893384ae7"
         ],
-        "timestamp": "2023-05-16T19:38:26+0000"
+        "timestamp": "2023-05-16T20:52:16+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
index 958a361e..b0fa8e18 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
@@ -13,13 +13,13 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-16T19:40:34+0000"
+        "timestamp": "2023-05-16T20:54:25+0000"
     },
     "software_versions": {
         "content": [
-            "software_versions.yml:md5,a1fb45ebb6c1d809de31398b910942dc"
+            "software_versions.yml:md5,9f477f11e8db6ac81cda776d0375fbb3"
         ],
-        "timestamp": "2023-05-16T19:40:34+0000"
+        "timestamp": "2023-05-16T20:54:25+0000"
     },
     "viralrecon_metadata": {
         "content": [
@@ -35,14 +35,14 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-16T19:40:34+0000"
+        "timestamp": "2023-05-16T20:54:25+0000"
     },
     "viralrecon_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-16T19:40:34+0000"
+        "timestamp": "2023-05-16T20:54:25+0000"
     },
     "atacseq_metadata": {
         "content": [
@@ -58,7 +58,7 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-16T19:40:34+0000"
+        "timestamp": "2023-05-16T20:54:25+0000"
     },
     "rnaseq_ena_metadata": {
         "content": [
@@ -74,21 +74,21 @@
             "SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1",
             "SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236"
         ],
-        "timestamp": "2023-05-16T19:40:34+0000"
+        "timestamp": "2023-05-16T20:54:25+0000"
     },
     "rnaseq_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-16T19:40:34+0000"
+        "timestamp": "2023-05-16T20:54:25+0000"
     },
     "rnaseq_samplesheet_specific_ena": {
         "content": [
             "id_mappings.csv:md5,0efde324e1818c0827390a17449a6e8a",
             "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd"
         ],
-        "timestamp": "2023-05-16T19:40:34+0000"
+        "timestamp": "2023-05-16T20:54:25+0000"
     },
     "rnaseq_metadata": {
         "content": [
@@ -104,35 +104,35 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-16T19:40:34+0000"
+        "timestamp": "2023-05-16T20:54:25+0000"
     },
     "rnaseq_specific_ena_samplesheet": {
         "content": [
             "id_mappings.csv:md5,0efde324e1818c0827390a17449a6e8a",
             "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd"
         ],
-        "timestamp": "2023-05-16T19:40:34+0000"
+        "timestamp": "2023-05-16T20:54:25+0000"
     },
     "atacseq_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-16T19:40:34+0000"
+        "timestamp": "2023-05-16T20:54:25+0000"
     },
     "rnaseq_ena_samplesheet": {
         "content": [
             "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f",
             "multiqc_config.yml:md5,6f6189ee58855de81eaf82ad86e21040"
         ],
-        "timestamp": "2023-05-16T19:40:34+0000"
+        "timestamp": "2023-05-16T20:54:25+0000"
     },
     "taxprofiler_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-16T19:40:34+0000"
+        "timestamp": "2023-05-16T20:54:25+0000"
     },
     "fastq": {
         "content": [
@@ -182,6 +182,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-05-16T19:40:34+0000"
+        "timestamp": "2023-05-16T20:54:25+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_sratools.nf.test.snap b/tests/pipeline/sra_with_sratools.nf.test.snap
index 13e1b5f6..9ebf0e55 100644
--- a/tests/pipeline/sra_with_sratools.nf.test.snap
+++ b/tests/pipeline/sra_with_sratools.nf.test.snap
@@ -13,20 +13,20 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-16T19:37:55+0000"
+        "timestamp": "2023-05-16T20:51:44+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-16T19:37:55+0000"
+        "timestamp": "2023-05-16T20:51:44+0000"
     },
     "software_versions": {
         "content": [
-            "software_versions.yml:md5,ece325a9469ecf48050340b577e252a1"
+            "software_versions.yml:md5,53061262d7600d38656f7373a7123159"
         ],
-        "timestamp": "2023-05-16T19:37:55+0000"
+        "timestamp": "2023-05-16T20:51:44+0000"
     },
     "fastq": {
         "content": [
@@ -55,6 +55,6 @@
             "SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7",
             "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af"
         ],
-        "timestamp": "2023-05-16T19:37:55+0000"
+        "timestamp": "2023-05-16T20:51:44+0000"
     }
 }
\ No newline at end of file

From c0e5d138dced843b00b019f6d990a0684cc9f93b Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Tue, 16 May 2023 18:47:13 -0400
Subject: [PATCH 331/852] update-ci-use-GITHUB_OUTPUT-for-nxf-ver

---
 .github/workflows/ci.yml | 2 +-
 .nf-core.yml             | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c54b696c..584b9967 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -33,7 +33,7 @@ jobs:
         id: get_version
         run: |
           VERSION=$(grep 'nextflowVersion' nextflow.config | awk -F'= ' '{print $2}' | tr -d '!>=" ')
-          echo "::set-output name=version::$VERSION"
+          echo "nxf_version=$VERSION" >> $GITHUB_OUTPUT
 
   test:
     name: Run ${{ matrix.profile }} pipeline test
diff --git a/.nf-core.yml b/.nf-core.yml
index 402025a7..f11657b7 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -3,4 +3,5 @@ lint:
   files_unchanged:
     - assets/sendmail_template.txt
     - lib/NfcoreTemplate.groovy
+    - .gitattributes
   actions_ci: False

From a119105d8861f21f6e6659498092f6b956535ddd Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Tue, 16 May 2023 19:38:47 -0400
Subject: [PATCH 332/852] fix-nxf-ver-output-name

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 584b9967..f1140334 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -33,7 +33,7 @@ jobs:
         id: get_version
         run: |
           VERSION=$(grep 'nextflowVersion' nextflow.config | awk -F'= ' '{print $2}' | tr -d '!>=" ')
-          echo "nxf_version=$VERSION" >> $GITHUB_OUTPUT
+          echo "version=$VERSION" >> $GITHUB_OUTPUT
 
   test:
     name: Run ${{ matrix.profile }} pipeline test

From 0374bcf5bff5ae8ea7ff7a21226b0e62f9d8afb5 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Wed, 17 May 2023 11:19:51 -0500
Subject: [PATCH 333/852] test: Remove docker profile

---
 .github/workflows/ci.yml                         | 2 +-
 tests/pipeline/sra.nf.test                       | 2 +-
 tests/pipeline/sra_skip_fastq.nf.test            | 2 +-
 tests/pipeline/sra_with_nf_core_pipeline.nf.test | 2 +-
 tests/pipeline/sra_with_sratools.nf.test         | 2 +-
 tests/pipeline/synapse.test                      | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f1140334..27216961 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -80,7 +80,7 @@ jobs:
       # Run nf-test with the specified aligner and output test results in TAP format
       - name: Run nf-test
         run: |
-          nf-test test tests/pipeline/ --tap=test.tap
+          nf-test test tests/pipeline/ --tap=test.tap --profile "${{ matrix.profile }}"
 
       # If the test fails, output the software_versions.yml using the 'batcat' utility
       - name: Output log on failure
diff --git a/tests/pipeline/sra.nf.test b/tests/pipeline/sra.nf.test
index 00d8ad0f..c82a8fff 100644
--- a/tests/pipeline/sra.nf.test
+++ b/tests/pipeline/sra.nf.test
@@ -2,7 +2,7 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
-    options "-profile test,docker"
+    profile "test"
     tag "pipeline"
 
     test("SRA FASTQ & Metadata") {
diff --git a/tests/pipeline/sra_skip_fastq.nf.test b/tests/pipeline/sra_skip_fastq.nf.test
index bdf992ef..caa11c75 100644
--- a/tests/pipeline/sra_skip_fastq.nf.test
+++ b/tests/pipeline/sra_skip_fastq.nf.test
@@ -2,7 +2,7 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
-    profile "test,docker"
+    profile "test"
     tag "pipeline"
 
     test("SRA Skip FASTQ") {
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
index 813c25da..231970be 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
@@ -2,7 +2,7 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
-    profile "test,docker"
+    profile "test"
     tag "pipeline"
 
     test("SRA NF-CORE/RNASEQ Samplesheet") {
diff --git a/tests/pipeline/sra_with_sratools.nf.test b/tests/pipeline/sra_with_sratools.nf.test
index 5bc903ac..cba77760 100644
--- a/tests/pipeline/sra_with_sratools.nf.test
+++ b/tests/pipeline/sra_with_sratools.nf.test
@@ -2,7 +2,7 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
-    profile "test,docker"
+    profile "test"
     tag "pipeline"
 
     test("Force SRA-Tools Download") {
diff --git a/tests/pipeline/synapse.test b/tests/pipeline/synapse.test
index a59ebf0b..464ad226 100644
--- a/tests/pipeline/synapse.test
+++ b/tests/pipeline/synapse.test
@@ -2,7 +2,7 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
-    profile "test_synapse,docker"
+    profile "test_synapse"
     tag "pipeline"
 
     test("Synapse Input Type") {

From 266fbe48fbf2be7c134f33bdfb6f1b57066e4f62 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Wed, 17 May 2023 11:22:40 -0500
Subject: [PATCH 334/852] ci: Remove matrix prefix of NXF_VER

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 27216961..c1ee8f7a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -69,7 +69,7 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
-          version: "${{ matrix.NXF_VER }}"
+          version: "$NXF_VER"
 
       # Install nf-test
       - name: Install nf-test

From 7e2ab293d3693f9aa756e1ed5d21f2edbd47769d Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Tue, 23 May 2023 14:31:44 -0400
Subject: [PATCH 335/852] rm-nxf-ver-snapshot

---
 .github/workflows/ci.yml                      |  4 +-
 nf-test.config                                |  2 +-
 tests/pipeline/sra.nf.test                    |  6 +-
 tests/pipeline/sra.nf.test.snap               | 36 ++++++++++--
 tests/pipeline/sra_skip_fastq.nf.test         |  6 +-
 tests/pipeline/sra_skip_fastq.nf.test.snap    | 28 +++++++--
 .../sra_with_nf_core_pipeline.nf.test         | 26 +++++++--
 .../sra_with_nf_core_pipeline.nf.test.snap    | 58 ++++++++++++++-----
 tests/pipeline/sra_with_sratools.nf.test      |  6 +-
 tests/pipeline/sra_with_sratools.nf.test.snap | 33 +++++++++--
 10 files changed, 160 insertions(+), 45 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c1ee8f7a..f1140334 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -69,7 +69,7 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
-          version: "$NXF_VER"
+          version: "${{ matrix.NXF_VER }}"
 
       # Install nf-test
       - name: Install nf-test
@@ -80,7 +80,7 @@ jobs:
       # Run nf-test with the specified aligner and output test results in TAP format
       - name: Run nf-test
         run: |
-          nf-test test tests/pipeline/ --tap=test.tap --profile "${{ matrix.profile }}"
+          nf-test test tests/pipeline/ --tap=test.tap
 
       # If the test fails, output the software_versions.yml using the 'batcat' utility
       - name: Output log on failure
diff --git a/nf-test.config b/nf-test.config
index 9d4198ff..f345cb2d 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -3,6 +3,6 @@ config {
     testsDir "tests"
     workDir ".nf-test"
     configFile "nextflow.config"
-    profile ""
+    profile "test,docker"
 
 }
diff --git a/tests/pipeline/sra.nf.test b/tests/pipeline/sra.nf.test
index c82a8fff..37749254 100644
--- a/tests/pipeline/sra.nf.test
+++ b/tests/pipeline/sra.nf.test
@@ -2,7 +2,6 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
-    profile "test"
     tag "pipeline"
 
     test("SRA FASTQ & Metadata") {
@@ -14,9 +13,12 @@ nextflow_pipeline {
         }
 
         then {
+            def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
+            if (softwareVersions.containsKey("Workflow")) { softwareVersions.Workflow.remove("Nextflow") }
+
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
+                { assert snapshot(softwareVersions).match("software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/").list()).match("metadata") },
                 { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
diff --git a/tests/pipeline/sra.nf.test.snap b/tests/pipeline/sra.nf.test.snap
index be0a6829..fc79907b 100644
--- a/tests/pipeline/sra.nf.test.snap
+++ b/tests/pipeline/sra.nf.test.snap
@@ -13,20 +13,46 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-16T21:05:23+0000"
+        "timestamp": "2023-05-23T18:30:12+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-16T21:05:23+0000"
+        "timestamp": "2023-05-23T18:30:12+0000"
     },
     "software_versions": {
         "content": [
-            "software_versions.yml:md5,9f477f11e8db6ac81cda776d0375fbb3"
+            {
+                "CUSTOM_DUMPSOFTWAREVERSIONS": {
+                    "python": "3.11.0",
+                    "yaml": "6.0"
+                },
+                "CUSTOM_SRATOOLSNCBISETTINGS": {
+                    "sratools": "2.11.0"
+                },
+                "MULTIQC_MAPPINGS_CONFIG": {
+                    "python": "3.9.5"
+                },
+                "SRA_FASTQ_FTP": {
+                    "curl": "7.81.0"
+                },
+                "SRA_IDS_TO_RUNINFO": {
+                    "python": "3.9.5"
+                },
+                "SRA_MERGE_SAMPLESHEET": {
+                    "sed": "4.7"
+                },
+                "SRA_RUNINFO_TO_FTP": {
+                    "python": "3.9.5"
+                },
+                "Workflow": {
+                    "nf-core/fetchngs": "1.11.0dev"
+                }
+            }
         ],
-        "timestamp": "2023-05-16T21:05:23+0000"
+        "timestamp": "2023-05-23T18:30:12+0000"
     },
     "fastq": {
         "content": [
@@ -76,6 +102,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-05-16T21:05:23+0000"
+        "timestamp": "2023-05-23T18:30:12+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_skip_fastq.nf.test b/tests/pipeline/sra_skip_fastq.nf.test
index caa11c75..8497af75 100644
--- a/tests/pipeline/sra_skip_fastq.nf.test
+++ b/tests/pipeline/sra_skip_fastq.nf.test
@@ -2,7 +2,6 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
-    profile "test"
     tag "pipeline"
 
     test("SRA Skip FASTQ") {
@@ -15,9 +14,12 @@ nextflow_pipeline {
         }
 
         then {
+            def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
+            if (softwareVersions.containsKey("Workflow")) { softwareVersions.Workflow.remove("Nextflow") }
+
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
+                { assert snapshot(softwareVersions).match("software_versions") },
                 { assert snapshot(path("$outputDir/metadata/").list()).match("metadata") },
                 { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
                                 path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
diff --git a/tests/pipeline/sra_skip_fastq.nf.test.snap b/tests/pipeline/sra_skip_fastq.nf.test.snap
index 116af376..456e101d 100644
--- a/tests/pipeline/sra_skip_fastq.nf.test.snap
+++ b/tests/pipeline/sra_skip_fastq.nf.test.snap
@@ -13,19 +13,39 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-16T20:52:16+0000"
+        "timestamp": "2023-05-23T18:17:54+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-16T20:52:16+0000"
+        "timestamp": "2023-05-23T18:17:54+0000"
     },
     "software_versions": {
         "content": [
-            "software_versions.yml:md5,5a1fd397bea2323067ca0a6893384ae7"
+            {
+                "CUSTOM_DUMPSOFTWAREVERSIONS": {
+                    "python": "3.11.0",
+                    "yaml": "6.0"
+                },
+                "MULTIQC_MAPPINGS_CONFIG": {
+                    "python": "3.9.5"
+                },
+                "SRA_IDS_TO_RUNINFO": {
+                    "python": "3.9.5"
+                },
+                "SRA_MERGE_SAMPLESHEET": {
+                    "sed": "4.7"
+                },
+                "SRA_RUNINFO_TO_FTP": {
+                    "python": "3.9.5"
+                },
+                "Workflow": {
+                    "nf-core/fetchngs": "1.11.0dev"
+                }
+            }
         ],
-        "timestamp": "2023-05-16T20:52:16+0000"
+        "timestamp": "2023-05-23T18:17:54+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
index 231970be..54cec435 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
@@ -2,7 +2,6 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
-    profile "test"
     tag "pipeline"
 
     test("SRA NF-CORE/RNASEQ Samplesheet") {
@@ -15,9 +14,12 @@ nextflow_pipeline {
         }
 
         then {
+            def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
+            if (softwareVersions.containsKey("Workflow")) { softwareVersions.Workflow.remove("Nextflow") }
+
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
+                { assert snapshot(softwareVersions).match("software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/").list()).match("rnaseq_metadata") },
                 { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
@@ -39,9 +41,12 @@ nextflow_pipeline {
         }
 
         then {
+            def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
+            if (softwareVersions.containsKey("Workflow")) { softwareVersions.Workflow.remove("Nextflow") }
+
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
+                { assert snapshot(softwareVersions).match("software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/").list()).match("rnaseq_ena_metadata") },
                 { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
@@ -61,9 +66,12 @@ nextflow_pipeline {
         }
 
         then {
+            def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
+            if (softwareVersions.containsKey("Workflow")) { softwareVersions.Workflow.remove("Nextflow") }
+
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
+                { assert snapshot(softwareVersions).match("software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/").list()).match("atacseq_metadata") },
                 { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
@@ -83,9 +91,12 @@ nextflow_pipeline {
         }
 
         then {
+            def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
+            if (softwareVersions.containsKey("Workflow")) { softwareVersions.Workflow.remove("Nextflow") }
+
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
+                { assert snapshot(softwareVersions).match("software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/").list()).match("viralrecon_metadata") },
                 { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
@@ -105,9 +116,12 @@ nextflow_pipeline {
         }
 
         then {
+            def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
+            if (softwareVersions.containsKey("Workflow")) { softwareVersions.Workflow.remove("Nextflow") }
+
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
+                { assert snapshot(softwareVersions).match("software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/").list()).match("taxprofiler_metadata") },
                 { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
index b0fa8e18..ef695ab0 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
@@ -6,20 +6,46 @@
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
             "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "GSM4907283.runinfo_ftp.tsv:md5,3d2c2395ee6690338f56fca84acb54ba",
+            "GSM4907283.runinfo_ftp.tsv:md5,92591968fa8fa37a9f7160fe8ada11a2",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-16T20:54:25+0000"
+        "timestamp": "2023-05-23T18:27:58+0000"
     },
     "software_versions": {
         "content": [
-            "software_versions.yml:md5,9f477f11e8db6ac81cda776d0375fbb3"
+            {
+                "CUSTOM_DUMPSOFTWAREVERSIONS": {
+                    "python": "3.11.0",
+                    "yaml": "6.0"
+                },
+                "CUSTOM_SRATOOLSNCBISETTINGS": {
+                    "sratools": "2.11.0"
+                },
+                "MULTIQC_MAPPINGS_CONFIG": {
+                    "python": "3.9.5"
+                },
+                "SRA_FASTQ_FTP": {
+                    "curl": "7.81.0"
+                },
+                "SRA_IDS_TO_RUNINFO": {
+                    "python": "3.9.5"
+                },
+                "SRA_MERGE_SAMPLESHEET": {
+                    "sed": "4.7"
+                },
+                "SRA_RUNINFO_TO_FTP": {
+                    "python": "3.9.5"
+                },
+                "Workflow": {
+                    "nf-core/fetchngs": "1.11.0dev"
+                }
+            }
         ],
-        "timestamp": "2023-05-16T20:54:25+0000"
+        "timestamp": "2023-05-23T18:27:57+0000"
     },
     "viralrecon_metadata": {
         "content": [
@@ -35,14 +61,14 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-16T20:54:25+0000"
+        "timestamp": "2023-05-23T18:27:57+0000"
     },
     "viralrecon_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-16T20:54:25+0000"
+        "timestamp": "2023-05-23T18:27:57+0000"
     },
     "atacseq_metadata": {
         "content": [
@@ -58,7 +84,7 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-16T20:54:25+0000"
+        "timestamp": "2023-05-23T18:27:57+0000"
     },
     "rnaseq_ena_metadata": {
         "content": [
@@ -74,21 +100,21 @@
             "SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1",
             "SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236"
         ],
-        "timestamp": "2023-05-16T20:54:25+0000"
+        "timestamp": "2023-05-23T18:27:57+0000"
     },
     "rnaseq_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-16T20:54:25+0000"
+        "timestamp": "2023-05-23T18:27:57+0000"
     },
     "rnaseq_samplesheet_specific_ena": {
         "content": [
             "id_mappings.csv:md5,0efde324e1818c0827390a17449a6e8a",
             "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd"
         ],
-        "timestamp": "2023-05-16T20:54:25+0000"
+        "timestamp": "2023-05-23T18:27:57+0000"
     },
     "rnaseq_metadata": {
         "content": [
@@ -104,35 +130,35 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-16T20:54:25+0000"
+        "timestamp": "2023-05-23T18:27:57+0000"
     },
     "rnaseq_specific_ena_samplesheet": {
         "content": [
             "id_mappings.csv:md5,0efde324e1818c0827390a17449a6e8a",
             "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd"
         ],
-        "timestamp": "2023-05-16T20:54:25+0000"
+        "timestamp": "2023-05-23T18:27:57+0000"
     },
     "atacseq_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-16T20:54:25+0000"
+        "timestamp": "2023-05-23T18:27:57+0000"
     },
     "rnaseq_ena_samplesheet": {
         "content": [
             "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f",
             "multiqc_config.yml:md5,6f6189ee58855de81eaf82ad86e21040"
         ],
-        "timestamp": "2023-05-16T20:54:25+0000"
+        "timestamp": "2023-05-23T18:27:57+0000"
     },
     "taxprofiler_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-16T20:54:25+0000"
+        "timestamp": "2023-05-23T18:27:57+0000"
     },
     "fastq": {
         "content": [
@@ -182,6 +208,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-05-16T20:54:25+0000"
+        "timestamp": "2023-05-23T18:27:57+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_sratools.nf.test b/tests/pipeline/sra_with_sratools.nf.test
index cba77760..7e50cc46 100644
--- a/tests/pipeline/sra_with_sratools.nf.test
+++ b/tests/pipeline/sra_with_sratools.nf.test
@@ -2,7 +2,6 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
-    profile "test"
     tag "pipeline"
 
     test("Force SRA-Tools Download") {
@@ -15,9 +14,12 @@ nextflow_pipeline {
         }
 
         then {
+            def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
+            if (softwareVersions.containsKey("Workflow")) { softwareVersions.Workflow.remove("Nextflow") }
+
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
+                { assert snapshot(softwareVersions).match("software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/").list()).match("metadata") },
                 { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
diff --git a/tests/pipeline/sra_with_sratools.nf.test.snap b/tests/pipeline/sra_with_sratools.nf.test.snap
index 9ebf0e55..d66ebc11 100644
--- a/tests/pipeline/sra_with_sratools.nf.test.snap
+++ b/tests/pipeline/sra_with_sratools.nf.test.snap
@@ -13,20 +13,43 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-16T20:51:44+0000"
+        "timestamp": "2023-05-23T18:17:22+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-16T20:51:44+0000"
+        "timestamp": "2023-05-23T18:17:22+0000"
     },
     "software_versions": {
         "content": [
-            "software_versions.yml:md5,53061262d7600d38656f7373a7123159"
+            {
+                "CUSTOM_DUMPSOFTWAREVERSIONS": {
+                    "python": "3.11.0",
+                    "yaml": "6.0"
+                },
+                "CUSTOM_SRATOOLSNCBISETTINGS": {
+                    "sratools": "2.11.0"
+                },
+                "MULTIQC_MAPPINGS_CONFIG": {
+                    "python": "3.9.5"
+                },
+                "SRA_IDS_TO_RUNINFO": {
+                    "python": "3.9.5"
+                },
+                "SRA_MERGE_SAMPLESHEET": {
+                    "sed": "4.7"
+                },
+                "SRA_RUNINFO_TO_FTP": {
+                    "python": "3.9.5"
+                },
+                "Workflow": {
+                    "nf-core/fetchngs": "1.11.0dev"
+                }
+            }
         ],
-        "timestamp": "2023-05-16T20:51:44+0000"
+        "timestamp": "2023-05-23T18:17:23+0000"
     },
     "fastq": {
         "content": [
@@ -55,6 +78,6 @@
             "SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7",
             "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af"
         ],
-        "timestamp": "2023-05-16T20:51:44+0000"
+        "timestamp": "2023-05-23T18:17:22+0000"
     }
 }
\ No newline at end of file

From e4a4fe9f536a89cc391aeb5741ec4b06e1e834ae Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Tue, 23 May 2023 14:34:48 -0400
Subject: [PATCH 336/852] fix-ci-setup-nxf-ver

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f1140334..a9c3aff0 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -69,7 +69,7 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
-          version: "${{ matrix.NXF_VER }}"
+          version: $NXF_VER
 
       # Install nf-test
       - name: Install nf-test

From 6510941e370aec34d5433969ef37582a0730bd09 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Tue, 23 May 2023 14:35:35 -0400
Subject: [PATCH 337/852] fix-ci-setup-nxf-ver

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index a9c3aff0..3e510594 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -69,7 +69,7 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
-          version: $NXF_VER
+          version: "$NXF_VER"
 
       # Install nf-test
       - name: Install nf-test

From de9ef6abbf45fbfbd4218254b2f1318d6047d593 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Tue, 23 May 2023 14:41:45 -0400
Subject: [PATCH 338/852] fix-ci-setup-nxf-ver

---
 .github/workflows/ci.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 3e510594..fc77b35e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -68,8 +68,6 @@ jobs:
       # Install the specified version of Nextflow
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
-        with:
-          version: "$NXF_VER"
 
       # Install nf-test
       - name: Install nf-test

From 17d1a36f7be2bba3b0378e1ec0388e0e27fe5533 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Tue, 23 May 2023 14:47:14 -0400
Subject: [PATCH 339/852] fix-ci-setup-nxf-ver

---
 .github/workflows/ci.yml | 23 ++++++-----------------
 1 file changed, 6 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index fc77b35e..38d0fce5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,7 +1,5 @@
-# This is the nf-core CI workflow configuration for GitHub Actions
 name: nf-core CI
 
-# This workflow is triggered when a pull request is made to the 'dev' branch or when a new release is published
 on:
   pull_request:
     branches:
@@ -9,16 +7,13 @@ on:
   release:
     types: [published]
 
-# Setting environment variable for Nextflow logs
 env:
   NXF_ANSI_LOG: false
 
-# Cancel if a newer run is started
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
-# Define the jobs to be run in parallel
 jobs:
   get_version:
     runs-on: ubuntu-latest
@@ -33,7 +28,7 @@ jobs:
         id: get_version
         run: |
           VERSION=$(grep 'nextflowVersion' nextflow.config | awk -F'= ' '{print $2}' | tr -d '!>=" ')
-          echo "version=$VERSION" >> $GITHUB_OUTPUT
+          echo "VERSION=$VERSION" >> $GITHUB_ENV
 
   test:
     name: Run ${{ matrix.profile }} pipeline test
@@ -56,29 +51,25 @@ jobs:
       - name: Use Nextflow version
         run: echo "Using Nextflow version $NXF_VER"
 
-      # Cache Test Data
       - name: Cache test data
         uses: actions/cache@v2
         with:
           path: /usr/local/bin/nextflow
           key: ${{ runner.os }}
-          restore-keys: |
-            ${{ runner.os }}-nextflow-
+          restore-keys: ${{ runner.os }}-nextflow-
 
-      # Install the specified version of Nextflow
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
+        with:
+          version: "$NXF_VER"
 
-      # Install nf-test
       - name: Install nf-test
         run: |
           wget -qO- https://code.askimed.com/install/nf-test | bash
           sudo mv nf-test /usr/local/bin/
 
-      # Run nf-test with the specified aligner and output test results in TAP format
       - name: Run nf-test
-        run: |
-          nf-test test tests/pipeline/ --tap=test.tap
+        run: nf-test test tests/pipeline/ --tap=test.tap
 
       # If the test fails, output the software_versions.yml using the 'batcat' utility
       - name: Output log on failure
@@ -87,8 +78,6 @@ jobs:
           sudo apt install bat > /dev/null
           batcat --decorations=always --color=always /home/runner/work/fetchngs/fetchngs/.nf-test/tests/*/output/pipeline_info/software_versions.yml
 
-      # Use TAP summary to display test results
       - uses: pcolby/tap-summary@v1
         with:
-          path: >-
-            test.tap
+          path: test.tap

From cac3b9f37e707f287f12b88d27455490064bed7e Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Tue, 23 May 2023 14:48:40 -0400
Subject: [PATCH 340/852] fix-ci-setup-nxf-ver

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 38d0fce5..de0f545f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -61,7 +61,7 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
-          version: "$NXF_VER"
+          version: ${{ matrix.NXF_VER }}
 
       - name: Install nf-test
         run: |

From 36033bef1b5d3762f586bda3156587bc4d7e6477 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Tue, 23 May 2023 14:50:05 -0400
Subject: [PATCH 341/852] fix-ci-setup-nxf-ver

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index de0f545f..f7559df1 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -38,7 +38,7 @@ jobs:
 
     runs-on: ubuntu-latest
     env:
-      NXF_VER: ${{ needs.get_version.outputs.version }}
+      NXF_VER: ${{ needs.get_version.outputs.VERSION }}
 
     strategy:
       matrix:

From 9683e029b9ee7e465609e78af3bb04161c48bfcc Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Tue, 23 May 2023 14:53:55 -0400
Subject: [PATCH 342/852] fix-ci-setup-nxf-ver

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f7559df1..960a7dca 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -28,7 +28,7 @@ jobs:
         id: get_version
         run: |
           VERSION=$(grep 'nextflowVersion' nextflow.config | awk -F'= ' '{print $2}' | tr -d '!>=" ')
-          echo "VERSION=$VERSION" >> $GITHUB_ENV
+          echo "VERSION=$VERSION" >> $GITHUB_OUTPUT
 
   test:
     name: Run ${{ matrix.profile }} pipeline test

From 1497db02a66719174832c4332daa35bfc27f85fa Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Tue, 23 May 2023 14:57:57 -0400
Subject: [PATCH 343/852] fix-ci-setup-nxf-ver

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 960a7dca..a23c68a4 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -61,7 +61,7 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
-          version: ${{ matrix.NXF_VER }}
+          version: ${{ needs.get_version.outputs.VERSION }}
 
       - name: Install nf-test
         run: |

From e3fa273ea636dd07db4bbbde9a2f5b1ecfdebf90 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Tue, 23 May 2023 14:59:27 -0400
Subject: [PATCH 344/852] fix-ci-setup-nxf-ver

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index a23c68a4..b090ef85 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -61,7 +61,7 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
-          version: ${{ needs.get_version.outputs.VERSION }}
+          version: "$NXF_VER"
 
       - name: Install nf-test
         run: |

From 84dbc4395a4deac65ac4509dd7f32f5cd9f9f2de Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Tue, 23 May 2023 15:09:53 -0400
Subject: [PATCH 345/852] fix-ci-setup-nxf-ver

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b090ef85..e8ef60fc 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -61,7 +61,7 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
-          version: "$NXF_VER"
+          version: "${{ env.NXF_VER }}"
 
       - name: Install nf-test
         run: |

From 143eed6d377b3b7839d75026fb37a9904a55b883 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Tue, 23 May 2023 22:09:25 -0400
Subject: [PATCH 346/852] revert-to-testing-2-nxf-vers

---
 .github/workflows/ci.yml | 48 +++++++++-------------------------------
 1 file changed, 10 insertions(+), 38 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index e8ef60fc..60259e4d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,9 +1,10 @@
 name: nf-core CI
-
+# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on:
-  pull_request:
+  push:
     branches:
       - dev
+  pull_request:
   release:
     types: [published]
 
@@ -11,57 +12,28 @@ env:
   NXF_ANSI_LOG: false
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
 
 jobs:
-  get_version:
-    runs-on: ubuntu-latest
-    outputs:
-      version: ${{ steps.get_version.outputs.version }}
-
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v3
-
-      - name: Get Minimum supported Nextflow version
-        id: get_version
-        run: |
-          VERSION=$(grep 'nextflowVersion' nextflow.config | awk -F'= ' '{print $2}' | tr -d '!>=" ')
-          echo "VERSION=$VERSION" >> $GITHUB_OUTPUT
-
   test:
-    name: Run ${{ matrix.profile }} pipeline test
-    needs: get_version
-
+    name: Run pipeline with test data
+    # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}"
-
     runs-on: ubuntu-latest
-    env:
-      NXF_VER: ${{ needs.get_version.outputs.VERSION }}
-
     strategy:
       matrix:
-        profile: ["docker"]
-
+        NXF_VER:
+          - "22.10.1"
+          - "latest-everything"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v3
 
-      - name: Use Nextflow version
-        run: echo "Using Nextflow version $NXF_VER"
-
-      - name: Cache test data
-        uses: actions/cache@v2
-        with:
-          path: /usr/local/bin/nextflow
-          key: ${{ runner.os }}
-          restore-keys: ${{ runner.os }}-nextflow-
-
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
-          version: "${{ env.NXF_VER }}"
+          version: "${{ matrix.NXF_VER }}"
 
       - name: Install nf-test
         run: |

From a26c031785771592d45a31f0f1c256f8bffdfec7 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Wed, 24 May 2023 00:09:00 -0400
Subject: [PATCH 347/852] update-snapshots

---
 tests/pipeline/sra.nf.test.snap               | 10 +++---
 tests/pipeline/sra_skip_fastq.nf.test.snap    |  8 ++---
 .../sra_with_nf_core_pipeline.nf.test.snap    | 34 +++++++++----------
 tests/pipeline/sra_with_sratools.nf.test.snap | 10 +++---
 4 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/tests/pipeline/sra.nf.test.snap b/tests/pipeline/sra.nf.test.snap
index fc79907b..9732de6f 100644
--- a/tests/pipeline/sra.nf.test.snap
+++ b/tests/pipeline/sra.nf.test.snap
@@ -6,21 +6,21 @@
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
             "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "GSM4907283.runinfo_ftp.tsv:md5,3d2c2395ee6690338f56fca84acb54ba",
+            "GSM4907283.runinfo_ftp.tsv:md5,92591968fa8fa37a9f7160fe8ada11a2",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-23T18:30:12+0000"
+        "timestamp": "2023-05-24T04:05:51+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-23T18:30:12+0000"
+        "timestamp": "2023-05-24T04:05:51+0000"
     },
     "software_versions": {
         "content": [
@@ -52,7 +52,7 @@
                 }
             }
         ],
-        "timestamp": "2023-05-23T18:30:12+0000"
+        "timestamp": "2023-05-24T04:05:51+0000"
     },
     "fastq": {
         "content": [
@@ -102,6 +102,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-05-23T18:30:12+0000"
+        "timestamp": "2023-05-24T04:05:51+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_skip_fastq.nf.test.snap b/tests/pipeline/sra_skip_fastq.nf.test.snap
index 456e101d..5452bd4a 100644
--- a/tests/pipeline/sra_skip_fastq.nf.test.snap
+++ b/tests/pipeline/sra_skip_fastq.nf.test.snap
@@ -6,21 +6,21 @@
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
             "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "GSM4907283.runinfo_ftp.tsv:md5,3d2c2395ee6690338f56fca84acb54ba",
+            "GSM4907283.runinfo_ftp.tsv:md5,92591968fa8fa37a9f7160fe8ada11a2",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-23T18:17:54+0000"
+        "timestamp": "2023-05-24T02:38:17+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-23T18:17:54+0000"
+        "timestamp": "2023-05-24T02:38:17+0000"
     },
     "software_versions": {
         "content": [
@@ -46,6 +46,6 @@
                 }
             }
         ],
-        "timestamp": "2023-05-23T18:17:54+0000"
+        "timestamp": "2023-05-24T02:38:17+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
index ef695ab0..c858773b 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
@@ -6,14 +6,14 @@
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
             "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "GSM4907283.runinfo_ftp.tsv:md5,92591968fa8fa37a9f7160fe8ada11a2",
+            "GSM4907283.runinfo_ftp.tsv:md5,3d2c2395ee6690338f56fca84acb54ba",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-23T18:27:58+0000"
+        "timestamp": "2023-05-24T03:54:13+0000"
     },
     "software_versions": {
         "content": [
@@ -45,7 +45,7 @@
                 }
             }
         ],
-        "timestamp": "2023-05-23T18:27:57+0000"
+        "timestamp": "2023-05-24T03:54:13+0000"
     },
     "viralrecon_metadata": {
         "content": [
@@ -54,21 +54,21 @@
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
             "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "GSM4907283.runinfo_ftp.tsv:md5,3d2c2395ee6690338f56fca84acb54ba",
+            "GSM4907283.runinfo_ftp.tsv:md5,92591968fa8fa37a9f7160fe8ada11a2",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-23T18:27:57+0000"
+        "timestamp": "2023-05-24T03:54:13+0000"
     },
     "viralrecon_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-23T18:27:57+0000"
+        "timestamp": "2023-05-24T03:54:13+0000"
     },
     "atacseq_metadata": {
         "content": [
@@ -84,7 +84,7 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-23T18:27:57+0000"
+        "timestamp": "2023-05-24T03:54:13+0000"
     },
     "rnaseq_ena_metadata": {
         "content": [
@@ -100,21 +100,21 @@
             "SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1",
             "SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236"
         ],
-        "timestamp": "2023-05-23T18:27:57+0000"
+        "timestamp": "2023-05-24T03:54:13+0000"
     },
     "rnaseq_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-23T18:27:57+0000"
+        "timestamp": "2023-05-24T03:54:13+0000"
     },
     "rnaseq_samplesheet_specific_ena": {
         "content": [
             "id_mappings.csv:md5,0efde324e1818c0827390a17449a6e8a",
             "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd"
         ],
-        "timestamp": "2023-05-23T18:27:57+0000"
+        "timestamp": "2023-05-24T03:54:13+0000"
     },
     "rnaseq_metadata": {
         "content": [
@@ -123,42 +123,42 @@
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
             "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "GSM4907283.runinfo_ftp.tsv:md5,3d2c2395ee6690338f56fca84acb54ba",
+            "GSM4907283.runinfo_ftp.tsv:md5,92591968fa8fa37a9f7160fe8ada11a2",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-23T18:27:57+0000"
+        "timestamp": "2023-05-24T03:54:13+0000"
     },
     "rnaseq_specific_ena_samplesheet": {
         "content": [
             "id_mappings.csv:md5,0efde324e1818c0827390a17449a6e8a",
             "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd"
         ],
-        "timestamp": "2023-05-23T18:27:57+0000"
+        "timestamp": "2023-05-24T03:54:13+0000"
     },
     "atacseq_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-23T18:27:57+0000"
+        "timestamp": "2023-05-24T03:54:13+0000"
     },
     "rnaseq_ena_samplesheet": {
         "content": [
             "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f",
             "multiqc_config.yml:md5,6f6189ee58855de81eaf82ad86e21040"
         ],
-        "timestamp": "2023-05-23T18:27:57+0000"
+        "timestamp": "2023-05-24T03:54:13+0000"
     },
     "taxprofiler_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-23T18:27:57+0000"
+        "timestamp": "2023-05-24T03:54:13+0000"
     },
     "fastq": {
         "content": [
@@ -208,6 +208,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-05-23T18:27:57+0000"
+        "timestamp": "2023-05-24T03:54:13+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_sratools.nf.test.snap b/tests/pipeline/sra_with_sratools.nf.test.snap
index d66ebc11..8844905b 100644
--- a/tests/pipeline/sra_with_sratools.nf.test.snap
+++ b/tests/pipeline/sra_with_sratools.nf.test.snap
@@ -6,21 +6,21 @@
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
             "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "GSM4907283.runinfo_ftp.tsv:md5,3d2c2395ee6690338f56fca84acb54ba",
+            "GSM4907283.runinfo_ftp.tsv:md5,92591968fa8fa37a9f7160fe8ada11a2",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-23T18:17:22+0000"
+        "timestamp": "2023-05-24T04:03:04+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-23T18:17:22+0000"
+        "timestamp": "2023-05-24T04:03:04+0000"
     },
     "software_versions": {
         "content": [
@@ -49,7 +49,7 @@
                 }
             }
         ],
-        "timestamp": "2023-05-23T18:17:23+0000"
+        "timestamp": "2023-05-24T04:03:04+0000"
     },
     "fastq": {
         "content": [
@@ -78,6 +78,6 @@
             "SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7",
             "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af"
         ],
-        "timestamp": "2023-05-23T18:17:22+0000"
+        "timestamp": "2023-05-24T04:03:04+0000"
     }
 }
\ No newline at end of file

From de7d5ab1533564e1b2c4d5d05a72a29cae09c393 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Wed, 24 May 2023 11:38:15 -0400
Subject: [PATCH 348/852] update-snapshots

---
 .../sra_with_nf_core_pipeline.nf.test         |  10 +-
 .../sra_with_nf_core_pipeline.nf.test.snap    | 174 +++++++++++++++---
 2 files changed, 149 insertions(+), 35 deletions(-)

diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
index 54cec435..9facceef 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
@@ -19,7 +19,7 @@ nextflow_pipeline {
 
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(softwareVersions).match("software_versions") },
+                { assert snapshot(softwareVersions).match("rnaseq_software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/").list()).match("rnaseq_metadata") },
                 { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
@@ -46,7 +46,7 @@ nextflow_pipeline {
 
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(softwareVersions).match("software_versions") },
+                { assert snapshot(softwareVersions).match("rnaseq_ena_software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/").list()).match("rnaseq_ena_metadata") },
                 { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
@@ -71,7 +71,7 @@ nextflow_pipeline {
 
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(softwareVersions).match("software_versions") },
+                { assert snapshot(softwareVersions).match("atacseq_software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/").list()).match("atacseq_metadata") },
                 { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
@@ -96,7 +96,7 @@ nextflow_pipeline {
 
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(softwareVersions).match("software_versions") },
+                { assert snapshot(softwareVersions).match("viralrecon_software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/").list()).match("viralrecon_metadata") },
                 { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
@@ -121,7 +121,7 @@ nextflow_pipeline {
 
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(softwareVersions).match("software_versions") },
+                { assert snapshot(softwareVersions).match("taxprofiler_software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/").list()).match("taxprofiler_metadata") },
                 { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
index c858773b..25a8308b 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
@@ -13,9 +13,9 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-24T03:54:13+0000"
+        "timestamp": "2023-05-24T14:53:28+0000"
     },
-    "software_versions": {
+    "rnaseq_software_versions": {
         "content": [
             {
                 "CUSTOM_DUMPSOFTWAREVERSIONS": {
@@ -45,7 +45,39 @@
                 }
             }
         ],
-        "timestamp": "2023-05-24T03:54:13+0000"
+        "timestamp": "2023-05-24T14:53:28+0000"
+    },
+    "rnaseq_ena_software_versions": {
+        "content": [
+            {
+                "CUSTOM_DUMPSOFTWAREVERSIONS": {
+                    "python": "3.11.0",
+                    "yaml": "6.0"
+                },
+                "CUSTOM_SRATOOLSNCBISETTINGS": {
+                    "sratools": "2.11.0"
+                },
+                "MULTIQC_MAPPINGS_CONFIG": {
+                    "python": "3.9.5"
+                },
+                "SRA_FASTQ_FTP": {
+                    "curl": "7.81.0"
+                },
+                "SRA_IDS_TO_RUNINFO": {
+                    "python": "3.9.5"
+                },
+                "SRA_MERGE_SAMPLESHEET": {
+                    "sed": "4.7"
+                },
+                "SRA_RUNINFO_TO_FTP": {
+                    "python": "3.9.5"
+                },
+                "Workflow": {
+                    "nf-core/fetchngs": "1.11.0dev"
+                }
+            }
+        ],
+        "timestamp": "2023-05-24T14:53:28+0000"
     },
     "viralrecon_metadata": {
         "content": [
@@ -54,21 +86,85 @@
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
             "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "GSM4907283.runinfo_ftp.tsv:md5,92591968fa8fa37a9f7160fe8ada11a2",
+            "GSM4907283.runinfo_ftp.tsv:md5,3d2c2395ee6690338f56fca84acb54ba",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-24T03:54:13+0000"
+        "timestamp": "2023-05-24T14:53:28+0000"
+    },
+    "viralrecon_software_versions": {
+        "content": [
+            {
+                "CUSTOM_DUMPSOFTWAREVERSIONS": {
+                    "python": "3.11.0",
+                    "yaml": "6.0"
+                },
+                "CUSTOM_SRATOOLSNCBISETTINGS": {
+                    "sratools": "2.11.0"
+                },
+                "MULTIQC_MAPPINGS_CONFIG": {
+                    "python": "3.9.5"
+                },
+                "SRA_FASTQ_FTP": {
+                    "curl": "7.81.0"
+                },
+                "SRA_IDS_TO_RUNINFO": {
+                    "python": "3.9.5"
+                },
+                "SRA_MERGE_SAMPLESHEET": {
+                    "sed": "4.7"
+                },
+                "SRA_RUNINFO_TO_FTP": {
+                    "python": "3.9.5"
+                },
+                "Workflow": {
+                    "nf-core/fetchngs": "1.11.0dev"
+                }
+            }
+        ],
+        "timestamp": "2023-05-24T14:53:28+0000"
     },
     "viralrecon_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-24T03:54:13+0000"
+        "timestamp": "2023-05-24T14:53:28+0000"
+    },
+    "taxprofiler_software_versions": {
+        "content": [
+            {
+                "CUSTOM_DUMPSOFTWAREVERSIONS": {
+                    "python": "3.11.0",
+                    "yaml": "6.0"
+                },
+                "CUSTOM_SRATOOLSNCBISETTINGS": {
+                    "sratools": "2.11.0"
+                },
+                "MULTIQC_MAPPINGS_CONFIG": {
+                    "python": "3.9.5"
+                },
+                "SRA_FASTQ_FTP": {
+                    "curl": "7.81.0"
+                },
+                "SRA_IDS_TO_RUNINFO": {
+                    "python": "3.9.5"
+                },
+                "SRA_MERGE_SAMPLESHEET": {
+                    "sed": "4.7"
+                },
+                "SRA_RUNINFO_TO_FTP": {
+                    "python": "3.9.5"
+                },
+                "Workflow": {
+                    "nf-core/fetchngs": "1.11.0dev"
+                }
+            }
+        ],
+        "timestamp": "2023-05-24T14:53:28+0000"
     },
     "atacseq_metadata": {
         "content": [
@@ -77,14 +173,14 @@
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
             "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "GSM4907283.runinfo_ftp.tsv:md5,3d2c2395ee6690338f56fca84acb54ba",
+            "GSM4907283.runinfo_ftp.tsv:md5,92591968fa8fa37a9f7160fe8ada11a2",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-24T03:54:13+0000"
+        "timestamp": "2023-05-24T14:53:28+0000"
     },
     "rnaseq_ena_metadata": {
         "content": [
@@ -100,21 +196,14 @@
             "SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1",
             "SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236"
         ],
-        "timestamp": "2023-05-24T03:54:13+0000"
+        "timestamp": "2023-05-24T14:53:28+0000"
     },
     "rnaseq_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-24T03:54:13+0000"
-    },
-    "rnaseq_samplesheet_specific_ena": {
-        "content": [
-            "id_mappings.csv:md5,0efde324e1818c0827390a17449a6e8a",
-            "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd"
-        ],
-        "timestamp": "2023-05-24T03:54:13+0000"
+        "timestamp": "2023-05-24T14:53:28+0000"
     },
     "rnaseq_metadata": {
         "content": [
@@ -123,42 +212,67 @@
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
             "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "GSM4907283.runinfo_ftp.tsv:md5,92591968fa8fa37a9f7160fe8ada11a2",
+            "GSM4907283.runinfo_ftp.tsv:md5,3d2c2395ee6690338f56fca84acb54ba",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-24T03:54:13+0000"
-    },
-    "rnaseq_specific_ena_samplesheet": {
-        "content": [
-            "id_mappings.csv:md5,0efde324e1818c0827390a17449a6e8a",
-            "multiqc_config.yml:md5,6af65b0ae40e1bba60a25361771624bd"
-        ],
-        "timestamp": "2023-05-24T03:54:13+0000"
+        "timestamp": "2023-05-24T14:53:28+0000"
     },
     "atacseq_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-24T03:54:13+0000"
+        "timestamp": "2023-05-24T14:53:28+0000"
     },
     "rnaseq_ena_samplesheet": {
         "content": [
             "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f",
             "multiqc_config.yml:md5,6f6189ee58855de81eaf82ad86e21040"
         ],
-        "timestamp": "2023-05-24T03:54:13+0000"
+        "timestamp": "2023-05-24T14:53:28+0000"
+    },
+    "atacseq_software_versions": {
+        "content": [
+            {
+                "CUSTOM_DUMPSOFTWAREVERSIONS": {
+                    "python": "3.11.0",
+                    "yaml": "6.0"
+                },
+                "CUSTOM_SRATOOLSNCBISETTINGS": {
+                    "sratools": "2.11.0"
+                },
+                "MULTIQC_MAPPINGS_CONFIG": {
+                    "python": "3.9.5"
+                },
+                "SRA_FASTQ_FTP": {
+                    "curl": "7.81.0"
+                },
+                "SRA_IDS_TO_RUNINFO": {
+                    "python": "3.9.5"
+                },
+                "SRA_MERGE_SAMPLESHEET": {
+                    "sed": "4.7"
+                },
+                "SRA_RUNINFO_TO_FTP": {
+                    "python": "3.9.5"
+                },
+                "Workflow": {
+                    "nf-core/fetchngs": "1.11.0dev"
+                }
+            }
+        ],
+        "timestamp": "2023-05-24T14:53:28+0000"
     },
     "taxprofiler_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-24T03:54:13+0000"
+        "timestamp": "2023-05-24T14:53:28+0000"
     },
     "fastq": {
         "content": [
@@ -208,6 +322,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-05-24T03:54:13+0000"
+        "timestamp": "2023-05-24T14:53:28+0000"
     }
 }
\ No newline at end of file

From 325264799b3b216337a996f5e648929941b951c4 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Wed, 24 May 2023 21:58:20 -0400
Subject: [PATCH 349/852] update-snapshots-metadata-runinfo

---
 tests/pipeline/sra.nf.test                    | 12 +++-
 tests/pipeline/sra.nf.test.snap               |  9 ++-
 tests/pipeline/sra_skip_fastq.nf.test         | 12 +++-
 tests/pipeline/sra_skip_fastq.nf.test.snap    |  7 +--
 .../sra_with_nf_core_pipeline.nf.test         | 60 +++++++++++++++++--
 .../sra_with_nf_core_pipeline.nf.test.snap    | 37 +++++-------
 tests/pipeline/sra_with_sratools.nf.test      | 12 +++-
 tests/pipeline/sra_with_sratools.nf.test.snap |  9 ++-
 8 files changed, 115 insertions(+), 43 deletions(-)

diff --git a/tests/pipeline/sra.nf.test b/tests/pipeline/sra.nf.test
index 37749254..970840de 100644
--- a/tests/pipeline/sra.nf.test
+++ b/tests/pipeline/sra.nf.test
@@ -20,7 +20,17 @@ nextflow_pipeline {
                 { assert workflow.success },
                 { assert snapshot(softwareVersions).match("software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
-                { assert snapshot(path("$outputDir/metadata/").list()).match("metadata") },
+                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") },
+                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
                 { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
                                 path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
                 { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
diff --git a/tests/pipeline/sra.nf.test.snap b/tests/pipeline/sra.nf.test.snap
index 9732de6f..86c6780e 100644
--- a/tests/pipeline/sra.nf.test.snap
+++ b/tests/pipeline/sra.nf.test.snap
@@ -6,21 +6,20 @@
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
             "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "GSM4907283.runinfo_ftp.tsv:md5,92591968fa8fa37a9f7160fe8ada11a2",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-24T04:05:51+0000"
+        "timestamp": "2023-05-25T01:31:04+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-24T04:05:51+0000"
+        "timestamp": "2023-05-25T01:31:04+0000"
     },
     "software_versions": {
         "content": [
@@ -52,7 +51,7 @@
                 }
             }
         ],
-        "timestamp": "2023-05-24T04:05:51+0000"
+        "timestamp": "2023-05-25T01:31:04+0000"
     },
     "fastq": {
         "content": [
@@ -102,6 +101,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-05-24T04:05:51+0000"
+        "timestamp": "2023-05-25T01:31:04+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_skip_fastq.nf.test b/tests/pipeline/sra_skip_fastq.nf.test
index 8497af75..e00dc66a 100644
--- a/tests/pipeline/sra_skip_fastq.nf.test
+++ b/tests/pipeline/sra_skip_fastq.nf.test
@@ -20,7 +20,17 @@ nextflow_pipeline {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(softwareVersions).match("software_versions") },
-                { assert snapshot(path("$outputDir/metadata/").list()).match("metadata") },
+                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") },
+                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
                 { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
                                 path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
                 { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() },
diff --git a/tests/pipeline/sra_skip_fastq.nf.test.snap b/tests/pipeline/sra_skip_fastq.nf.test.snap
index 5452bd4a..c2edd1c3 100644
--- a/tests/pipeline/sra_skip_fastq.nf.test.snap
+++ b/tests/pipeline/sra_skip_fastq.nf.test.snap
@@ -6,21 +6,20 @@
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
             "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "GSM4907283.runinfo_ftp.tsv:md5,92591968fa8fa37a9f7160fe8ada11a2",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-24T02:38:17+0000"
+        "timestamp": "2023-05-24T23:49:24+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-24T02:38:17+0000"
+        "timestamp": "2023-05-24T23:49:24+0000"
     },
     "software_versions": {
         "content": [
@@ -46,6 +45,6 @@
                 }
             }
         ],
-        "timestamp": "2023-05-24T02:38:17+0000"
+        "timestamp": "2023-05-24T23:49:24+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
index 9facceef..3015311a 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
@@ -21,7 +21,17 @@ nextflow_pipeline {
                 { assert workflow.success },
                 { assert snapshot(softwareVersions).match("rnaseq_software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
-                { assert snapshot(path("$outputDir/metadata/").list()).match("rnaseq_metadata") },
+                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("rnaseq_metadata") },
+                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
                 { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
                                 path("$outputDir/samplesheet/multiqc_config.yml")).match("rnaseq_samplesheet") },
                 { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
@@ -48,7 +58,17 @@ nextflow_pipeline {
                 { assert workflow.success },
                 { assert snapshot(softwareVersions).match("rnaseq_ena_software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
-                { assert snapshot(path("$outputDir/metadata/").list()).match("rnaseq_ena_metadata") },
+                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("rnaseq_ena_metadata") },
+                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
                 { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
                                 path("$outputDir/samplesheet/multiqc_config.yml")).match("rnaseq_ena_samplesheet") },
                 { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
@@ -73,7 +93,17 @@ nextflow_pipeline {
                 { assert workflow.success },
                 { assert snapshot(softwareVersions).match("atacseq_software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
-                { assert snapshot(path("$outputDir/metadata/").list()).match("atacseq_metadata") },
+                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("atacseq_metadata") },
+                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
                 { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
                                 path("$outputDir/samplesheet/multiqc_config.yml")).match("atacseq_samplesheet") },
                 { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
@@ -98,7 +128,17 @@ nextflow_pipeline {
                 { assert workflow.success },
                 { assert snapshot(softwareVersions).match("viralrecon_software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
-                { assert snapshot(path("$outputDir/metadata/").list()).match("viralrecon_metadata") },
+                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("viralrecon_metadata") },
+                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
                 { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
                                 path("$outputDir/samplesheet/multiqc_config.yml")).match("viralrecon_samplesheet") },
                 { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
@@ -123,7 +163,17 @@ nextflow_pipeline {
                 { assert workflow.success },
                 { assert snapshot(softwareVersions).match("taxprofiler_software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
-                { assert snapshot(path("$outputDir/metadata/").list()).match("taxprofiler_metadata") },
+                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("taxprofiler_metadata") },
+                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
                 { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
                                 path("$outputDir/samplesheet/multiqc_config.yml")).match("taxprofiler_samplesheet") },
                 { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
index 25a8308b..ca946dc8 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
@@ -6,14 +6,13 @@
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
             "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "GSM4907283.runinfo_ftp.tsv:md5,3d2c2395ee6690338f56fca84acb54ba",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-24T14:53:28+0000"
+        "timestamp": "2023-05-25T01:47:31+0000"
     },
     "rnaseq_software_versions": {
         "content": [
@@ -45,7 +44,7 @@
                 }
             }
         ],
-        "timestamp": "2023-05-24T14:53:28+0000"
+        "timestamp": "2023-05-25T01:47:31+0000"
     },
     "rnaseq_ena_software_versions": {
         "content": [
@@ -77,7 +76,7 @@
                 }
             }
         ],
-        "timestamp": "2023-05-24T14:53:28+0000"
+        "timestamp": "2023-05-25T01:47:31+0000"
     },
     "viralrecon_metadata": {
         "content": [
@@ -86,14 +85,13 @@
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
             "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "GSM4907283.runinfo_ftp.tsv:md5,3d2c2395ee6690338f56fca84acb54ba",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-24T14:53:28+0000"
+        "timestamp": "2023-05-25T01:47:31+0000"
     },
     "viralrecon_software_versions": {
         "content": [
@@ -125,14 +123,14 @@
                 }
             }
         ],
-        "timestamp": "2023-05-24T14:53:28+0000"
+        "timestamp": "2023-05-25T01:47:31+0000"
     },
     "viralrecon_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-24T14:53:28+0000"
+        "timestamp": "2023-05-25T01:47:31+0000"
     },
     "taxprofiler_software_versions": {
         "content": [
@@ -164,7 +162,7 @@
                 }
             }
         ],
-        "timestamp": "2023-05-24T14:53:28+0000"
+        "timestamp": "2023-05-25T01:47:31+0000"
     },
     "atacseq_metadata": {
         "content": [
@@ -173,14 +171,13 @@
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
             "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "GSM4907283.runinfo_ftp.tsv:md5,92591968fa8fa37a9f7160fe8ada11a2",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-24T14:53:28+0000"
+        "timestamp": "2023-05-25T01:47:31+0000"
     },
     "rnaseq_ena_metadata": {
         "content": [
@@ -189,21 +186,20 @@
             "ERR1109373.runinfo_ftp.tsv:md5,868897310855c50b1d5fc77d1195a1f9",
             "ERR1160846.runinfo_ftp.tsv:md5,146d7f2ec778b32b7da7ad040e554114",
             "GSE214215.runinfo_ftp.tsv:md5,adf62affe371dc9bad8e271450bdc2fe",
-            "GSM4907283.runinfo_ftp.tsv:md5,5758453402e82490c4841c8e85a6aa53",
             "SRR12848126.runinfo_ftp.tsv:md5,cf8827612a76645824e83418d7d76cbf",
             "SRR13191702.runinfo_ftp.tsv:md5,2031ca9b7ab736dbde37d05b10cdb0ad",
             "SRR14593545.runinfo_ftp.tsv:md5,3a1ac14d71744224a61ab542f869e180",
             "SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1",
             "SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236"
         ],
-        "timestamp": "2023-05-24T14:53:28+0000"
+        "timestamp": "2023-05-25T01:47:31+0000"
     },
     "rnaseq_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-24T14:53:28+0000"
+        "timestamp": "2023-05-25T01:47:31+0000"
     },
     "rnaseq_metadata": {
         "content": [
@@ -212,28 +208,27 @@
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
             "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "GSM4907283.runinfo_ftp.tsv:md5,3d2c2395ee6690338f56fca84acb54ba",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-24T14:53:28+0000"
+        "timestamp": "2023-05-25T01:47:31+0000"
     },
     "atacseq_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-24T14:53:28+0000"
+        "timestamp": "2023-05-25T01:47:31+0000"
     },
     "rnaseq_ena_samplesheet": {
         "content": [
             "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f",
             "multiqc_config.yml:md5,6f6189ee58855de81eaf82ad86e21040"
         ],
-        "timestamp": "2023-05-24T14:53:28+0000"
+        "timestamp": "2023-05-25T01:47:31+0000"
     },
     "atacseq_software_versions": {
         "content": [
@@ -265,14 +260,14 @@
                 }
             }
         ],
-        "timestamp": "2023-05-24T14:53:28+0000"
+        "timestamp": "2023-05-25T01:47:31+0000"
     },
     "taxprofiler_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-24T14:53:28+0000"
+        "timestamp": "2023-05-25T01:47:31+0000"
     },
     "fastq": {
         "content": [
@@ -322,6 +317,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-05-24T14:53:28+0000"
+        "timestamp": "2023-05-25T01:47:31+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_sratools.nf.test b/tests/pipeline/sra_with_sratools.nf.test
index 7e50cc46..755f0c9c 100644
--- a/tests/pipeline/sra_with_sratools.nf.test
+++ b/tests/pipeline/sra_with_sratools.nf.test
@@ -21,7 +21,17 @@ nextflow_pipeline {
                 { assert workflow.success },
                 { assert snapshot(softwareVersions).match("software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
-                { assert snapshot(path("$outputDir/metadata/").list()).match("metadata") },
+                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") },
+                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
                 { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
                                 path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
                 { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
diff --git a/tests/pipeline/sra_with_sratools.nf.test.snap b/tests/pipeline/sra_with_sratools.nf.test.snap
index 8844905b..ee8278a9 100644
--- a/tests/pipeline/sra_with_sratools.nf.test.snap
+++ b/tests/pipeline/sra_with_sratools.nf.test.snap
@@ -6,21 +6,20 @@
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
             "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "GSM4907283.runinfo_ftp.tsv:md5,92591968fa8fa37a9f7160fe8ada11a2",
             "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
             "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
             "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-24T04:03:04+0000"
+        "timestamp": "2023-05-24T23:48:56+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-24T04:03:04+0000"
+        "timestamp": "2023-05-24T23:48:56+0000"
     },
     "software_versions": {
         "content": [
@@ -49,7 +48,7 @@
                 }
             }
         ],
-        "timestamp": "2023-05-24T04:03:04+0000"
+        "timestamp": "2023-05-24T23:48:56+0000"
     },
     "fastq": {
         "content": [
@@ -78,6 +77,6 @@
             "SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7",
             "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af"
         ],
-        "timestamp": "2023-05-24T04:03:04+0000"
+        "timestamp": "2023-05-24T23:48:56+0000"
     }
 }
\ No newline at end of file

From 6886432d55d3babeca24d36fea8d1068513eab0c Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Wed, 24 May 2023 22:01:03 -0400
Subject: [PATCH 350/852] CI-add-master-tests

---
 .github/workflows/ci.yml | 49 ++++++++++++++++++++++++++++++++++------
 1 file changed, 42 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 60259e4d..37a33264 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -5,6 +5,9 @@ on:
     branches:
       - dev
   pull_request:
+    branches:
+      - dev
+      - master
   release:
     types: [published]
 
@@ -16,16 +19,48 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  test:
-    name: Run pipeline with test data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}"
+  test-dev:
+    if: github.base_ref == 'dev' || github.event_name == 'push'
+    name: Run pipeline with test data on dev
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        NXF_VER: ["latest-everything"]
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v3
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Install nf-test
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Run nf-test
+        run: nf-test test tests/pipeline/ --tap=test.tap
+
+      # If the test fails, output the software_versions.yml using the 'batcat' utility
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always /home/runner/work/fetchngs/fetchngs/.nf-test/tests/*/output/pipeline_info/software_versions.yml
+
+      - uses: pcolby/tap-summary@v1
+        with:
+          path: test.tap
+
+  test-master:
+    if: github.base_ref == 'master'
+    name: Run pipeline with test data on master
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        NXF_VER:
-          - "22.10.1"
-          - "latest-everything"
+        NXF_VER: ["22.10.1", "latest-everything"]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v3

From 0c00e742f8395f7d67083c27bc83c0565943c241 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Thu, 25 May 2023 15:19:11 -0400
Subject: [PATCH 351/852] CI-comment-pr-test-tap-results

---
 .github/workflows/ci.yml | 19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 37a33264..4abae6d9 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -20,6 +20,7 @@ concurrency:
 
 jobs:
   test-dev:
+    # Only run on dev branch or when a PR is opened against dev
     if: github.base_ref == 'dev' || github.event_name == 'push'
     name: Run pipeline with test data on dev
     runs-on: ubuntu-latest
@@ -30,16 +31,19 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v3
 
+      # Install Nextflow
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      # Install nf-test
       - name: Install nf-test
         run: |
           wget -qO- https://code.askimed.com/install/nf-test | bash
           sudo mv nf-test /usr/local/bin/
 
+      # Run nf-test
       - name: Run nf-test
         run: nf-test test tests/pipeline/ --tap=test.tap
 
@@ -50,9 +54,11 @@ jobs:
           sudo apt install bat > /dev/null
           batcat --decorations=always --color=always /home/runner/work/fetchngs/fetchngs/.nf-test/tests/*/output/pipeline_info/software_versions.yml
 
-      - uses: pcolby/tap-summary@v1
+      # Comment on the PR with the test results
+      - name: PR comment with file
+        uses: thollander/actions-comment-pull-request@v2
         with:
-          path: test.tap
+          filePath: test.tap
 
   test-master:
     if: github.base_ref == 'master'
@@ -65,16 +71,19 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v3
 
+      # Install Nextflow
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      # Install nf-test
       - name: Install nf-test
         run: |
           wget -qO- https://code.askimed.com/install/nf-test | bash
           sudo mv nf-test /usr/local/bin/
 
+      # Run nf-test
       - name: Run nf-test
         run: nf-test test tests/pipeline/ --tap=test.tap
 
@@ -85,6 +94,8 @@ jobs:
           sudo apt install bat > /dev/null
           batcat --decorations=always --color=always /home/runner/work/fetchngs/fetchngs/.nf-test/tests/*/output/pipeline_info/software_versions.yml
 
-      - uses: pcolby/tap-summary@v1
+      # Comment on the PR with the test results
+      - name: PR comment with file
+        uses: thollander/actions-comment-pull-request@v2
         with:
-          path: test.tap
+          filePath: test.tap

From 4e4a5c39dffd996ab7832ff0d8f1a75c04a36fad Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Thu, 25 May 2023 20:28:17 -0400
Subject: [PATCH 352/852] CI-fix-comment-pr-pull-request

---
 .github/workflows/ci.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4abae6d9..7f65ab67 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -56,6 +56,7 @@ jobs:
 
       # Comment on the PR with the test results
       - name: PR comment with file
+        if: github.event_name == 'pull_request'
         uses: thollander/actions-comment-pull-request@v2
         with:
           filePath: test.tap
@@ -96,6 +97,7 @@ jobs:
 
       # Comment on the PR with the test results
       - name: PR comment with file
+        if: github.event_name == 'pull_request'
         uses: thollander/actions-comment-pull-request@v2
         with:
           filePath: test.tap

From 3b7be1d51c7a5d48de4244d92e521b5a91ca7928 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Thu, 25 May 2023 20:29:20 -0400
Subject: [PATCH 353/852] CI-fix-comment-pr-pull-request

---
 .github/workflows/ci.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 7f65ab67..f541dc19 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -24,6 +24,7 @@ jobs:
     if: github.base_ref == 'dev' || github.event_name == 'push'
     name: Run pipeline with test data on dev
     runs-on: ubuntu-latest
+    # Define the matrix of different Nextflow versions to test
     strategy:
       matrix:
         NXF_VER: ["latest-everything"]
@@ -62,9 +63,11 @@ jobs:
           filePath: test.tap
 
   test-master:
+    # Only run on master branch or when a PR is opened against master
     if: github.base_ref == 'master'
     name: Run pipeline with test data on master
     runs-on: ubuntu-latest
+    # Define the matrix of different Nextflow versions to test
     strategy:
       matrix:
         NXF_VER: ["22.10.1", "latest-everything"]

From a148806aa52c8843b955b5ab96a01b567d800aa7 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Sun, 28 May 2023 11:26:41 -0400
Subject: [PATCH 354/852] CI-add-nf-test-ver-to-matrix

---
 .github/workflows/ci.yml | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f541dc19..ab3a10de 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,5 +1,5 @@
-name: nf-core CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+name: nf-core CI
 on:
   push:
     branches:
@@ -14,20 +14,22 @@ on:
 env:
   NXF_ANSI_LOG: false
 
+# cancel-in-progress: true ensures that if a new push is made to the same branch while a previous run is still in progress, the previous run is cancelled
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
 
 jobs:
   test-dev:
-    # Only run on dev branch or when a PR is opened against dev
-    if: github.base_ref == 'dev' || github.event_name == 'push'
+    # Only run if the pull request is against the dev branch or if the push is to the dev branch
+    if: ${{ (github.base_ref == 'dev' || (github.event_name == 'push')) }}
     name: Run pipeline with test data on dev
     runs-on: ubuntu-latest
     # Define the matrix of different Nextflow versions to test
     strategy:
       matrix:
         NXF_VER: ["latest-everything"]
+        NFTEST_VER: ["0.7.3"]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v3
@@ -41,7 +43,7 @@ jobs:
       # Install nf-test
       - name: Install nf-test
         run: |
-          wget -qO- https://code.askimed.com/install/nf-test | bash
+          wget -qO- https://code.askimed.com/install/nf-test | bash -s ${{ matrix.NFTEST_VER }}
           sudo mv nf-test /usr/local/bin/
 
       # Run nf-test
@@ -64,13 +66,14 @@ jobs:
 
   test-master:
     # Only run on master branch or when a PR is opened against master
-    if: github.base_ref == 'master'
+    if: ${{ (github.base_ref == 'master') }}
     name: Run pipeline with test data on master
     runs-on: ubuntu-latest
     # Define the matrix of different Nextflow versions to test
     strategy:
       matrix:
         NXF_VER: ["22.10.1", "latest-everything"]
+        NFTEST_VER: ["0.7.3"]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v3
@@ -84,7 +87,7 @@ jobs:
       # Install nf-test
       - name: Install nf-test
         run: |
-          wget -qO- https://code.askimed.com/install/nf-test | bash
+          wget -qO- https://code.askimed.com/install/nf-test | bash -s ${{ matrix.NFTEST_VER }}
           sudo mv nf-test /usr/local/bin/
 
       # Run nf-test

From a4a86d88865274e201209b05023d720ec51740a8 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Sun, 28 May 2023 11:27:20 -0400
Subject: [PATCH 355/852] add-utils-groovy-update-snapshots

---
 nf-test.config                                |  12 +-
 tests/pipeline/lib/UTILS.groovy               |  11 +
 tests/pipeline/sra.nf.test                    |   7 +-
 tests/pipeline/sra.nf.test.snap               |  36 +---
 tests/pipeline/sra_skip_fastq.nf.test         |   7 +-
 tests/pipeline/sra_skip_fastq.nf.test.snap    |  28 +--
 .../sra_with_nf_core_pipeline.nf.test         |  27 +--
 .../sra_with_nf_core_pipeline.nf.test.snap    | 198 +++---------------
 tests/pipeline/sra_with_sratools.nf.test      |   7 +-
 tests/pipeline/sra_with_sratools.nf.test.snap |  33 +--
 10 files changed, 81 insertions(+), 285 deletions(-)
 create mode 100644 tests/pipeline/lib/UTILS.groovy

diff --git a/nf-test.config b/nf-test.config
index f345cb2d..7d705067 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -1,8 +1,16 @@
 config {
-
+    // location for all nf-tests
     testsDir "tests"
+
+    // nf-test directory including temporary files for each test
     workDir ".nf-test"
+
+    // location of library folder that is added automatically to the classpath
+    libDir "tests/pipeline/lib/"
+
+    // location of an optional nextflow.config file specific for executing tests
     configFile "nextflow.config"
-    profile "test,docker"
 
+    // run all test with the defined docker profile from the main nextflow.config
+    profile "test,docker"
 }
diff --git a/tests/pipeline/lib/UTILS.groovy b/tests/pipeline/lib/UTILS.groovy
new file mode 100644
index 00000000..311403cc
--- /dev/null
+++ b/tests/pipeline/lib/UTILS.groovy
@@ -0,0 +1,11 @@
+// Function to remove Nextflow version from software_versions.yml
+
+class UTILS {
+    public static String removeNextflowVersion(outputDir) {
+        def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
+        if (softwareVersions.containsKey("Workflow")) {
+            softwareVersions.Workflow.remove("Nextflow")
+        }
+        return softwareVersions
+    }
+}
diff --git a/tests/pipeline/sra.nf.test b/tests/pipeline/sra.nf.test
index 970840de..96f4dc93 100644
--- a/tests/pipeline/sra.nf.test
+++ b/tests/pipeline/sra.nf.test
@@ -2,7 +2,7 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
-    tag "pipeline"
+    tag "sra"
 
     test("SRA FASTQ & Metadata") {
 
@@ -13,12 +13,9 @@ nextflow_pipeline {
         }
 
         then {
-            def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
-            if (softwareVersions.containsKey("Workflow")) { softwareVersions.Workflow.remove("Nextflow") }
-
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(softwareVersions).match("software_versions") },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
                                 path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
diff --git a/tests/pipeline/sra.nf.test.snap b/tests/pipeline/sra.nf.test.snap
index 86c6780e..366b20f6 100644
--- a/tests/pipeline/sra.nf.test.snap
+++ b/tests/pipeline/sra.nf.test.snap
@@ -12,46 +12,20 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-25T01:31:04+0000"
+        "timestamp": "2023-05-28T15:25:33+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-25T01:31:04+0000"
+        "timestamp": "2023-05-28T15:25:33+0000"
     },
     "software_versions": {
         "content": [
-            {
-                "CUSTOM_DUMPSOFTWAREVERSIONS": {
-                    "python": "3.11.0",
-                    "yaml": "6.0"
-                },
-                "CUSTOM_SRATOOLSNCBISETTINGS": {
-                    "sratools": "2.11.0"
-                },
-                "MULTIQC_MAPPINGS_CONFIG": {
-                    "python": "3.9.5"
-                },
-                "SRA_FASTQ_FTP": {
-                    "curl": "7.81.0"
-                },
-                "SRA_IDS_TO_RUNINFO": {
-                    "python": "3.9.5"
-                },
-                "SRA_MERGE_SAMPLESHEET": {
-                    "sed": "4.7"
-                },
-                "SRA_RUNINFO_TO_FTP": {
-                    "python": "3.9.5"
-                },
-                "Workflow": {
-                    "nf-core/fetchngs": "1.11.0dev"
-                }
-            }
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0dev}}"
         ],
-        "timestamp": "2023-05-25T01:31:04+0000"
+        "timestamp": "2023-05-28T15:25:33+0000"
     },
     "fastq": {
         "content": [
@@ -101,6 +75,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-05-25T01:31:04+0000"
+        "timestamp": "2023-05-28T15:25:33+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_skip_fastq.nf.test b/tests/pipeline/sra_skip_fastq.nf.test
index e00dc66a..7d8a6789 100644
--- a/tests/pipeline/sra_skip_fastq.nf.test
+++ b/tests/pipeline/sra_skip_fastq.nf.test
@@ -2,7 +2,7 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
-    tag "pipeline"
+    tag "sra_skip_fastq"
 
     test("SRA Skip FASTQ") {
 
@@ -14,12 +14,9 @@ nextflow_pipeline {
         }
 
         then {
-            def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
-            if (softwareVersions.containsKey("Workflow")) { softwareVersions.Workflow.remove("Nextflow") }
-
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(softwareVersions).match("software_versions") },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
                 { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
                                 path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
                                 path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
diff --git a/tests/pipeline/sra_skip_fastq.nf.test.snap b/tests/pipeline/sra_skip_fastq.nf.test.snap
index c2edd1c3..e5fcb176 100644
--- a/tests/pipeline/sra_skip_fastq.nf.test.snap
+++ b/tests/pipeline/sra_skip_fastq.nf.test.snap
@@ -12,39 +12,19 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-24T23:49:24+0000"
+        "timestamp": "2023-05-28T15:07:52+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-24T23:49:24+0000"
+        "timestamp": "2023-05-28T15:07:52+0000"
     },
     "software_versions": {
         "content": [
-            {
-                "CUSTOM_DUMPSOFTWAREVERSIONS": {
-                    "python": "3.11.0",
-                    "yaml": "6.0"
-                },
-                "MULTIQC_MAPPINGS_CONFIG": {
-                    "python": "3.9.5"
-                },
-                "SRA_IDS_TO_RUNINFO": {
-                    "python": "3.9.5"
-                },
-                "SRA_MERGE_SAMPLESHEET": {
-                    "sed": "4.7"
-                },
-                "SRA_RUNINFO_TO_FTP": {
-                    "python": "3.9.5"
-                },
-                "Workflow": {
-                    "nf-core/fetchngs": "1.11.0dev"
-                }
-            }
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0dev}}"
         ],
-        "timestamp": "2023-05-24T23:49:24+0000"
+        "timestamp": "2023-05-28T15:07:52+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
index 3015311a..17324e60 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
@@ -2,7 +2,7 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
-    tag "pipeline"
+    tag "sra_nf-core"
 
     test("SRA NF-CORE/RNASEQ Samplesheet") {
 
@@ -14,12 +14,9 @@ nextflow_pipeline {
         }
 
         then {
-            def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
-            if (softwareVersions.containsKey("Workflow")) { softwareVersions.Workflow.remove("Nextflow") }
-
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(softwareVersions).match("rnaseq_software_versions") },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("rnaseq_software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
                                 path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
@@ -51,12 +48,9 @@ nextflow_pipeline {
         }
 
         then {
-            def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
-            if (softwareVersions.containsKey("Workflow")) { softwareVersions.Workflow.remove("Nextflow") }
-
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(softwareVersions).match("rnaseq_ena_software_versions") },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("rnaseq_ena_software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
                                 path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
@@ -86,12 +80,9 @@ nextflow_pipeline {
         }
 
         then {
-            def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
-            if (softwareVersions.containsKey("Workflow")) { softwareVersions.Workflow.remove("Nextflow") }
-
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(softwareVersions).match("atacseq_software_versions") },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("atacseq_software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
                                 path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
@@ -121,12 +112,9 @@ nextflow_pipeline {
         }
 
         then {
-            def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
-            if (softwareVersions.containsKey("Workflow")) { softwareVersions.Workflow.remove("Nextflow") }
-
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(softwareVersions).match("viralrecon_software_versions") },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("viralrecon_software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
                                 path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
@@ -156,12 +144,9 @@ nextflow_pipeline {
         }
 
         then {
-            def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
-            if (softwareVersions.containsKey("Workflow")) { softwareVersions.Workflow.remove("Nextflow") }
-
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(softwareVersions).match("taxprofiler_software_versions") },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("taxprofiler_software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
                                 path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
index ca946dc8..edd1e910 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
@@ -12,71 +12,7 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-25T01:47:31+0000"
-    },
-    "rnaseq_software_versions": {
-        "content": [
-            {
-                "CUSTOM_DUMPSOFTWAREVERSIONS": {
-                    "python": "3.11.0",
-                    "yaml": "6.0"
-                },
-                "CUSTOM_SRATOOLSNCBISETTINGS": {
-                    "sratools": "2.11.0"
-                },
-                "MULTIQC_MAPPINGS_CONFIG": {
-                    "python": "3.9.5"
-                },
-                "SRA_FASTQ_FTP": {
-                    "curl": "7.81.0"
-                },
-                "SRA_IDS_TO_RUNINFO": {
-                    "python": "3.9.5"
-                },
-                "SRA_MERGE_SAMPLESHEET": {
-                    "sed": "4.7"
-                },
-                "SRA_RUNINFO_TO_FTP": {
-                    "python": "3.9.5"
-                },
-                "Workflow": {
-                    "nf-core/fetchngs": "1.11.0dev"
-                }
-            }
-        ],
-        "timestamp": "2023-05-25T01:47:31+0000"
-    },
-    "rnaseq_ena_software_versions": {
-        "content": [
-            {
-                "CUSTOM_DUMPSOFTWAREVERSIONS": {
-                    "python": "3.11.0",
-                    "yaml": "6.0"
-                },
-                "CUSTOM_SRATOOLSNCBISETTINGS": {
-                    "sratools": "2.11.0"
-                },
-                "MULTIQC_MAPPINGS_CONFIG": {
-                    "python": "3.9.5"
-                },
-                "SRA_FASTQ_FTP": {
-                    "curl": "7.81.0"
-                },
-                "SRA_IDS_TO_RUNINFO": {
-                    "python": "3.9.5"
-                },
-                "SRA_MERGE_SAMPLESHEET": {
-                    "sed": "4.7"
-                },
-                "SRA_RUNINFO_TO_FTP": {
-                    "python": "3.9.5"
-                },
-                "Workflow": {
-                    "nf-core/fetchngs": "1.11.0dev"
-                }
-            }
-        ],
-        "timestamp": "2023-05-25T01:47:31+0000"
+        "timestamp": "2023-05-28T15:19:39+0000"
     },
     "viralrecon_metadata": {
         "content": [
@@ -91,78 +27,38 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-25T01:47:31+0000"
+        "timestamp": "2023-05-28T15:19:39+0000"
     },
-    "viralrecon_software_versions": {
+    "rnaseq_software_versions": {
+        "content": [
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0dev}}"
+        ],
+        "timestamp": "2023-05-28T15:19:39+0000"
+    },
+    "rnaseq_ena_software_versions": {
         "content": [
-            {
-                "CUSTOM_DUMPSOFTWAREVERSIONS": {
-                    "python": "3.11.0",
-                    "yaml": "6.0"
-                },
-                "CUSTOM_SRATOOLSNCBISETTINGS": {
-                    "sratools": "2.11.0"
-                },
-                "MULTIQC_MAPPINGS_CONFIG": {
-                    "python": "3.9.5"
-                },
-                "SRA_FASTQ_FTP": {
-                    "curl": "7.81.0"
-                },
-                "SRA_IDS_TO_RUNINFO": {
-                    "python": "3.9.5"
-                },
-                "SRA_MERGE_SAMPLESHEET": {
-                    "sed": "4.7"
-                },
-                "SRA_RUNINFO_TO_FTP": {
-                    "python": "3.9.5"
-                },
-                "Workflow": {
-                    "nf-core/fetchngs": "1.11.0dev"
-                }
-            }
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0dev}}"
         ],
-        "timestamp": "2023-05-25T01:47:31+0000"
+        "timestamp": "2023-05-28T15:19:39+0000"
     },
     "viralrecon_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-25T01:47:31+0000"
+        "timestamp": "2023-05-28T15:19:39+0000"
+    },
+    "viralrecon_software_versions": {
+        "content": [
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0dev}}"
+        ],
+        "timestamp": "2023-05-28T15:19:39+0000"
     },
     "taxprofiler_software_versions": {
         "content": [
-            {
-                "CUSTOM_DUMPSOFTWAREVERSIONS": {
-                    "python": "3.11.0",
-                    "yaml": "6.0"
-                },
-                "CUSTOM_SRATOOLSNCBISETTINGS": {
-                    "sratools": "2.11.0"
-                },
-                "MULTIQC_MAPPINGS_CONFIG": {
-                    "python": "3.9.5"
-                },
-                "SRA_FASTQ_FTP": {
-                    "curl": "7.81.0"
-                },
-                "SRA_IDS_TO_RUNINFO": {
-                    "python": "3.9.5"
-                },
-                "SRA_MERGE_SAMPLESHEET": {
-                    "sed": "4.7"
-                },
-                "SRA_RUNINFO_TO_FTP": {
-                    "python": "3.9.5"
-                },
-                "Workflow": {
-                    "nf-core/fetchngs": "1.11.0dev"
-                }
-            }
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0dev}}"
         ],
-        "timestamp": "2023-05-25T01:47:31+0000"
+        "timestamp": "2023-05-28T15:19:39+0000"
     },
     "atacseq_metadata": {
         "content": [
@@ -177,7 +73,7 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-25T01:47:31+0000"
+        "timestamp": "2023-05-28T15:19:39+0000"
     },
     "rnaseq_ena_metadata": {
         "content": [
@@ -192,14 +88,14 @@
             "SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1",
             "SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236"
         ],
-        "timestamp": "2023-05-25T01:47:31+0000"
+        "timestamp": "2023-05-28T15:19:39+0000"
     },
     "rnaseq_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-25T01:47:31+0000"
+        "timestamp": "2023-05-28T15:19:39+0000"
     },
     "rnaseq_metadata": {
         "content": [
@@ -214,60 +110,34 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-25T01:47:31+0000"
+        "timestamp": "2023-05-28T15:19:39+0000"
     },
     "atacseq_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-25T01:47:31+0000"
+        "timestamp": "2023-05-28T15:19:39+0000"
     },
     "rnaseq_ena_samplesheet": {
         "content": [
             "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f",
             "multiqc_config.yml:md5,6f6189ee58855de81eaf82ad86e21040"
         ],
-        "timestamp": "2023-05-25T01:47:31+0000"
-    },
-    "atacseq_software_versions": {
-        "content": [
-            {
-                "CUSTOM_DUMPSOFTWAREVERSIONS": {
-                    "python": "3.11.0",
-                    "yaml": "6.0"
-                },
-                "CUSTOM_SRATOOLSNCBISETTINGS": {
-                    "sratools": "2.11.0"
-                },
-                "MULTIQC_MAPPINGS_CONFIG": {
-                    "python": "3.9.5"
-                },
-                "SRA_FASTQ_FTP": {
-                    "curl": "7.81.0"
-                },
-                "SRA_IDS_TO_RUNINFO": {
-                    "python": "3.9.5"
-                },
-                "SRA_MERGE_SAMPLESHEET": {
-                    "sed": "4.7"
-                },
-                "SRA_RUNINFO_TO_FTP": {
-                    "python": "3.9.5"
-                },
-                "Workflow": {
-                    "nf-core/fetchngs": "1.11.0dev"
-                }
-            }
-        ],
-        "timestamp": "2023-05-25T01:47:31+0000"
+        "timestamp": "2023-05-28T15:19:39+0000"
     },
     "taxprofiler_samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-25T01:47:31+0000"
+        "timestamp": "2023-05-28T15:19:39+0000"
+    },
+    "atacseq_software_versions": {
+        "content": [
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0dev}}"
+        ],
+        "timestamp": "2023-05-28T15:19:39+0000"
     },
     "fastq": {
         "content": [
@@ -317,6 +187,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-05-25T01:47:31+0000"
+        "timestamp": "2023-05-28T15:19:39+0000"
     }
 }
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_sratools.nf.test b/tests/pipeline/sra_with_sratools.nf.test
index 755f0c9c..863f050c 100644
--- a/tests/pipeline/sra_with_sratools.nf.test
+++ b/tests/pipeline/sra_with_sratools.nf.test
@@ -2,7 +2,7 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
-    tag "pipeline"
+    tag "sratools_force"
 
     test("Force SRA-Tools Download") {
 
@@ -14,12 +14,9 @@ nextflow_pipeline {
         }
 
         then {
-            def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
-            if (softwareVersions.containsKey("Workflow")) { softwareVersions.Workflow.remove("Nextflow") }
-
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(softwareVersions).match("software_versions") },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
                                 path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
diff --git a/tests/pipeline/sra_with_sratools.nf.test.snap b/tests/pipeline/sra_with_sratools.nf.test.snap
index ee8278a9..75ccd0a6 100644
--- a/tests/pipeline/sra_with_sratools.nf.test.snap
+++ b/tests/pipeline/sra_with_sratools.nf.test.snap
@@ -12,43 +12,20 @@
             "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
             "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
         ],
-        "timestamp": "2023-05-24T23:48:56+0000"
+        "timestamp": "2023-05-28T15:07:23+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
             "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
         ],
-        "timestamp": "2023-05-24T23:48:56+0000"
+        "timestamp": "2023-05-28T15:07:23+0000"
     },
     "software_versions": {
         "content": [
-            {
-                "CUSTOM_DUMPSOFTWAREVERSIONS": {
-                    "python": "3.11.0",
-                    "yaml": "6.0"
-                },
-                "CUSTOM_SRATOOLSNCBISETTINGS": {
-                    "sratools": "2.11.0"
-                },
-                "MULTIQC_MAPPINGS_CONFIG": {
-                    "python": "3.9.5"
-                },
-                "SRA_IDS_TO_RUNINFO": {
-                    "python": "3.9.5"
-                },
-                "SRA_MERGE_SAMPLESHEET": {
-                    "sed": "4.7"
-                },
-                "SRA_RUNINFO_TO_FTP": {
-                    "python": "3.9.5"
-                },
-                "Workflow": {
-                    "nf-core/fetchngs": "1.11.0dev"
-                }
-            }
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0dev}}"
         ],
-        "timestamp": "2023-05-24T23:48:56+0000"
+        "timestamp": "2023-05-28T15:07:23+0000"
     },
     "fastq": {
         "content": [
@@ -77,6 +54,6 @@
             "SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7",
             "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af"
         ],
-        "timestamp": "2023-05-24T23:48:56+0000"
+        "timestamp": "2023-05-28T15:07:23+0000"
     }
 }
\ No newline at end of file

From d6263a0b38e3b0a92e11a8f169c3340797d79c35 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Sun, 28 May 2023 11:27:56 -0400
Subject: [PATCH 356/852] rm-old-module-test

---
 tests/modules/sra_ids_to_runinfo/main.nf.test | 43 -------------------
 .../sra_ids_to_runinfo/main.nf.test.snap      | 40 -----------------
 2 files changed, 83 deletions(-)
 delete mode 100644 tests/modules/sra_ids_to_runinfo/main.nf.test
 delete mode 100644 tests/modules/sra_ids_to_runinfo/main.nf.test.snap

diff --git a/tests/modules/sra_ids_to_runinfo/main.nf.test b/tests/modules/sra_ids_to_runinfo/main.nf.test
deleted file mode 100644
index f5467e75..00000000
--- a/tests/modules/sra_ids_to_runinfo/main.nf.test
+++ /dev/null
@@ -1,43 +0,0 @@
-nextflow_process {
-
-    name "Test Process SRA_IDS_TO_RUNINFO"
-    script "modules/local/sra_ids_to_runinfo.nf"
-    process "SRA_IDS_TO_RUNINFO"
-
-    test("Should run without failures without fields") {
-
-        when {
-            process {
-                """
-                input[0] = 'SRR9984183'
-                input[1] = ''
-                """
-            }
-        }
-
-        then {
-            assert process.success
-            assert snapshot(process.out).match()
-        }
-
-    }
-
-    test("Should run without failures with fields") {
-
-        when {
-            process {
-                """
-                input[0] = 'SRR9984183'
-                input[1] = 'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'
-                """
-            }
-        }
-
-        then {
-            assert process.success
-            assert snapshot(process.out).match()
-        }
-
-    }
-
-}
diff --git a/tests/modules/sra_ids_to_runinfo/main.nf.test.snap b/tests/modules/sra_ids_to_runinfo/main.nf.test.snap
deleted file mode 100644
index e13c470f..00000000
--- a/tests/modules/sra_ids_to_runinfo/main.nf.test.snap
+++ /dev/null
@@ -1,40 +0,0 @@
-{
-    "Should run without failures without fields": {
-        "content": [
-            {
-                "0": [
-                    "SRR9984183.runinfo.tsv:md5,6bc8bfb7058412e5a54b83e08d3d1673"
-                ],
-                "1": [
-                    "versions.yml:md5,61ebf47bc00075513ff16295beddb197"
-                ],
-                "tsv": [
-                    "SRR9984183.runinfo.tsv:md5,6bc8bfb7058412e5a54b83e08d3d1673"
-                ],
-                "versions": [
-                    "versions.yml:md5,61ebf47bc00075513ff16295beddb197"
-                ]
-            }
-        ],
-        "timestamp": "2023-05-09T02:22:52+0000"
-    },
-    "Should run without failures with fields": {
-        "content": [
-            {
-                "0": [
-                    "SRR9984183.runinfo.tsv:md5,6419f18c29ab09634b3dd97a6b2acd06"
-                ],
-                "1": [
-                    "versions.yml:md5,61ebf47bc00075513ff16295beddb197"
-                ],
-                "tsv": [
-                    "SRR9984183.runinfo.tsv:md5,6419f18c29ab09634b3dd97a6b2acd06"
-                ],
-                "versions": [
-                    "versions.yml:md5,61ebf47bc00075513ff16295beddb197"
-                ]
-            }
-        ],
-        "timestamp": "2023-05-09T02:22:52+0000"
-    }
-}
\ No newline at end of file

From 1db801fe6bb600c5c34cbfe0750fbbefd304e6d8 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Wed, 31 May 2023 13:15:32 -0400
Subject: [PATCH 357/852] rm-docker-hardcode.nf-test-config-add-pipeline-tag

---
 nf-test.config                                   | 2 +-
 tests/pipeline/sra.nf.test                       | 1 +
 tests/pipeline/sra_skip_fastq.nf.test            | 1 +
 tests/pipeline/sra_with_nf_core_pipeline.nf.test | 1 +
 tests/pipeline/sra_with_sratools.nf.test         | 1 +
 5 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/nf-test.config b/nf-test.config
index 7d705067..cd432d43 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -12,5 +12,5 @@ config {
     configFile "nextflow.config"
 
     // run all test with the defined docker profile from the main nextflow.config
-    profile "test,docker"
+    profile ""
 }
diff --git a/tests/pipeline/sra.nf.test b/tests/pipeline/sra.nf.test
index 96f4dc93..f545d93d 100644
--- a/tests/pipeline/sra.nf.test
+++ b/tests/pipeline/sra.nf.test
@@ -3,6 +3,7 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "main.nf"
     tag "sra"
+    tag "pipeline"
 
     test("SRA FASTQ & Metadata") {
 
diff --git a/tests/pipeline/sra_skip_fastq.nf.test b/tests/pipeline/sra_skip_fastq.nf.test
index 7d8a6789..b0237a81 100644
--- a/tests/pipeline/sra_skip_fastq.nf.test
+++ b/tests/pipeline/sra_skip_fastq.nf.test
@@ -3,6 +3,7 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "main.nf"
     tag "sra_skip_fastq"
+    tag "pipeline"
 
     test("SRA Skip FASTQ") {
 
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
index 17324e60..d0c41baf 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
@@ -3,6 +3,7 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "main.nf"
     tag "sra_nf-core"
+    tag "pipeline"
 
     test("SRA NF-CORE/RNASEQ Samplesheet") {
 
diff --git a/tests/pipeline/sra_with_sratools.nf.test b/tests/pipeline/sra_with_sratools.nf.test
index 863f050c..2fd06ba8 100644
--- a/tests/pipeline/sra_with_sratools.nf.test
+++ b/tests/pipeline/sra_with_sratools.nf.test
@@ -3,6 +3,7 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "main.nf"
     tag "sratools_force"
+    tag "pipeline"
 
     test("Force SRA-Tools Download") {
 

From 3e2158c1f5d9b4ff89442d02942d0bcb687acdce Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Wed, 31 May 2023 13:16:03 -0400
Subject: [PATCH 358/852] CI-add-matrix-profile-nf-test-run-update-pr-commenter

---
 .github/workflows/ci.yml | 45 +++++++++++++++++++++++++---------------
 1 file changed, 28 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index ab3a10de..3b9936f5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -9,10 +9,12 @@ on:
       - dev
       - master
   release:
-    types: [published]
+    types:
+      - "published"
 
 env:
   NXF_ANSI_LOG: false
+  NFTEST_VER: "0.7.3"
 
 # cancel-in-progress: true ensures that if a new push is made to the same branch while a previous run is still in progress, the previous run is cancelled
 concurrency:
@@ -22,14 +24,16 @@ concurrency:
 jobs:
   test-dev:
     # Only run if the pull request is against the dev branch or if the push is to the dev branch
-    if: ${{ (github.base_ref == 'dev' || (github.event_name == 'push')) }}
+    if: (github.base_ref == 'dev' || (github.event_name == 'push'))
     name: Run pipeline with test data on dev
     runs-on: ubuntu-latest
     # Define the matrix of different Nextflow versions to test
     strategy:
       matrix:
-        NXF_VER: ["latest-everything"]
-        NFTEST_VER: ["0.7.3"]
+        NXF_VER:
+          - "latest-everything"
+        profile: # TODO ["singularity", "conda"]
+          - "docker"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v3
@@ -43,12 +47,12 @@ jobs:
       # Install nf-test
       - name: Install nf-test
         run: |
-          wget -qO- https://code.askimed.com/install/nf-test | bash -s ${{ matrix.NFTEST_VER }}
+          wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
           sudo mv nf-test /usr/local/bin/
 
       # Run nf-test
       - name: Run nf-test
-        run: nf-test test tests/pipeline/ --tap=test.tap
+        run: nf-test test tests/pipeline/ --profile "test,${{ matrix.profile }}" --tap=test.tap
 
       # If the test fails, output the software_versions.yml using the 'batcat' utility
       - name: Output log on failure
@@ -58,22 +62,27 @@ jobs:
           batcat --decorations=always --color=always /home/runner/work/fetchngs/fetchngs/.nf-test/tests/*/output/pipeline_info/software_versions.yml
 
       # Comment on the PR with the test results
-      - name: PR comment with file
-        if: github.event_name == 'pull_request'
+      - name: Comment PR with execution number
         uses: thollander/actions-comment-pull-request@v2
         with:
-          filePath: test.tap
+          message: |
+            _(execution **${{ github.run_id }}** / attempt **${{ github.run_attempt }}**)_
+          comment_tag: execution
+          reactions: eyes
 
   test-master:
     # Only run on master branch or when a PR is opened against master
-    if: ${{ (github.base_ref == 'master') }}
+    if: github.base_ref == 'master'
     name: Run pipeline with test data on master
     runs-on: ubuntu-latest
     # Define the matrix of different Nextflow versions to test
     strategy:
       matrix:
-        NXF_VER: ["22.10.1", "latest-everything"]
-        NFTEST_VER: ["0.7.3"]
+        NXF_VER:
+          - "22.10.1"
+          - "latest-everything"
+        profile:
+          - "docker"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v3
@@ -87,12 +96,12 @@ jobs:
       # Install nf-test
       - name: Install nf-test
         run: |
-          wget -qO- https://code.askimed.com/install/nf-test | bash -s ${{ matrix.NFTEST_VER }}
+          wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
           sudo mv nf-test /usr/local/bin/
 
       # Run nf-test
       - name: Run nf-test
-        run: nf-test test tests/pipeline/ --tap=test.tap
+        run: nf-test test tests/pipeline/ --profile "test,${{ matrix.profile }}" --tap=test.tap
 
       # If the test fails, output the software_versions.yml using the 'batcat' utility
       - name: Output log on failure
@@ -102,8 +111,10 @@ jobs:
           batcat --decorations=always --color=always /home/runner/work/fetchngs/fetchngs/.nf-test/tests/*/output/pipeline_info/software_versions.yml
 
       # Comment on the PR with the test results
-      - name: PR comment with file
-        if: github.event_name == 'pull_request'
+      - name: Comment PR with execution number
         uses: thollander/actions-comment-pull-request@v2
         with:
-          filePath: test.tap
+          message: |
+            _(execution **${{ github.run_id }}** / attempt **${{ github.run_attempt }}**)_
+          comment_tag: execution
+          reactions: eyes

From 75e1cb5618048dd96ed194d381ab322b28edebac Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Thu, 1 Jun 2023 17:57:34 -0400
Subject: [PATCH 359/852] CI-disable-pr-commenter-ref-dev

---
 .github/workflows/ci.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 3b9936f5..a5b6b592 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -63,6 +63,7 @@ jobs:
 
       # Comment on the PR with the test results
       - name: Comment PR with execution number
+        if: github.event_name == 'pull_request' && github.ref != 'refs/heads/dev'
         uses: thollander/actions-comment-pull-request@v2
         with:
           message: |
@@ -112,6 +113,7 @@ jobs:
 
       # Comment on the PR with the test results
       - name: Comment PR with execution number
+        if: github.event_name == 'pull_request' && github.ref != 'refs/heads/dev'
         uses: thollander/actions-comment-pull-request@v2
         with:
           message: |

From d4a7830b4bbc4b01add191b36a5e4cb834133ff8 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Fri, 9 Jun 2023 09:38:38 -0400
Subject: [PATCH 360/852] CI-skip-condition-for-dev

---
 .github/workflows/ci.yml | 89 ++++++++--------------------------------
 1 file changed, 18 insertions(+), 71 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index a5b6b592..c3d8511a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -16,67 +16,14 @@ env:
   NXF_ANSI_LOG: false
   NFTEST_VER: "0.7.3"
 
-# cancel-in-progress: true ensures that if a new push is made to the same branch while a previous run is still in progress, the previous run is cancelled
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
 
 jobs:
-  test-dev:
-    # Only run if the pull request is against the dev branch or if the push is to the dev branch
-    if: (github.base_ref == 'dev' || (github.event_name == 'push'))
-    name: Run pipeline with test data on dev
+  test:
+    name: Run pipeline with test data
     runs-on: ubuntu-latest
-    # Define the matrix of different Nextflow versions to test
-    strategy:
-      matrix:
-        NXF_VER:
-          - "latest-everything"
-        profile: # TODO ["singularity", "conda"]
-          - "docker"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v3
-
-      # Install Nextflow
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      # Install nf-test
-      - name: Install nf-test
-        run: |
-          wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
-          sudo mv nf-test /usr/local/bin/
-
-      # Run nf-test
-      - name: Run nf-test
-        run: nf-test test tests/pipeline/ --profile "test,${{ matrix.profile }}" --tap=test.tap
-
-      # If the test fails, output the software_versions.yml using the 'batcat' utility
-      - name: Output log on failure
-        if: failure()
-        run: |
-          sudo apt install bat > /dev/null
-          batcat --decorations=always --color=always /home/runner/work/fetchngs/fetchngs/.nf-test/tests/*/output/pipeline_info/software_versions.yml
-
-      # Comment on the PR with the test results
-      - name: Comment PR with execution number
-        if: github.event_name == 'pull_request' && github.ref != 'refs/heads/dev'
-        uses: thollander/actions-comment-pull-request@v2
-        with:
-          message: |
-            _(execution **${{ github.run_id }}** / attempt **${{ github.run_attempt }}**)_
-          comment_tag: execution
-          reactions: eyes
-
-  test-master:
-    # Only run on master branch or when a PR is opened against master
-    if: github.base_ref == 'master'
-    name: Run pipeline with test data on master
-    runs-on: ubuntu-latest
-    # Define the matrix of different Nextflow versions to test
     strategy:
       matrix:
         NXF_VER:
@@ -84,39 +31,39 @@ jobs:
           - "latest-everything"
         profile:
           - "docker"
+
     steps:
+      # Skip if it's a pull_request to dev and NXF_VER is '22.10.1'
+      - name: Skip condition
+        id: condition
+        run: |
+          if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
+            echo "skip=true" >> $GITHUB_OUTPUT
+          fi
+
       - name: Check out pipeline code
+        if: steps.condition.outputs.skip != 'true'
         uses: actions/checkout@v3
 
-      # Install Nextflow
       - name: Install Nextflow
+        if: steps.condition.outputs.skip != 'true'
         uses: nf-core/setup-nextflow@v1
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      # Install nf-test
       - name: Install nf-test
+        if: steps.condition.outputs.skip != 'true'
         run: |
           wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
           sudo mv nf-test /usr/local/bin/
 
-      # Run nf-test
       - name: Run nf-test
-        run: nf-test test tests/pipeline/ --profile "test,${{ matrix.profile }}" --tap=test.tap
+        if: steps.condition.outputs.skip != 'true'
+        run: |
+          nf-test test tests/pipeline/ --profile "test,${{ matrix.profile }}" --tap=test.tap
 
-      # If the test fails, output the software_versions.yml using the 'batcat' utility
       - name: Output log on failure
         if: failure()
         run: |
           sudo apt install bat > /dev/null
-          batcat --decorations=always --color=always /home/runner/work/fetchngs/fetchngs/.nf-test/tests/*/output/pipeline_info/software_versions.yml
-
-      # Comment on the PR with the test results
-      - name: Comment PR with execution number
-        if: github.event_name == 'pull_request' && github.ref != 'refs/heads/dev'
-        uses: thollander/actions-comment-pull-request@v2
-        with:
-          message: |
-            _(execution **${{ github.run_id }}** / attempt **${{ github.run_attempt }}**)_
-          comment_tag: execution
-          reactions: eyes
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml

From 23c6e24608cd9162ba817a31e56eddb71957c3a5 Mon Sep 17 00:00:00 2001
From: MCMandR <136441313+MCMandR@users.noreply.github.com>
Date: Tue, 13 Jun 2023 10:48:00 +0200
Subject: [PATCH 361/852] sra_runinfo_to_ftp.py: Avoid dependency on Python 3.8

The ":=" assignment was introduced in Python 3.8. On HPC environments this is not always available.
---
 bin/sra_runinfo_to_ftp.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/bin/sra_runinfo_to_ftp.py b/bin/sra_runinfo_to_ftp.py
index ef80ec80..c220f74e 100755
--- a/bin/sra_runinfo_to_ftp.py
+++ b/bin/sra_runinfo_to_ftp.py
@@ -61,7 +61,8 @@ def parse_sra_runinfo(file_in):
     with open(file_in, "r", newline="") as fin:
         reader = csv.DictReader(fin, delimiter="\t", skipinitialspace=True)
         header = list(reader.fieldnames)
-        if missing := frozenset(columns).difference(frozenset(header)):
+        missing = frozenset(columns).difference(frozenset(header))
+        if missing:
             logger.critical(f"The following expected columns are missing from {file_in}: " f"{', '.join(missing)}.")
             sys.exit(1)
         for row in reader:

From 80ead031899101715d6d97363a67c52cbd17a02c Mon Sep 17 00:00:00 2001
From: davidecarlson <david.carlson@stonybrook.edu>
Date: Thu, 15 Jun 2023 10:17:07 -0400
Subject: [PATCH 362/852] updated usage with info on downloading 10X data.

---
 docs/usage.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/docs/usage.md b/docs/usage.md
index 0720a680..5bef3bcb 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -70,6 +70,12 @@ From v1.9 of this pipeline the default `strandedness` in the output samplesheet
 
 If FTP connections are blocked on your network use the [`--force_sratools_download`](https://nf-co.re/fetchngs/parameters#force_sratools_download) parameter to force the pipeline to download data using sra-tools instead of the ENA FTP.
 
+### Downloading 10X Genomics Data
+
+As of v1.010.0, this pipeline now supports downloading of 10X Genomics data. For 10X data sets, the output needs to  be split into three fastq files, consisting of the feature barcode+UMI, cDNA sequence reads, and sample index. Adding the `--force_sratools_download` parameter will cause the pipeline to use the sra-tools fasterq-dump program with appropriate setting to ensure that all three files are generated.
+
+Please note that in our experience the downloaded R1, R2, and R3 fastq files do not always correspond to the same data types across different submissions.  In many cases, R1 will be the cell barcode + UMI, R2 is the cDNA sequence, and R3 is the sample index.  However, this is not alway the case.  Users are strongly encouraged to verify their data before proceeding with downstream analysis.
+
 ### Downloading dbGAP data with JWT
 
 As of v1.10.0, the SRA Toolkit used in this pipeline can be configured to access protected data from dbGAP using a [JWT cart file](https://www.ncbi.nlm.nih.gov/sra/docs/sra-dbGAP-cloud-download/) on a supported cloud computing environment (Amazon Web Services or Google Cloud Platform). The JWT cart file can be specified with `--dbgap_key /path/to/cart.jwt`.

From 944bb3abb792a91ceb318f27cddcd1779ce75462 Mon Sep 17 00:00:00 2001
From: davidecarlson <david.carlson@stonybrook.edu>
Date: Thu, 15 Jun 2023 10:54:53 -0400
Subject: [PATCH 363/852] prettier formatting

---
 docs/usage.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/usage.md b/docs/usage.md
index 5bef3bcb..8fe801fd 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -72,9 +72,9 @@ If FTP connections are blocked on your network use the [`--force_sratools_downlo
 
 ### Downloading 10X Genomics Data
 
-As of v1.010.0, this pipeline now supports downloading of 10X Genomics data. For 10X data sets, the output needs to  be split into three fastq files, consisting of the feature barcode+UMI, cDNA sequence reads, and sample index. Adding the `--force_sratools_download` parameter will cause the pipeline to use the sra-tools fasterq-dump program with appropriate setting to ensure that all three files are generated.
+As of v1.010.0, this pipeline now supports downloading of 10X Genomics data. For 10X data sets, the output needs to be split into three fastq files, consisting of the feature barcode+UMI, cDNA sequence reads, and sample index. Adding the `--force_sratools_download` parameter will cause the pipeline to use the sra-tools fasterq-dump program with appropriate setting to ensure that all three files are generated.
 
-Please note that in our experience the downloaded R1, R2, and R3 fastq files do not always correspond to the same data types across different submissions.  In many cases, R1 will be the cell barcode + UMI, R2 is the cDNA sequence, and R3 is the sample index.  However, this is not alway the case.  Users are strongly encouraged to verify their data before proceeding with downstream analysis.
+Please note that in our experience the downloaded R1, R2, and R3 fastq files do not always correspond to the same data types across different submissions. In many cases, R1 will be the cell barcode + UMI, R2 is the cDNA sequence, and R3 is the sample index. However, this is not alway the case. Users are strongly encouraged to verify their data before proceeding with downstream analysis.
 
 ### Downloading dbGAP data with JWT
 

From f3b8cf872ccb3e7b2b893909fd70a9f2605036ad Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Thu, 15 Jun 2023 17:23:36 +0100
Subject: [PATCH 364/852] Update docs/usage.md

---
 docs/usage.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/usage.md b/docs/usage.md
index 8fe801fd..b2cd7b50 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -72,7 +72,7 @@ If FTP connections are blocked on your network use the [`--force_sratools_downlo
 
 ### Downloading 10X Genomics Data
 
-As of v1.010.0, this pipeline now supports downloading of 10X Genomics data. For 10X data sets, the output needs to be split into three fastq files, consisting of the feature barcode+UMI, cDNA sequence reads, and sample index. Adding the `--force_sratools_download` parameter will cause the pipeline to use the sra-tools fasterq-dump program with appropriate setting to ensure that all three files are generated.
+As of v1.10.0, this pipeline now supports downloading of 10X Genomics data. For 10X data sets, the output needs to be split into three fastq files, consisting of the feature barcode+UMI, cDNA sequence reads, and sample index. Adding the `--force_sratools_download` parameter will cause the pipeline to use the sra-tools fasterq-dump program with appropriate setting to ensure that all three files are generated.
 
 Please note that in our experience the downloaded R1, R2, and R3 fastq files do not always correspond to the same data types across different submissions. In many cases, R1 will be the cell barcode + UMI, R2 is the cDNA sequence, and R3 is the sample index. However, this is not alway the case. Users are strongly encouraged to verify their data before proceeding with downstream analysis.
 

From 385d0884eaa5797270a5182fc525378f6041571c Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Sat, 17 Jun 2023 09:24:43 -0400
Subject: [PATCH 365/852] CI to use dynamic matrix nextflow versions based on
 target branch

---
 .github/workflows/ci.yml | 39 +++++++++++++++++++++++----------------
 1 file changed, 23 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c3d8511a..d0198cae 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -21,49 +21,56 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  define_nxf_versions:
+    name: Choose nextflow versions to test against depending on target branch
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.nxf_versions.outputs.matrix }}
+    steps:
+      - id: nxf_versions
+        run: |
+          if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
+            echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT
+          else
+            echo matrix='["latest-everything", "22.10.1"]' | tee -a $GITHUB_OUTPUT
+          fi
+
   test:
     name: Run pipeline with test data
+    needs: define_nxf_versions
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        NXF_VER:
-          - "22.10.1"
-          - "latest-everything"
+        NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
         profile:
           - "docker"
 
     steps:
-      # Skip if it's a pull_request to dev and NXF_VER is '22.10.1'
-      - name: Skip condition
-        id: condition
-        run: |
-          if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
-            echo "skip=true" >> $GITHUB_OUTPUT
-          fi
-
       - name: Check out pipeline code
-        if: steps.condition.outputs.skip != 'true'
         uses: actions/checkout@v3
 
       - name: Install Nextflow
-        if: steps.condition.outputs.skip != 'true'
         uses: nf-core/setup-nextflow@v1
         with:
           version: "${{ matrix.NXF_VER }}"
 
       - name: Install nf-test
-        if: steps.condition.outputs.skip != 'true'
         run: |
           wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
           sudo mv nf-test /usr/local/bin/
 
       - name: Run nf-test
-        if: steps.condition.outputs.skip != 'true'
         run: |
-          nf-test test tests/pipeline/ --profile "test,${{ matrix.profile }}" --tap=test.tap
+          nf-test test tests/pipeline/ --profile "test,${{ matrix.profile }}" --junitxml=test.xml
 
       - name: Output log on failure
         if: failure()
         run: |
           sudo apt install bat > /dev/null
           batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: test.xml

From 6e9a0adf506f09f92c46f0cb13d1254e483ae0aa Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Wed, 28 Jun 2023 09:24:47 -0400
Subject: [PATCH 366/852] bump version

---
 nextflow.config                                       |  2 +-
 tests/pipeline/sra.nf.test.snap                       |  2 +-
 tests/pipeline/sra_skip_fastq.nf.test.snap            |  2 +-
 tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap | 10 +++++-----
 tests/pipeline/sra_with_sratools.nf.test.snap         |  2 +-
 5 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 0e0886e4..fff1910c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -212,7 +212,7 @@ manifest {
     description     = """Pipeline to fetch metadata and raw FastQ files from public databases"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '1.11.0dev'
+    version         = '1.11.0'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
 
diff --git a/tests/pipeline/sra.nf.test.snap b/tests/pipeline/sra.nf.test.snap
index 366b20f6..bcfbd5c3 100644
--- a/tests/pipeline/sra.nf.test.snap
+++ b/tests/pipeline/sra.nf.test.snap
@@ -23,7 +23,7 @@
     },
     "software_versions": {
         "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0dev}}"
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0}}"
         ],
         "timestamp": "2023-05-28T15:25:33+0000"
     },
diff --git a/tests/pipeline/sra_skip_fastq.nf.test.snap b/tests/pipeline/sra_skip_fastq.nf.test.snap
index e5fcb176..3033bb7e 100644
--- a/tests/pipeline/sra_skip_fastq.nf.test.snap
+++ b/tests/pipeline/sra_skip_fastq.nf.test.snap
@@ -23,7 +23,7 @@
     },
     "software_versions": {
         "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0dev}}"
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0}}"
         ],
         "timestamp": "2023-05-28T15:07:52+0000"
     }
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
index edd1e910..0d0b8cb3 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
@@ -31,13 +31,13 @@
     },
     "rnaseq_software_versions": {
         "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0dev}}"
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0}}"
         ],
         "timestamp": "2023-05-28T15:19:39+0000"
     },
     "rnaseq_ena_software_versions": {
         "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0dev}}"
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0}}"
         ],
         "timestamp": "2023-05-28T15:19:39+0000"
     },
@@ -50,13 +50,13 @@
     },
     "viralrecon_software_versions": {
         "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0dev}}"
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0}}"
         ],
         "timestamp": "2023-05-28T15:19:39+0000"
     },
     "taxprofiler_software_versions": {
         "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0dev}}"
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0}}"
         ],
         "timestamp": "2023-05-28T15:19:39+0000"
     },
@@ -135,7 +135,7 @@
     },
     "atacseq_software_versions": {
         "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0dev}}"
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0}}"
         ],
         "timestamp": "2023-05-28T15:19:39+0000"
     },
diff --git a/tests/pipeline/sra_with_sratools.nf.test.snap b/tests/pipeline/sra_with_sratools.nf.test.snap
index 75ccd0a6..c31fde9f 100644
--- a/tests/pipeline/sra_with_sratools.nf.test.snap
+++ b/tests/pipeline/sra_with_sratools.nf.test.snap
@@ -23,7 +23,7 @@
     },
     "software_versions": {
         "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0dev}}"
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0}}"
         ],
         "timestamp": "2023-05-28T15:07:23+0000"
     },

From 473db19f6e650ac54c9ea326ac27730a846a8dc8 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Thu, 29 Jun 2023 08:52:15 -0400
Subject: [PATCH 367/852] update changelog

---
 CHANGELOG.md | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2bd283e9..146b93b6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,10 +3,22 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unpublished Version / DEV]
+## [[1.10.1](https://github.com/nf-core/fetchngs/releases/tag/1.10.1)] - 2023-06-29
+
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Sateesh Peri](https://github.com/sateeshperi)
+- [Edmund Miller](https://github.com/Emiller88)
+- [Maxime Garcia](https://github.com/maxulysse)
+
+Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
 
 ### Enhancements & fixes
 
+- [#166](https://github.com/nf-core/fetchngs/issues/175) - Add NF-TEST pipeline end-to-end tests for existing CI tests
+
 ## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-16
 
 ### Credits

From e5fa57a3c90f595f324f4688e327fb79f10f5d0f Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Thu, 29 Jun 2023 16:20:57 +0200
Subject: [PATCH 368/852] Update nextflow.config

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index fff1910c..6eb5c18d 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -212,7 +212,7 @@ manifest {
     description     = """Pipeline to fetch metadata and raw FastQ files from public databases"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '1.11.0'
+    version         = '1.10.1'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
 

From c7f7df926b93677aee4bb0cf9bb09d46fcba2c0b Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Thu, 29 Jun 2023 16:35:40 +0200
Subject: [PATCH 369/852] Apply suggestions from code review

---
 tests/pipeline/sra.nf.test.snap                       |  2 +-
 tests/pipeline/sra_skip_fastq.nf.test.snap            |  2 +-
 tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap | 10 +++++-----
 tests/pipeline/sra_with_sratools.nf.test.snap         |  2 +-
 4 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/tests/pipeline/sra.nf.test.snap b/tests/pipeline/sra.nf.test.snap
index bcfbd5c3..02cf5541 100644
--- a/tests/pipeline/sra.nf.test.snap
+++ b/tests/pipeline/sra.nf.test.snap
@@ -23,7 +23,7 @@
     },
     "software_versions": {
         "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0}}"
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
         "timestamp": "2023-05-28T15:25:33+0000"
     },
diff --git a/tests/pipeline/sra_skip_fastq.nf.test.snap b/tests/pipeline/sra_skip_fastq.nf.test.snap
index 3033bb7e..4f2efb49 100644
--- a/tests/pipeline/sra_skip_fastq.nf.test.snap
+++ b/tests/pipeline/sra_skip_fastq.nf.test.snap
@@ -23,7 +23,7 @@
     },
     "software_versions": {
         "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0}}"
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
         "timestamp": "2023-05-28T15:07:52+0000"
     }
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
index 0d0b8cb3..ea9e25d8 100644
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
+++ b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
@@ -31,13 +31,13 @@
     },
     "rnaseq_software_versions": {
         "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0}}"
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
         "timestamp": "2023-05-28T15:19:39+0000"
     },
     "rnaseq_ena_software_versions": {
         "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0}}"
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
         "timestamp": "2023-05-28T15:19:39+0000"
     },
@@ -50,13 +50,13 @@
     },
     "viralrecon_software_versions": {
         "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0}}"
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
         "timestamp": "2023-05-28T15:19:39+0000"
     },
     "taxprofiler_software_versions": {
         "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0}}"
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
         "timestamp": "2023-05-28T15:19:39+0000"
     },
@@ -135,7 +135,7 @@
     },
     "atacseq_software_versions": {
         "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0}}"
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
         "timestamp": "2023-05-28T15:19:39+0000"
     },
diff --git a/tests/pipeline/sra_with_sratools.nf.test.snap b/tests/pipeline/sra_with_sratools.nf.test.snap
index c31fde9f..285b9ce1 100644
--- a/tests/pipeline/sra_with_sratools.nf.test.snap
+++ b/tests/pipeline/sra_with_sratools.nf.test.snap
@@ -23,7 +23,7 @@
     },
     "software_versions": {
         "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.11.0}}"
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
         "timestamp": "2023-05-28T15:07:23+0000"
     },

From 93f1aa368220bf38b2164ec99560a5c5a2129f75 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Sun, 9 Jul 2023 07:36:08 -0400
Subject: [PATCH 370/852] restrucutre local modules workflow dirs for tests

---
 .github/workflows/ci.yml                      |  13 +-
 .nf-core.yml                                  |  10 +-
 conf/test_data.config                         |  14 ++
 lib/NftestUtils.groovy                        |  38 ++++
 main.nf                                       |   4 +-
 .../multiqc_mappings_config.nf                |   0
 .../multiqc_mappings_config.nf.test           |  31 +++
 .../multiqc_mappings_config.nf.test.snap      |  27 +++
 .../{ => sra_fastq_ftp}/sra_fastq_ftp.nf      |   0
 .../local/sra_fastq_ftp/sra_fastq_ftp.nf.test |  33 +++
 .../sra_ids_to_runinfo.nf                     |   0
 .../sra_ids_to_runinfo.nf.test                |  32 +++
 .../sra_ids_to_runinfo.nf.test.snap           |  21 ++
 .../sra_merge_samplesheet.nf                  |   0
 .../sra_merge_samplesheet.nf.test             |  32 +++
 .../sra_merge_samplesheet.nf.test.snap        |  27 +++
 .../sra_runinfo_to_ftp.nf                     |   0
 .../sra_runinfo_to_ftp.nf.test                |  31 +++
 .../sra_runinfo_to_ftp.nf.test.snap           |  21 ++
 .../sra_to_samplesheet.nf                     |   0
 .../sra_to_samplesheet.nf.test                |  33 +++
 .../local/{ => synapse_get}/synapse_get.nf    |   0
 .../local/{ => synapse_list}/synapse_list.nf  |   0
 .../synapse_merge_samplesheet.nf              |   0
 .../local/{ => synapse_show}/synapse_show.nf  |   0
 .../synapse_to_samplesheet.nf                 |   0
 nf-test.config                                |   4 +-
 tests/config/tags.yml                         |  14 --
 tests/pipeline/lib/UTILS.groovy               |  11 -
 tests/pipeline/sra_skip_fastq.nf.test.snap    |  30 ---
 .../sra_with_nf_core_pipeline.nf.test         | 170 ----------------
 .../sra_with_nf_core_pipeline.nf.test.snap    | 192 ------------------
 workflows/{sra.nf => sra/main.nf}             |  16 +-
 .../sra/tests/skip_fastq.nf.test              |   4 +-
 workflows/sra/tests/skip_fastq.nf.test.snap   |  30 +++
 .../sra/tests}/sra.nf.test                    |   4 +-
 .../sra/tests}/sra.nf.test.snap               |  30 +--
 .../tests/with_atacseq_samplesheet.nf.test    |  39 ++++
 .../with_atacseq_samplesheet.nf.test.snap     |  80 ++++++++
 .../sra/tests/with_rnaseq_samplesheet.nf.test |  39 ++++
 .../with_rnaseq_samplesheet.nf.test.snap      |  80 ++++++++
 .../with_rnaseq_specific_ena_metadata.nf.test |  41 ++++
 ..._rnaseq_specific_ena_metadata.nf.test.snap |  80 ++++++++
 .../sra/tests/with_sratools.nf.test           |   6 +-
 .../sra/tests/with_sratools.nf.test.snap      |  30 +--
 .../with_taxprofiler_samplesheet.nf.test      |  40 ++++
 .../with_taxprofiler_samplesheet.nf.test.snap |  80 ++++++++
 .../tests/with_viralrecon_samplesheet.nf.test |  39 ++++
 .../with_viralrecon_samplesheet.nf.test.snap  |  80 ++++++++
 workflows/{synapse.nf => synapse/main.nf}     |  12 +-
 .../synapse/tests}/synapse.test               |   0
 51 files changed, 1044 insertions(+), 474 deletions(-)
 create mode 100644 conf/test_data.config
 create mode 100644 lib/NftestUtils.groovy
 rename modules/local/{ => multiqc_mappings_config}/multiqc_mappings_config.nf (100%)
 create mode 100644 modules/local/multiqc_mappings_config/multiqc_mappings_config.nf.test
 create mode 100644 modules/local/multiqc_mappings_config/multiqc_mappings_config.nf.test.snap
 rename modules/local/{ => sra_fastq_ftp}/sra_fastq_ftp.nf (100%)
 create mode 100644 modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test
 rename modules/local/{ => sra_ids_to_runinfo}/sra_ids_to_runinfo.nf (100%)
 create mode 100644 modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test
 create mode 100644 modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test.snap
 rename modules/local/{ => sra_merge_samplesheet}/sra_merge_samplesheet.nf (100%)
 create mode 100644 modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test
 create mode 100644 modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test.snap
 rename modules/local/{ => sra_runinfo_to_ftp}/sra_runinfo_to_ftp.nf (100%)
 create mode 100644 modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test
 create mode 100644 modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test.snap
 rename modules/local/{ => sra_to_samplesheet}/sra_to_samplesheet.nf (100%)
 create mode 100644 modules/local/sra_to_samplesheet/sra_to_samplesheet.nf.test
 rename modules/local/{ => synapse_get}/synapse_get.nf (100%)
 rename modules/local/{ => synapse_list}/synapse_list.nf (100%)
 rename modules/local/{ => synapse_merge_samplesheet}/synapse_merge_samplesheet.nf (100%)
 rename modules/local/{ => synapse_show}/synapse_show.nf (100%)
 rename modules/local/{ => synapse_to_sampleshee}/synapse_to_samplesheet.nf (100%)
 delete mode 100644 tests/config/tags.yml
 delete mode 100644 tests/pipeline/lib/UTILS.groovy
 delete mode 100644 tests/pipeline/sra_skip_fastq.nf.test.snap
 delete mode 100644 tests/pipeline/sra_with_nf_core_pipeline.nf.test
 delete mode 100644 tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
 rename workflows/{sra.nf => sra/main.nf} (87%)
 rename tests/pipeline/sra_skip_fastq.nf.test => workflows/sra/tests/skip_fastq.nf.test (95%)
 create mode 100644 workflows/sra/tests/skip_fastq.nf.test.snap
 rename {tests/pipeline => workflows/sra/tests}/sra.nf.test (92%)
 rename {tests/pipeline => workflows/sra/tests}/sra.nf.test.snap (81%)
 create mode 100644 workflows/sra/tests/with_atacseq_samplesheet.nf.test
 create mode 100644 workflows/sra/tests/with_atacseq_samplesheet.nf.test.snap
 create mode 100644 workflows/sra/tests/with_rnaseq_samplesheet.nf.test
 create mode 100644 workflows/sra/tests/with_rnaseq_samplesheet.nf.test.snap
 create mode 100644 workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test
 create mode 100644 workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test.snap
 rename tests/pipeline/sra_with_sratools.nf.test => workflows/sra/tests/with_sratools.nf.test (91%)
 rename tests/pipeline/sra_with_sratools.nf.test.snap => workflows/sra/tests/with_sratools.nf.test.snap (71%)
 create mode 100644 workflows/sra/tests/with_taxprofiler_samplesheet.nf.test
 create mode 100644 workflows/sra/tests/with_taxprofiler_samplesheet.nf.test.snap
 create mode 100644 workflows/sra/tests/with_viralrecon_samplesheet.nf.test
 create mode 100644 workflows/sra/tests/with_viralrecon_samplesheet.nf.test.snap
 rename workflows/{synapse.nf => synapse/main.nf} (89%)
 rename {tests/pipeline => workflows/synapse/tests}/synapse.test (100%)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d0198cae..0abe1037 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -40,8 +40,19 @@ jobs:
     needs: define_nxf_versions
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
         NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
+        test_tags:
+          - "sra"
+          - "sra_force_sratools_download"
+          - "sra_skip_fastq"
+          - "sra_with_atacseq"
+          - "sra_with_rnaseq"
+          - "sra_with_rnaseq_specific_ena"
+          - "sra_with_taxprofiler"
+          - "sra_with_viralrecon"
+          - "modules_local"
         profile:
           - "docker"
 
@@ -61,7 +72,7 @@ jobs:
 
       - name: Run nf-test
         run: |
-          nf-test test tests/pipeline/ --profile "test,${{ matrix.profile }}" --junitxml=test.xml
+          nf-test test --tag ${{ matrix.test_tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml
 
       - name: Output log on failure
         if: failure()
diff --git a/.nf-core.yml b/.nf-core.yml
index f11657b7..253f86e2 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,7 +1,15 @@
 repository_type: pipeline
 lint:
   files_unchanged:
+    - .github/CONTRIBUTING.md
+    - .github/ISSUE_TEMPLATE/bug_report.yml
+    - assets/nf-core-fetchngs_logo_light.png
     - assets/sendmail_template.txt
     - lib/NfcoreTemplate.groovy
     - .gitattributes
-  actions_ci: False
+  actions_ci: false
+  multiqc_config: false
+  nextflow_config:
+    - "params.validationShowHiddenParams"
+    - "params.validationSchemaIgnoreParams"
+  schema_params: false
diff --git a/conf/test_data.config b/conf/test_data.config
new file mode 100644
index 00000000..31639250
--- /dev/null
+++ b/conf/test_data.config
@@ -0,0 +1,14 @@
+params {
+    // Base directory for test data
+    test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs"
+
+    modules {
+        'local' {
+                multiqc_mappings_config = "${params.test_data_base}/modules/local/multiqc_mappings_config/"
+                sra_merge_samplesheet   = "${params.test_data_base}/modules/local/sra_merge_samplesheet/"
+                sra_to_samplesheet      = "${params.test_data_base}/modules/local/sra_to_samplesheet/"
+                sra_fastq_ftp           = "${params.test_data_base}/modules/local/sra_fastq_ftp/"
+                sra_runinfo_to_ftp      = "${params.test_data_base}/modules/local/sra_runinfo_to_ftp/"
+        }
+    }
+}
diff --git a/lib/NftestUtils.groovy b/lib/NftestUtils.groovy
new file mode 100644
index 00000000..ce6fc8b4
--- /dev/null
+++ b/lib/NftestUtils.groovy
@@ -0,0 +1,38 @@
+// Helper functions for pipeline tests
+
+class NftestUtils {
+
+    // Function to remove Nextflow version from software_versions.yml
+    public static String removeNextflowVersion(outputDir) {
+        def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
+        if (softwareVersions.containsKey("Workflow")) {
+            softwareVersions.Workflow.remove("Nextflow")
+        }
+        return softwareVersions
+    }
+
+    // Function to filter lines from a file and return a new file
+    public static File filterLines(String inFilePath, int linesToSkip) {
+        if (linesToSkip >= 0) {
+            File inputFile = new File(inFilePath)
+            File outputFile = new File(inFilePath + ".filtered")
+            def lineCount = 0
+            inputFile.eachLine { line ->
+                lineCount++
+                if (lineCount > linesToSkip) {
+                    outputFile.append(line + '\n')
+                }
+            }
+            return outputFile
+        } else {
+            File inputFile = new File(inFilePath)
+            File outputFile = new File(inFilePath + ".filtered")
+            def lines = inputFile.readLines()
+            def totalLines = lines.size()
+            lines.take(totalLines + linesToSkip).each { line ->
+                outputFile.append(line + '\n')
+            }
+            return outputFile
+        }
+    }
+}
diff --git a/main.nf b/main.nf
index 6da732be..f856a93c 100644
--- a/main.nf
+++ b/main.nf
@@ -49,9 +49,9 @@ if (WorkflowMain.isSraId(ch_input)) {
 
 if (params.input_type == input_type) {
     if (params.input_type == 'sra') {
-        include { SRA } from './workflows/sra'
+        include { SRA } from './workflows/sra/main'
     } else if (params.input_type == 'synapse') {
-        include { SYNAPSE } from './workflows/synapse'
+        include { SYNAPSE } from './workflows/synapse/main'
     }
 } else {
     exit 1, "Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!"
diff --git a/modules/local/multiqc_mappings_config.nf b/modules/local/multiqc_mappings_config/multiqc_mappings_config.nf
similarity index 100%
rename from modules/local/multiqc_mappings_config.nf
rename to modules/local/multiqc_mappings_config/multiqc_mappings_config.nf
diff --git a/modules/local/multiqc_mappings_config/multiqc_mappings_config.nf.test b/modules/local/multiqc_mappings_config/multiqc_mappings_config.nf.test
new file mode 100644
index 00000000..7a0fe2dd
--- /dev/null
+++ b/modules/local/multiqc_mappings_config/multiqc_mappings_config.nf.test
@@ -0,0 +1,31 @@
+nextflow_process {
+
+    name "Test Process MULTIQC_MAPPINGS_CONFIG"
+    script "modules/local/multiqc_mappings_config.nf"
+    process "MULTIQC_MAPPINGS_CONFIG"
+    tag "multiqc_mappings_config"
+    tag "modules_local"
+
+    test("SRX9626017_SRR13191702") {
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = file("$baseDir/modules/local/tests/input/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv", checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+
+    }
+
+}
diff --git a/modules/local/multiqc_mappings_config/multiqc_mappings_config.nf.test.snap b/modules/local/multiqc_mappings_config/multiqc_mappings_config.nf.test.snap
new file mode 100644
index 00000000..e8914aea
--- /dev/null
+++ b/modules/local/multiqc_mappings_config/multiqc_mappings_config.nf.test.snap
@@ -0,0 +1,27 @@
+{
+    "SRX9626017_SRR13191702": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
+                        "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                ],
+                "versions": [
+                    "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                ],
+                "yml": [
+                    [
+                        "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
+                        "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2023-07-05T15:01:18+0000"
+    }
+}
\ No newline at end of file
diff --git a/modules/local/sra_fastq_ftp.nf b/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf
similarity index 100%
rename from modules/local/sra_fastq_ftp.nf
rename to modules/local/sra_fastq_ftp/sra_fastq_ftp.nf
diff --git a/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test b/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test
new file mode 100644
index 00000000..fb8d53e2
--- /dev/null
+++ b/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test
@@ -0,0 +1,33 @@
+nextflow_process {
+
+    name "Test Process SRA_FASTQ_FTP"
+    script "modules/local/sra_fastq_ftp.nf"
+    process "SRA_FASTQ_FTP"
+    tag "sra_fastq_ftp"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                            [ id:'SRX9626017_SRR13191702', single_end:false ], // meta map
+                            [ SRR13191702 ]
+                        ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+
+    }
+
+}
diff --git a/modules/local/sra_ids_to_runinfo.nf b/modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf
similarity index 100%
rename from modules/local/sra_ids_to_runinfo.nf
rename to modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf
diff --git a/modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test b/modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test
new file mode 100644
index 00000000..36699bb4
--- /dev/null
+++ b/modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test
@@ -0,0 +1,32 @@
+nextflow_process {
+
+    name "Test Process SRA_IDS_TO_RUNINFO"
+    script "modules/local/sra_ids_to_runinfo.nf"
+    process "SRA_IDS_TO_RUNINFO"
+    tag "sra_ids_to_runinfo"
+    tag "modules_local"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = 'SRR9984183'
+                input[1] = ''
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+
+    }
+
+}
diff --git a/modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test.snap b/modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test.snap
new file mode 100644
index 00000000..d4e1e05d
--- /dev/null
+++ b/modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test.snap
@@ -0,0 +1,21 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    "SRR9984183.runinfo.tsv:md5,51cba5fab4d6f0c0386e4397672240b9"
+                ],
+                "1": [
+                    "versions.yml:md5,1c14442e9b494b586eafe41e77300fae"
+                ],
+                "tsv": [
+                    "SRR9984183.runinfo.tsv:md5,51cba5fab4d6f0c0386e4397672240b9"
+                ],
+                "versions": [
+                    "versions.yml:md5,1c14442e9b494b586eafe41e77300fae"
+                ]
+            }
+        ],
+        "timestamp": "2023-07-06T13:16:51+0000"
+    }
+}
\ No newline at end of file
diff --git a/modules/local/sra_merge_samplesheet.nf b/modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf
similarity index 100%
rename from modules/local/sra_merge_samplesheet.nf
rename to modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf
diff --git a/modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test b/modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test
new file mode 100644
index 00000000..00c23f19
--- /dev/null
+++ b/modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test
@@ -0,0 +1,32 @@
+nextflow_process {
+
+    name "Test Process SRA_MERGE_SAMPLESHEET"
+    script "modules/local/sra_merge_samplesheet.nf"
+    process "SRA_MERGE_SAMPLESHEET"
+    tag "sra_merge_samplesheet"
+    tag "modules_local"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = file("$baseDir/modules/local/tests/input/sra_merge_samplesheet/samplesheets/*", checkIfExists: true)
+                input[1] = file("$baseDir/modules/local/tests/input/sra_merge_samplesheet/mappings/*", checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+
+    }
+
+}
diff --git a/modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test.snap b/modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test.snap
new file mode 100644
index 00000000..c5f06aac
--- /dev/null
+++ b/modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test.snap
@@ -0,0 +1,27 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    "samplesheet.csv:md5,ef756557b0735becd2574c2a3f5840b2"
+                ],
+                "1": [
+                    "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253"
+                ],
+                "2": [
+                    "versions.yml:md5,410006679d5e496d8c55e58e78ca6b34"
+                ],
+                "mappings": [
+                    "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253"
+                ],
+                "samplesheet": [
+                    "samplesheet.csv:md5,ef756557b0735becd2574c2a3f5840b2"
+                ],
+                "versions": [
+                    "versions.yml:md5,410006679d5e496d8c55e58e78ca6b34"
+                ]
+            }
+        ],
+        "timestamp": "2023-07-06T13:16:36+0000"
+    }
+}
\ No newline at end of file
diff --git a/modules/local/sra_runinfo_to_ftp.nf b/modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf
similarity index 100%
rename from modules/local/sra_runinfo_to_ftp.nf
rename to modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf
diff --git a/modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test b/modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test
new file mode 100644
index 00000000..14bb829b
--- /dev/null
+++ b/modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test
@@ -0,0 +1,31 @@
+nextflow_process {
+
+    name "Test Process SRA_RUNINFO_TO_FTP"
+    script "modules/local/sra_runinfo_to_ftp.nf"
+    process "SRA_RUNINFO_TO_FTP"
+    tag "sra_runinfo_to_ftp"
+    tag "modules_local"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = file("$baseDir/modules/local/tests/input/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv", checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+
+    }
+
+}
diff --git a/modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test.snap b/modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test.snap
new file mode 100644
index 00000000..03cf80e8
--- /dev/null
+++ b/modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test.snap
@@ -0,0 +1,21 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e"
+                ],
+                "1": [
+                    "versions.yml:md5,e95f8185f665127a73622a19d321bcca"
+                ],
+                "tsv": [
+                    "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e"
+                ],
+                "versions": [
+                    "versions.yml:md5,e95f8185f665127a73622a19d321bcca"
+                ]
+            }
+        ],
+        "timestamp": "2023-07-06T02:05:52+0000"
+    }
+}
\ No newline at end of file
diff --git a/modules/local/sra_to_samplesheet.nf b/modules/local/sra_to_samplesheet/sra_to_samplesheet.nf
similarity index 100%
rename from modules/local/sra_to_samplesheet.nf
rename to modules/local/sra_to_samplesheet/sra_to_samplesheet.nf
diff --git a/modules/local/sra_to_samplesheet/sra_to_samplesheet.nf.test b/modules/local/sra_to_samplesheet/sra_to_samplesheet.nf.test
new file mode 100644
index 00000000..413c6410
--- /dev/null
+++ b/modules/local/sra_to_samplesheet/sra_to_samplesheet.nf.test
@@ -0,0 +1,33 @@
+nextflow_process {
+
+    name "Test Process SRA_TO_SAMPLESHEET"
+    script "modules/local/sra_to_samplesheet.nf"
+    process "SRA_TO_SAMPLESHEET"
+    tag "sra_to_samplesheet"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[1] =
+                input[2] =
+                input[3] =
+                input[4] = file("$baseDir/modules/local/tests/input/sra_to_samplesheet/SRX9626017_SRR13191702.mappings.csv", checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+
+    }
+
+}
diff --git a/modules/local/synapse_get.nf b/modules/local/synapse_get/synapse_get.nf
similarity index 100%
rename from modules/local/synapse_get.nf
rename to modules/local/synapse_get/synapse_get.nf
diff --git a/modules/local/synapse_list.nf b/modules/local/synapse_list/synapse_list.nf
similarity index 100%
rename from modules/local/synapse_list.nf
rename to modules/local/synapse_list/synapse_list.nf
diff --git a/modules/local/synapse_merge_samplesheet.nf b/modules/local/synapse_merge_samplesheet/synapse_merge_samplesheet.nf
similarity index 100%
rename from modules/local/synapse_merge_samplesheet.nf
rename to modules/local/synapse_merge_samplesheet/synapse_merge_samplesheet.nf
diff --git a/modules/local/synapse_show.nf b/modules/local/synapse_show/synapse_show.nf
similarity index 100%
rename from modules/local/synapse_show.nf
rename to modules/local/synapse_show/synapse_show.nf
diff --git a/modules/local/synapse_to_samplesheet.nf b/modules/local/synapse_to_sampleshee/synapse_to_samplesheet.nf
similarity index 100%
rename from modules/local/synapse_to_samplesheet.nf
rename to modules/local/synapse_to_sampleshee/synapse_to_samplesheet.nf
diff --git a/nf-test.config b/nf-test.config
index cd432d43..0799cb40 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -1,12 +1,12 @@
 config {
     // location for all nf-tests
-    testsDir "tests"
+    testsDir "."
 
     // nf-test directory including temporary files for each test
     workDir ".nf-test"
 
     // location of library folder that is added automatically to the classpath
-    libDir "tests/pipeline/lib/"
+    libDir "lib/"
 
     // location of an optional nextflow.config file specific for executing tests
     configFile "nextflow.config"
diff --git a/tests/config/tags.yml b/tests/config/tags.yml
deleted file mode 100644
index 9214c834..00000000
--- a/tests/config/tags.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-default:
-  - bin/**
-  - conf/**
-  - lib/**
-  - modules/**
-  - subworkflows/**
-  - tests/**
-  - workflows/**
-  - nextflow.config
-  - main.nf
-
-sra_ids_to_runinfo:
-  - modules/local/sra_ids_to_runinfo.nf
-  - tests/modules/sra_ids_to_runinfo/**
diff --git a/tests/pipeline/lib/UTILS.groovy b/tests/pipeline/lib/UTILS.groovy
deleted file mode 100644
index 311403cc..00000000
--- a/tests/pipeline/lib/UTILS.groovy
+++ /dev/null
@@ -1,11 +0,0 @@
-// Function to remove Nextflow version from software_versions.yml
-
-class UTILS {
-    public static String removeNextflowVersion(outputDir) {
-        def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
-        if (softwareVersions.containsKey("Workflow")) {
-            softwareVersions.Workflow.remove("Nextflow")
-        }
-        return softwareVersions
-    }
-}
diff --git a/tests/pipeline/sra_skip_fastq.nf.test.snap b/tests/pipeline/sra_skip_fastq.nf.test.snap
deleted file mode 100644
index 4f2efb49..00000000
--- a/tests/pipeline/sra_skip_fastq.nf.test.snap
+++ /dev/null
@@ -1,30 +0,0 @@
-{
-    "metadata": {
-        "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,c5ab92f6f50717b8163580b642b37aec",
-            "DRR028935.runinfo_ftp.tsv:md5,9db5d6cba5ce2cccd9b2cc3faaa092e2",
-            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
-            "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
-            "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
-            "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
-            "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
-            "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
-            "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
-        ],
-        "timestamp": "2023-05-28T15:07:52+0000"
-    },
-    "samplesheet": {
-        "content": [
-            "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
-            "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
-        ],
-        "timestamp": "2023-05-28T15:07:52+0000"
-    },
-    "software_versions": {
-        "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
-        ],
-        "timestamp": "2023-05-28T15:07:52+0000"
-    }
-}
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test b/tests/pipeline/sra_with_nf_core_pipeline.nf.test
deleted file mode 100644
index d0c41baf..00000000
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test
+++ /dev/null
@@ -1,170 +0,0 @@
-nextflow_pipeline {
-
-    name "Test Workflow main.nf"
-    script "main.nf"
-    tag "sra_nf-core"
-    tag "pipeline"
-
-    test("SRA NF-CORE/RNASEQ Samplesheet") {
-
-        when {
-            params {
-                outdir           = "$outputDir"
-                nf_core_pipeline = "rnaseq"
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("rnaseq_software_versions") },
-                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
-                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("rnaseq_metadata") },
-                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
-                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
-                                path("$outputDir/samplesheet/multiqc_config.yml")).match("rnaseq_samplesheet") },
-                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
-            )
-        }
-    }
-
-    test("SRA NF-CORE/RNASEQ Samplesheet With Specific ENA metadata") {
-
-        when {
-            params {
-                outdir                = "$outputDir"
-                nf_core_pipeline      = "rnaseq"
-                ena_metadata_fields   = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5"
-                sample_mapping_fields = "run_accession,library_layout"
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("rnaseq_ena_software_versions") },
-                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
-                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("rnaseq_ena_metadata") },
-                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
-                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
-                                path("$outputDir/samplesheet/multiqc_config.yml")).match("rnaseq_ena_samplesheet") },
-                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
-            )
-        }
-    }
-
-    test("SRA NF-CORE/ATACSEQ Samplesheet") {
-
-        when {
-            params {
-                outdir           = "$outputDir"
-                nf_core_pipeline = "atacseq"
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("atacseq_software_versions") },
-                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
-                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("atacseq_metadata") },
-                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
-                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
-                                path("$outputDir/samplesheet/multiqc_config.yml")).match("atacseq_samplesheet") },
-                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
-            )
-        }
-    }
-
-    test("SRA NF-CORE/VIRALRECON Samplesheet") {
-
-        when {
-            params {
-                outdir           = "$outputDir"
-                nf_core_pipeline = "viralrecon"
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("viralrecon_software_versions") },
-                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
-                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("viralrecon_metadata") },
-                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
-                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
-                                path("$outputDir/samplesheet/multiqc_config.yml")).match("viralrecon_samplesheet") },
-                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
-            )
-        }
-    }
-
-    test("SRA NF-CORE/TAXPROFILER Samplesheet") {
-
-        when {
-            params {
-                outdir           = "$outputDir"
-                nf_core_pipeline = "taxprofiler"
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("taxprofiler_software_versions") },
-                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
-                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("taxprofiler_metadata") },
-                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
-                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
-                                path("$outputDir/samplesheet/multiqc_config.yml")).match("taxprofiler_samplesheet") },
-                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
-            )
-        }
-    }
-
-}
diff --git a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap b/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
deleted file mode 100644
index ea9e25d8..00000000
--- a/tests/pipeline/sra_with_nf_core_pipeline.nf.test.snap
+++ /dev/null
@@ -1,192 +0,0 @@
-{
-    "taxprofiler_metadata": {
-        "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,c5ab92f6f50717b8163580b642b37aec",
-            "DRR028935.runinfo_ftp.tsv:md5,9db5d6cba5ce2cccd9b2cc3faaa092e2",
-            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
-            "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
-            "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
-            "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
-            "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
-            "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
-            "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
-        ],
-        "timestamp": "2023-05-28T15:19:39+0000"
-    },
-    "viralrecon_metadata": {
-        "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,c5ab92f6f50717b8163580b642b37aec",
-            "DRR028935.runinfo_ftp.tsv:md5,9db5d6cba5ce2cccd9b2cc3faaa092e2",
-            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
-            "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
-            "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
-            "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
-            "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
-            "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
-            "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
-        ],
-        "timestamp": "2023-05-28T15:19:39+0000"
-    },
-    "rnaseq_software_versions": {
-        "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
-        ],
-        "timestamp": "2023-05-28T15:19:39+0000"
-    },
-    "rnaseq_ena_software_versions": {
-        "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
-        ],
-        "timestamp": "2023-05-28T15:19:39+0000"
-    },
-    "viralrecon_samplesheet": {
-        "content": [
-            "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
-            "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
-        ],
-        "timestamp": "2023-05-28T15:19:39+0000"
-    },
-    "viralrecon_software_versions": {
-        "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
-        ],
-        "timestamp": "2023-05-28T15:19:39+0000"
-    },
-    "taxprofiler_software_versions": {
-        "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
-        ],
-        "timestamp": "2023-05-28T15:19:39+0000"
-    },
-    "atacseq_metadata": {
-        "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,c5ab92f6f50717b8163580b642b37aec",
-            "DRR028935.runinfo_ftp.tsv:md5,9db5d6cba5ce2cccd9b2cc3faaa092e2",
-            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
-            "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
-            "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
-            "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
-            "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
-            "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
-            "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
-        ],
-        "timestamp": "2023-05-28T15:19:39+0000"
-    },
-    "rnaseq_ena_metadata": {
-        "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,74a5f7058f27a565ce59db481355ca54",
-            "DRR028935.runinfo_ftp.tsv:md5,07a98fdcec207686a4ea2c9a3997edf3",
-            "ERR1109373.runinfo_ftp.tsv:md5,868897310855c50b1d5fc77d1195a1f9",
-            "ERR1160846.runinfo_ftp.tsv:md5,146d7f2ec778b32b7da7ad040e554114",
-            "GSE214215.runinfo_ftp.tsv:md5,adf62affe371dc9bad8e271450bdc2fe",
-            "SRR12848126.runinfo_ftp.tsv:md5,cf8827612a76645824e83418d7d76cbf",
-            "SRR13191702.runinfo_ftp.tsv:md5,2031ca9b7ab736dbde37d05b10cdb0ad",
-            "SRR14593545.runinfo_ftp.tsv:md5,3a1ac14d71744224a61ab542f869e180",
-            "SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1",
-            "SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236"
-        ],
-        "timestamp": "2023-05-28T15:19:39+0000"
-    },
-    "rnaseq_samplesheet": {
-        "content": [
-            "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
-            "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
-        ],
-        "timestamp": "2023-05-28T15:19:39+0000"
-    },
-    "rnaseq_metadata": {
-        "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,c5ab92f6f50717b8163580b642b37aec",
-            "DRR028935.runinfo_ftp.tsv:md5,9db5d6cba5ce2cccd9b2cc3faaa092e2",
-            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
-            "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
-            "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
-            "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
-            "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
-            "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
-            "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
-        ],
-        "timestamp": "2023-05-28T15:19:39+0000"
-    },
-    "atacseq_samplesheet": {
-        "content": [
-            "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
-            "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
-        ],
-        "timestamp": "2023-05-28T15:19:39+0000"
-    },
-    "rnaseq_ena_samplesheet": {
-        "content": [
-            "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f",
-            "multiqc_config.yml:md5,6f6189ee58855de81eaf82ad86e21040"
-        ],
-        "timestamp": "2023-05-28T15:19:39+0000"
-    },
-    "taxprofiler_samplesheet": {
-        "content": [
-            "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
-            "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
-        ],
-        "timestamp": "2023-05-28T15:19:39+0000"
-    },
-    "atacseq_software_versions": {
-        "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
-        ],
-        "timestamp": "2023-05-28T15:19:39+0000"
-    },
-    "fastq": {
-        "content": [
-            "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791",
-            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
-            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30",
-            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
-            "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6",
-            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
-            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
-            "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
-            "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64",
-            "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83",
-            "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544",
-            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
-            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
-            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
-            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962",
-            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
-            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76",
-            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
-            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88",
-            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
-            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04",
-            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98",
-            [
-                "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d",
-                "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9",
-                "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f",
-                "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86",
-                "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499",
-                "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff",
-                "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75",
-                "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85",
-                "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4",
-                "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc",
-                "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0",
-                "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368",
-                "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8",
-                "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f",
-                "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3",
-                "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8",
-                "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882",
-                "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
-                "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
-            ]
-        ],
-        "timestamp": "2023-05-28T15:19:39+0000"
-    }
-}
\ No newline at end of file
diff --git a/workflows/sra.nf b/workflows/sra/main.nf
similarity index 87%
rename from workflows/sra.nf
rename to workflows/sra/main.nf
index 44ff8346..05b9a80d 100644
--- a/workflows/sra.nf
+++ b/workflows/sra/main.nf
@@ -19,12 +19,12 @@ WorkflowSra.initialise(params, valid_params)
 ========================================================================================
 */
 
-include { SRA_IDS_TO_RUNINFO      } from '../modules/local/sra_ids_to_runinfo'
-include { SRA_RUNINFO_TO_FTP      } from '../modules/local/sra_runinfo_to_ftp'
-include { SRA_FASTQ_FTP           } from '../modules/local/sra_fastq_ftp'
-include { SRA_TO_SAMPLESHEET      } from '../modules/local/sra_to_samplesheet'
-include { SRA_MERGE_SAMPLESHEET   } from '../modules/local/sra_merge_samplesheet'
-include { MULTIQC_MAPPINGS_CONFIG } from '../modules/local/multiqc_mappings_config'
+include { SRA_IDS_TO_RUNINFO      } from '../../modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo'
+include { SRA_RUNINFO_TO_FTP      } from '../../modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp'
+include { SRA_FASTQ_FTP           } from '../../modules/local/sra_fastq_ftp/sra_fastq_ftp'
+include { SRA_TO_SAMPLESHEET      } from '../../modules/local/sra_to_samplesheet/sra_to_samplesheet'
+include { SRA_MERGE_SAMPLESHEET   } from '../../modules/local/sra_merge_samplesheet/sra_merge_samplesheet'
+include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_config/multiqc_mappings_config'
 
 /*
 ========================================================================================
@@ -32,9 +32,9 @@ include { MULTIQC_MAPPINGS_CONFIG } from '../modules/local/multiqc_mappings_conf
 ========================================================================================
 */
 
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
+include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions/main'
 
-include { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS } from '../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main'
+include { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS } from '../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main'
 
 /*
 ========================================================================================
diff --git a/tests/pipeline/sra_skip_fastq.nf.test b/workflows/sra/tests/skip_fastq.nf.test
similarity index 95%
rename from tests/pipeline/sra_skip_fastq.nf.test
rename to workflows/sra/tests/skip_fastq.nf.test
index b0237a81..38814a77 100644
--- a/tests/pipeline/sra_skip_fastq.nf.test
+++ b/workflows/sra/tests/skip_fastq.nf.test
@@ -3,7 +3,7 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "main.nf"
     tag "sra_skip_fastq"
-    tag "pipeline"
+    tag "workflow"
 
     test("SRA Skip FASTQ") {
 
@@ -17,7 +17,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
+                { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") },
                 { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
                                 path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
                                 path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
diff --git a/workflows/sra/tests/skip_fastq.nf.test.snap b/workflows/sra/tests/skip_fastq.nf.test.snap
new file mode 100644
index 00000000..6d3201e8
--- /dev/null
+++ b/workflows/sra/tests/skip_fastq.nf.test.snap
@@ -0,0 +1,30 @@
+{
+    "metadata": {
+        "content": [
+            "DRR026872.runinfo_ftp.tsv:md5,ef90876b2cbcb3721251b4cdef8cc47b",
+            "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
+            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
+            "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
+            "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
+            "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
+            "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
+            "SRR14593545.runinfo_ftp.tsv:md5,888eaa19fd0b7fea4dc3e9800c1d26f2",
+            "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
+            "SRR9984183.runinfo_ftp.tsv:md5,911a48308f76387b97842d35abc43c8f"
+        ],
+        "timestamp": "2023-07-06T14:02:03+0000"
+    },
+    "samplesheet": {
+        "content": [
+            "id_mappings.csv:md5,aa5eab8068e59a3866fd6d1fa8fe1b5a",
+            "multiqc_config.yml:md5,1337fdab76cbca9b78dbf06d7344a3b8"
+        ],
+        "timestamp": "2023-07-06T14:02:03+0000"
+    },
+    "software_versions": {
+        "content": [
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
+        ],
+        "timestamp": "2023-07-06T14:02:03+0000"
+    }
+}
\ No newline at end of file
diff --git a/tests/pipeline/sra.nf.test b/workflows/sra/tests/sra.nf.test
similarity index 92%
rename from tests/pipeline/sra.nf.test
rename to workflows/sra/tests/sra.nf.test
index f545d93d..16074b64 100644
--- a/tests/pipeline/sra.nf.test
+++ b/workflows/sra/tests/sra.nf.test
@@ -3,7 +3,7 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "main.nf"
     tag "sra"
-    tag "pipeline"
+    tag "workflow"
 
     test("SRA FASTQ & Metadata") {
 
@@ -16,7 +16,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
+                { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
                                 path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
diff --git a/tests/pipeline/sra.nf.test.snap b/workflows/sra/tests/sra.nf.test.snap
similarity index 81%
rename from tests/pipeline/sra.nf.test.snap
rename to workflows/sra/tests/sra.nf.test.snap
index 02cf5541..a4276e94 100644
--- a/tests/pipeline/sra.nf.test.snap
+++ b/workflows/sra/tests/sra.nf.test.snap
@@ -1,31 +1,31 @@
 {
     "metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,c5ab92f6f50717b8163580b642b37aec",
-            "DRR028935.runinfo_ftp.tsv:md5,9db5d6cba5ce2cccd9b2cc3faaa092e2",
+            "DRR026872.runinfo_ftp.tsv:md5,ef90876b2cbcb3721251b4cdef8cc47b",
+            "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
-            "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
-            "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
-            "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
-            "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
-            "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
-            "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
+            "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
+            "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
+            "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
+            "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
+            "SRR14593545.runinfo_ftp.tsv:md5,888eaa19fd0b7fea4dc3e9800c1d26f2",
+            "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
+            "SRR9984183.runinfo_ftp.tsv:md5,911a48308f76387b97842d35abc43c8f"
         ],
-        "timestamp": "2023-05-28T15:25:33+0000"
+        "timestamp": "2023-07-06T14:10:16+0000"
     },
     "samplesheet": {
         "content": [
-            "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
-            "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
+            "id_mappings.csv:md5,aa5eab8068e59a3866fd6d1fa8fe1b5a",
+            "multiqc_config.yml:md5,1337fdab76cbca9b78dbf06d7344a3b8"
         ],
-        "timestamp": "2023-05-28T15:25:33+0000"
+        "timestamp": "2023-07-06T14:10:16+0000"
     },
     "software_versions": {
         "content": [
             "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
-        "timestamp": "2023-05-28T15:25:33+0000"
+        "timestamp": "2023-07-06T14:10:16+0000"
     },
     "fastq": {
         "content": [
@@ -75,6 +75,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-05-28T15:25:33+0000"
+        "timestamp": "2023-07-06T14:10:16+0000"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/with_atacseq_samplesheet.nf.test b/workflows/sra/tests/with_atacseq_samplesheet.nf.test
new file mode 100644
index 00000000..4ebc9352
--- /dev/null
+++ b/workflows/sra/tests/with_atacseq_samplesheet.nf.test
@@ -0,0 +1,39 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    tag "sra_with_atacseq"
+    tag "workflow"
+
+    test("SRA NF-CORE/ATACSEQ Samplesheet") {
+
+        when {
+            params {
+                outdir           = "$outputDir"
+                nf_core_pipeline = "atacseq"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") },
+                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
+                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") },
+                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
+                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
+                                path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
+                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
+            )
+        }
+    }
+}
diff --git a/workflows/sra/tests/with_atacseq_samplesheet.nf.test.snap b/workflows/sra/tests/with_atacseq_samplesheet.nf.test.snap
new file mode 100644
index 00000000..e49f6010
--- /dev/null
+++ b/workflows/sra/tests/with_atacseq_samplesheet.nf.test.snap
@@ -0,0 +1,80 @@
+{
+    "metadata": {
+        "content": [
+            "DRR026872.runinfo_ftp.tsv:md5,ef90876b2cbcb3721251b4cdef8cc47b",
+            "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
+            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
+            "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
+            "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
+            "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
+            "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
+            "SRR14593545.runinfo_ftp.tsv:md5,888eaa19fd0b7fea4dc3e9800c1d26f2",
+            "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
+            "SRR9984183.runinfo_ftp.tsv:md5,911a48308f76387b97842d35abc43c8f"
+        ],
+        "timestamp": "2023-07-06T14:03:45+0000"
+    },
+    "samplesheet": {
+        "content": [
+            "id_mappings.csv:md5,aa5eab8068e59a3866fd6d1fa8fe1b5a",
+            "multiqc_config.yml:md5,1337fdab76cbca9b78dbf06d7344a3b8"
+        ],
+        "timestamp": "2023-07-06T14:03:45+0000"
+    },
+    "software_versions": {
+        "content": [
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
+        ],
+        "timestamp": "2023-07-06T14:03:45+0000"
+    },
+    "fastq": {
+        "content": [
+            "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791",
+            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
+            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30",
+            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
+            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
+            "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6",
+            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
+            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
+            "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
+            "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64",
+            "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83",
+            "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544",
+            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
+            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
+            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
+            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962",
+            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
+            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76",
+            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
+            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88",
+            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
+            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04",
+            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98",
+            [
+                "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d",
+                "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9",
+                "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f",
+                "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86",
+                "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499",
+                "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff",
+                "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75",
+                "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85",
+                "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4",
+                "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc",
+                "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0",
+                "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368",
+                "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8",
+                "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f",
+                "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3",
+                "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8",
+                "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882",
+                "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
+                "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
+            ]
+        ],
+        "timestamp": "2023-07-06T14:03:45+0000"
+    }
+}
\ No newline at end of file
diff --git a/workflows/sra/tests/with_rnaseq_samplesheet.nf.test b/workflows/sra/tests/with_rnaseq_samplesheet.nf.test
new file mode 100644
index 00000000..ca77778c
--- /dev/null
+++ b/workflows/sra/tests/with_rnaseq_samplesheet.nf.test
@@ -0,0 +1,39 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    tag "sra_with_rnaseq"
+    tag "workflow"
+
+    test("SRA NF-CORE/RNASEQ Samplesheet") {
+
+        when {
+            params {
+                outdir           = "$outputDir"
+                nf_core_pipeline = "rnaseq"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") },
+                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
+                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") },
+                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
+                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
+                                path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
+                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
+            )
+        }
+    }
+}
diff --git a/workflows/sra/tests/with_rnaseq_samplesheet.nf.test.snap b/workflows/sra/tests/with_rnaseq_samplesheet.nf.test.snap
new file mode 100644
index 00000000..1efae9c1
--- /dev/null
+++ b/workflows/sra/tests/with_rnaseq_samplesheet.nf.test.snap
@@ -0,0 +1,80 @@
+{
+    "metadata": {
+        "content": [
+            "DRR026872.runinfo_ftp.tsv:md5,ef90876b2cbcb3721251b4cdef8cc47b",
+            "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
+            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
+            "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
+            "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
+            "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
+            "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
+            "SRR14593545.runinfo_ftp.tsv:md5,888eaa19fd0b7fea4dc3e9800c1d26f2",
+            "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
+            "SRR9984183.runinfo_ftp.tsv:md5,911a48308f76387b97842d35abc43c8f"
+        ],
+        "timestamp": "2023-07-06T14:12:03+0000"
+    },
+    "samplesheet": {
+        "content": [
+            "id_mappings.csv:md5,aa5eab8068e59a3866fd6d1fa8fe1b5a",
+            "multiqc_config.yml:md5,1337fdab76cbca9b78dbf06d7344a3b8"
+        ],
+        "timestamp": "2023-07-06T14:12:03+0000"
+    },
+    "software_versions": {
+        "content": [
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
+        ],
+        "timestamp": "2023-07-06T14:12:03+0000"
+    },
+    "fastq": {
+        "content": [
+            "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791",
+            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
+            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30",
+            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
+            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
+            "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6",
+            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
+            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
+            "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
+            "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64",
+            "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83",
+            "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544",
+            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
+            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
+            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
+            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962",
+            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
+            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76",
+            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
+            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88",
+            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
+            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04",
+            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98",
+            [
+                "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d",
+                "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9",
+                "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f",
+                "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86",
+                "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499",
+                "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff",
+                "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75",
+                "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85",
+                "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4",
+                "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc",
+                "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0",
+                "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368",
+                "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8",
+                "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f",
+                "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3",
+                "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8",
+                "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882",
+                "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
+                "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
+            ]
+        ],
+        "timestamp": "2023-07-06T14:12:03+0000"
+    }
+}
\ No newline at end of file
diff --git a/workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test b/workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test
new file mode 100644
index 00000000..2fc12241
--- /dev/null
+++ b/workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test
@@ -0,0 +1,41 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    tag "sra_with_rnaseq_specific_ena"
+    tag "workflow"
+
+    test("SRA NF-CORE/RNASEQ Samplesheet With Specific ENA metadata") {
+
+        when {
+            params {
+                outdir                = "$outputDir"
+                nf_core_pipeline      = "rnaseq"
+                ena_metadata_fields   = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5"
+                sample_mapping_fields = "run_accession,library_layout"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") },
+                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
+                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") },
+                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
+                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
+                                path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
+                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
+            )
+        }
+    }
+}
diff --git a/workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test.snap b/workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test.snap
new file mode 100644
index 00000000..bfa3c9cd
--- /dev/null
+++ b/workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test.snap
@@ -0,0 +1,80 @@
+{
+    "metadata": {
+        "content": [
+            "DRR026872.runinfo_ftp.tsv:md5,74a5f7058f27a565ce59db481355ca54",
+            "DRR028935.runinfo_ftp.tsv:md5,07a98fdcec207686a4ea2c9a3997edf3",
+            "ERR1109373.runinfo_ftp.tsv:md5,868897310855c50b1d5fc77d1195a1f9",
+            "ERR1160846.runinfo_ftp.tsv:md5,146d7f2ec778b32b7da7ad040e554114",
+            "GSE214215.runinfo_ftp.tsv:md5,adf62affe371dc9bad8e271450bdc2fe",
+            "SRR12848126.runinfo_ftp.tsv:md5,cf8827612a76645824e83418d7d76cbf",
+            "SRR13191702.runinfo_ftp.tsv:md5,2031ca9b7ab736dbde37d05b10cdb0ad",
+            "SRR14593545.runinfo_ftp.tsv:md5,3a1ac14d71744224a61ab542f869e180",
+            "SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1",
+            "SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236"
+        ],
+        "timestamp": "2023-07-03T23:38:27+0000"
+    },
+    "samplesheet": {
+        "content": [
+            "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f",
+            "multiqc_config.yml:md5,6f6189ee58855de81eaf82ad86e21040"
+        ],
+        "timestamp": "2023-07-03T23:38:27+0000"
+    },
+    "software_versions": {
+        "content": [
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
+        ],
+        "timestamp": "2023-07-03T23:38:27+0000"
+    },
+    "fastq": {
+        "content": [
+            "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791",
+            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
+            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30",
+            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
+            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
+            "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6",
+            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
+            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
+            "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
+            "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64",
+            "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83",
+            "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544",
+            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
+            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
+            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
+            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962",
+            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
+            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76",
+            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
+            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88",
+            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
+            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04",
+            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98",
+            [
+                "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d",
+                "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9",
+                "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f",
+                "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86",
+                "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499",
+                "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff",
+                "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75",
+                "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85",
+                "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4",
+                "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc",
+                "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0",
+                "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368",
+                "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8",
+                "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f",
+                "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3",
+                "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8",
+                "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882",
+                "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
+                "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
+            ]
+        ],
+        "timestamp": "2023-07-03T23:38:27+0000"
+    }
+}
\ No newline at end of file
diff --git a/tests/pipeline/sra_with_sratools.nf.test b/workflows/sra/tests/with_sratools.nf.test
similarity index 91%
rename from tests/pipeline/sra_with_sratools.nf.test
rename to workflows/sra/tests/with_sratools.nf.test
index 2fd06ba8..839e3089 100644
--- a/tests/pipeline/sra_with_sratools.nf.test
+++ b/workflows/sra/tests/with_sratools.nf.test
@@ -2,8 +2,8 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
-    tag "sratools_force"
-    tag "pipeline"
+    tag "sra_force_sratools_download"
+    tag "workflow"
 
     test("Force SRA-Tools Download") {
 
@@ -17,7 +17,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
+                { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
                 { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
                                 path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
diff --git a/tests/pipeline/sra_with_sratools.nf.test.snap b/workflows/sra/tests/with_sratools.nf.test.snap
similarity index 71%
rename from tests/pipeline/sra_with_sratools.nf.test.snap
rename to workflows/sra/tests/with_sratools.nf.test.snap
index 285b9ce1..7d6d007a 100644
--- a/tests/pipeline/sra_with_sratools.nf.test.snap
+++ b/workflows/sra/tests/with_sratools.nf.test.snap
@@ -1,31 +1,31 @@
 {
     "metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,c5ab92f6f50717b8163580b642b37aec",
-            "DRR028935.runinfo_ftp.tsv:md5,9db5d6cba5ce2cccd9b2cc3faaa092e2",
+            "DRR026872.runinfo_ftp.tsv:md5,ef90876b2cbcb3721251b4cdef8cc47b",
+            "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
-            "ERR1160846.runinfo_ftp.tsv:md5,5611622d583e6bc6d45d8f934696ff1e",
-            "GSE214215.runinfo_ftp.tsv:md5,4224b5733b92daa40689538de9498ab9",
-            "SRR12848126.runinfo_ftp.tsv:md5,9563f91d4cc6aa58d2ed5fba2eb30baf",
-            "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e",
-            "SRR14593545.runinfo_ftp.tsv:md5,302271a4a1d99865362d0228e6439580",
-            "SRR14709033.runinfo_ftp.tsv:md5,e059c4a0dfdddd70c1998a1ea9c1e65f",
-            "SRR9984183.runinfo_ftp.tsv:md5,1e299191d23e0f3bd0aabf98c9d8133e"
+            "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
+            "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
+            "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
+            "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
+            "SRR14593545.runinfo_ftp.tsv:md5,888eaa19fd0b7fea4dc3e9800c1d26f2",
+            "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
+            "SRR9984183.runinfo_ftp.tsv:md5,911a48308f76387b97842d35abc43c8f"
         ],
-        "timestamp": "2023-05-28T15:07:23+0000"
+        "timestamp": "2023-07-06T14:08:40+0000"
     },
     "samplesheet": {
         "content": [
-            "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253",
-            "multiqc_config.yml:md5,a24e0e280fa03b95bb678c17e4c36d93"
+            "id_mappings.csv:md5,aa5eab8068e59a3866fd6d1fa8fe1b5a",
+            "multiqc_config.yml:md5,1337fdab76cbca9b78dbf06d7344a3b8"
         ],
-        "timestamp": "2023-05-28T15:07:23+0000"
+        "timestamp": "2023-07-06T14:08:40+0000"
     },
     "software_versions": {
         "content": [
             "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
-        "timestamp": "2023-05-28T15:07:23+0000"
+        "timestamp": "2023-07-06T14:08:40+0000"
     },
     "fastq": {
         "content": [
@@ -54,6 +54,6 @@
             "SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7",
             "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af"
         ],
-        "timestamp": "2023-05-28T15:07:23+0000"
+        "timestamp": "2023-07-06T14:08:40+0000"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test b/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test
new file mode 100644
index 00000000..7ffbca59
--- /dev/null
+++ b/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test
@@ -0,0 +1,40 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    tag "sra_with_taxprofiler"
+    tag "workflow"
+
+    test("SRA NF-CORE/TAXPROFILER Samplesheet") {
+
+        when {
+            params {
+                outdir           = "$outputDir"
+                nf_core_pipeline = "taxprofiler"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") },
+                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
+                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") },
+                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
+                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
+                                path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
+                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
+            )
+        }
+    }
+
+}
diff --git a/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test.snap b/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test.snap
new file mode 100644
index 00000000..1e10d64b
--- /dev/null
+++ b/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test.snap
@@ -0,0 +1,80 @@
+{
+    "metadata": {
+        "content": [
+            "DRR026872.runinfo_ftp.tsv:md5,ef90876b2cbcb3721251b4cdef8cc47b",
+            "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
+            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
+            "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
+            "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
+            "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
+            "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
+            "SRR14593545.runinfo_ftp.tsv:md5,888eaa19fd0b7fea4dc3e9800c1d26f2",
+            "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
+            "SRR9984183.runinfo_ftp.tsv:md5,911a48308f76387b97842d35abc43c8f"
+        ],
+        "timestamp": "2023-07-06T14:05:23+0000"
+    },
+    "samplesheet": {
+        "content": [
+            "id_mappings.csv:md5,aa5eab8068e59a3866fd6d1fa8fe1b5a",
+            "multiqc_config.yml:md5,1337fdab76cbca9b78dbf06d7344a3b8"
+        ],
+        "timestamp": "2023-07-06T14:05:23+0000"
+    },
+    "software_versions": {
+        "content": [
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
+        ],
+        "timestamp": "2023-07-06T14:05:23+0000"
+    },
+    "fastq": {
+        "content": [
+            "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791",
+            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
+            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30",
+            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
+            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
+            "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6",
+            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
+            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
+            "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
+            "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64",
+            "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83",
+            "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544",
+            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
+            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
+            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
+            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962",
+            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
+            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76",
+            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
+            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88",
+            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
+            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04",
+            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98",
+            [
+                "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d",
+                "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9",
+                "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f",
+                "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86",
+                "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499",
+                "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff",
+                "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75",
+                "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85",
+                "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4",
+                "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc",
+                "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0",
+                "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368",
+                "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8",
+                "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f",
+                "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3",
+                "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8",
+                "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882",
+                "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
+                "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
+            ]
+        ],
+        "timestamp": "2023-07-06T14:05:23+0000"
+    }
+}
\ No newline at end of file
diff --git a/workflows/sra/tests/with_viralrecon_samplesheet.nf.test b/workflows/sra/tests/with_viralrecon_samplesheet.nf.test
new file mode 100644
index 00000000..e10e2db8
--- /dev/null
+++ b/workflows/sra/tests/with_viralrecon_samplesheet.nf.test
@@ -0,0 +1,39 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    tag "sra_with_viralrecon"
+    tag "workflow"
+
+    test("SRA NF-CORE/VIRALRECON Samplesheet") {
+
+        when {
+            params {
+                outdir           = "$outputDir"
+                nf_core_pipeline = "viralrecon"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") },
+                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
+                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
+                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") },
+                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
+                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
+                                path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
+                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
+            )
+        }
+    }
+}
diff --git a/workflows/sra/tests/with_viralrecon_samplesheet.nf.test.snap b/workflows/sra/tests/with_viralrecon_samplesheet.nf.test.snap
new file mode 100644
index 00000000..34e8a234
--- /dev/null
+++ b/workflows/sra/tests/with_viralrecon_samplesheet.nf.test.snap
@@ -0,0 +1,80 @@
+{
+    "metadata": {
+        "content": [
+            "DRR026872.runinfo_ftp.tsv:md5,ef90876b2cbcb3721251b4cdef8cc47b",
+            "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
+            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
+            "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
+            "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
+            "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
+            "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
+            "SRR14593545.runinfo_ftp.tsv:md5,888eaa19fd0b7fea4dc3e9800c1d26f2",
+            "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
+            "SRR9984183.runinfo_ftp.tsv:md5,911a48308f76387b97842d35abc43c8f"
+        ],
+        "timestamp": "2023-07-06T13:44:03+0000"
+    },
+    "samplesheet": {
+        "content": [
+            "id_mappings.csv:md5,aa5eab8068e59a3866fd6d1fa8fe1b5a",
+            "multiqc_config.yml:md5,1337fdab76cbca9b78dbf06d7344a3b8"
+        ],
+        "timestamp": "2023-07-06T13:44:03+0000"
+    },
+    "software_versions": {
+        "content": [
+            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
+        ],
+        "timestamp": "2023-07-06T13:44:03+0000"
+    },
+    "fastq": {
+        "content": [
+            "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791",
+            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
+            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30",
+            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
+            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
+            "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6",
+            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
+            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
+            "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
+            "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64",
+            "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83",
+            "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544",
+            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
+            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
+            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
+            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962",
+            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
+            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76",
+            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
+            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88",
+            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
+            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04",
+            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98",
+            [
+                "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d",
+                "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9",
+                "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f",
+                "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86",
+                "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499",
+                "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff",
+                "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75",
+                "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85",
+                "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4",
+                "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc",
+                "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0",
+                "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368",
+                "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8",
+                "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f",
+                "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3",
+                "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8",
+                "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882",
+                "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
+                "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
+            ]
+        ],
+        "timestamp": "2023-07-06T13:44:03+0000"
+    }
+}
\ No newline at end of file
diff --git a/workflows/synapse.nf b/workflows/synapse/main.nf
similarity index 89%
rename from workflows/synapse.nf
rename to workflows/synapse/main.nf
index f2138a60..7d871659 100644
--- a/workflows/synapse.nf
+++ b/workflows/synapse/main.nf
@@ -19,11 +19,11 @@ if (params.synapse_config) {
 ========================================================================================
 */
 
-include { SYNAPSE_LIST              } from '../modules/local/synapse_list'
-include { SYNAPSE_SHOW              } from '../modules/local/synapse_show'
-include { SYNAPSE_GET               } from '../modules/local/synapse_get'
-include { SYNAPSE_TO_SAMPLESHEET    } from '../modules/local/synapse_to_samplesheet'
-include { SYNAPSE_MERGE_SAMPLESHEET } from '../modules/local/synapse_merge_samplesheet'
+include { SYNAPSE_LIST              } from '../../modules/local/synapse_list'
+include { SYNAPSE_SHOW              } from '../../modules/local/synapse_show'
+include { SYNAPSE_GET               } from '../../modules/local/synapse_get'
+include { SYNAPSE_TO_SAMPLESHEET    } from '../../modules/local/synapse_to_samplesheet'
+include { SYNAPSE_MERGE_SAMPLESHEET } from '../../modules/local/synapse_merge_samplesheet'
 
 /*
 ========================================================================================
@@ -31,7 +31,7 @@ include { SYNAPSE_MERGE_SAMPLESHEET } from '../modules/local/synapse_merge_sampl
 ========================================================================================
 */
 
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
+include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions/main'
 
 /*
 ========================================================================================
diff --git a/tests/pipeline/synapse.test b/workflows/synapse/tests/synapse.test
similarity index 100%
rename from tests/pipeline/synapse.test
rename to workflows/synapse/tests/synapse.test

From 65fc8d2d4ec98ed1635ed604f87c983bcb692bb6 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Wed, 19 Jul 2023 08:28:15 -0400
Subject: [PATCH 371/852] include test_data config to point to
 nf-core/test-datasets

---
 conf/test.config                                  |  3 +++
 conf/test_data.config                             | 15 ++++++++-------
 .../multiqc_mappings_config.nf.test               |  4 ++--
 modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test |  3 ++-
 .../sra_merge_samplesheet.nf.test                 |  6 +++---
 .../sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test |  4 ++--
 .../sra_to_samplesheet/sra_to_samplesheet.nf.test |  5 +++--
 7 files changed, 23 insertions(+), 17 deletions(-)

diff --git a/conf/test.config b/conf/test.config
index 3c58e9cf..0bc98595 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -22,3 +22,6 @@ params {
     // Input data
     input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv'
 }
+
+// Load test_data.config for nf-tests
+includeConfig 'test_data.config'
diff --git a/conf/test_data.config b/conf/test_data.config
index 31639250..16acdabf 100644
--- a/conf/test_data.config
+++ b/conf/test_data.config
@@ -2,13 +2,14 @@ params {
     // Base directory for test data
     test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs"
 
-    modules {
-        'local' {
-                multiqc_mappings_config = "${params.test_data_base}/modules/local/multiqc_mappings_config/"
-                sra_merge_samplesheet   = "${params.test_data_base}/modules/local/sra_merge_samplesheet/"
-                sra_to_samplesheet      = "${params.test_data_base}/modules/local/sra_to_samplesheet/"
-                sra_fastq_ftp           = "${params.test_data_base}/modules/local/sra_fastq_ftp/"
-                sra_runinfo_to_ftp      = "${params.test_data_base}/modules/local/sra_runinfo_to_ftp/"
+    test_data {
+        'modules_local' {
+                multiqc_mappings_config             = "${params.test_data_base}/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv"
+                sra_merge_samplesheet_samplesheets  = "${params.test_data_base}/modules/local/sra_merge_samplesheet/samplesheets/"
+                sra_merge_samplesheet_mappings      = "${params.test_data_base}/modules/local/sra_merge_samplesheet/mappings/"
+                sra_to_samplesheet                  = "${params.test_data_base}/modules/local/sra_to_samplesheet/SRX9626017_SRR13191702.mappings.csv"
+                sra_fastq_ftp                       = "${params.test_data_base}/modules/local/sra_fastq_ftp/"
+                sra_runinfo_to_ftp                  = "${params.test_data_base}/modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv"
         }
     }
 }
diff --git a/modules/local/multiqc_mappings_config/multiqc_mappings_config.nf.test b/modules/local/multiqc_mappings_config/multiqc_mappings_config.nf.test
index 7a0fe2dd..a5c148dc 100644
--- a/modules/local/multiqc_mappings_config/multiqc_mappings_config.nf.test
+++ b/modules/local/multiqc_mappings_config/multiqc_mappings_config.nf.test
@@ -1,7 +1,7 @@
 nextflow_process {
 
     name "Test Process MULTIQC_MAPPINGS_CONFIG"
-    script "modules/local/multiqc_mappings_config.nf"
+    script "modules/local/multiqc_mappings_config/multiqc_mappings_config.nf"
     process "MULTIQC_MAPPINGS_CONFIG"
     tag "multiqc_mappings_config"
     tag "modules_local"
@@ -14,7 +14,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = file("$baseDir/modules/local/tests/input/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv", checkIfExists: true)
+                input[0] = file(params.test_data['modules_local']['multiqc_mappings_config'], checkIfExists: true)
                 """
             }
         }
diff --git a/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test b/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test
index fb8d53e2..7ba37846 100644
--- a/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test
+++ b/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test
@@ -1,9 +1,10 @@
 nextflow_process {
 
     name "Test Process SRA_FASTQ_FTP"
-    script "modules/local/sra_fastq_ftp.nf"
+    script "modules/local/sra_fastq_ftp/sra_fastq_ftp.nf"
     process "SRA_FASTQ_FTP"
     tag "sra_fastq_ftp"
+    tag "modules_local"
 
     test("Should run without failures") {
 
diff --git a/modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test b/modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test
index 00c23f19..fae3fdf1 100644
--- a/modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test
+++ b/modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test
@@ -1,7 +1,7 @@
 nextflow_process {
 
     name "Test Process SRA_MERGE_SAMPLESHEET"
-    script "modules/local/sra_merge_samplesheet.nf"
+    script "modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf"
     process "SRA_MERGE_SAMPLESHEET"
     tag "sra_merge_samplesheet"
     tag "modules_local"
@@ -14,8 +14,8 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = file("$baseDir/modules/local/tests/input/sra_merge_samplesheet/samplesheets/*", checkIfExists: true)
-                input[1] = file("$baseDir/modules/local/tests/input/sra_merge_samplesheet/mappings/*", checkIfExists: true)
+                input[0] = file(params.test_data['modules_local']['sra_merge_samplesheet_samplesheets'], checkIfExists: true)
+                input[1] = file(params.test_data['modules_local']['sra_merge_samplesheet_mappings'], checkIfExists: true)
                 """
             }
         }
diff --git a/modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test b/modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test
index 14bb829b..dfff36fe 100644
--- a/modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test
+++ b/modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test
@@ -1,7 +1,7 @@
 nextflow_process {
 
     name "Test Process SRA_RUNINFO_TO_FTP"
-    script "modules/local/sra_runinfo_to_ftp.nf"
+    script "modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf"
     process "SRA_RUNINFO_TO_FTP"
     tag "sra_runinfo_to_ftp"
     tag "modules_local"
@@ -14,7 +14,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = file("$baseDir/modules/local/tests/input/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv", checkIfExists: true)
+                input[0] = file(params.test_data['modules_local']['sra_runinfo_to_ftp'], checkIfExists: true)
                 """
             }
         }
diff --git a/modules/local/sra_to_samplesheet/sra_to_samplesheet.nf.test b/modules/local/sra_to_samplesheet/sra_to_samplesheet.nf.test
index 413c6410..a9e8c1f7 100644
--- a/modules/local/sra_to_samplesheet/sra_to_samplesheet.nf.test
+++ b/modules/local/sra_to_samplesheet/sra_to_samplesheet.nf.test
@@ -1,9 +1,10 @@
 nextflow_process {
 
     name "Test Process SRA_TO_SAMPLESHEET"
-    script "modules/local/sra_to_samplesheet.nf"
+    script "modules/local/sra_to_samplesheet/sra_to_samplesheet.nf"
     process "SRA_TO_SAMPLESHEET"
     tag "sra_to_samplesheet"
+    tag "modules_local"
 
     test("Should run without failures") {
 
@@ -16,7 +17,7 @@ nextflow_process {
                 input[1] =
                 input[2] =
                 input[3] =
-                input[4] = file("$baseDir/modules/local/tests/input/sra_to_samplesheet/SRX9626017_SRR13191702.mappings.csv", checkIfExists: true)
+                input[4] = file(params.test_data['modules_local']['sra_to_samplesheet'], checkIfExists: true)
                 """
             }
         }

From 2011565650099d464a19971d35b292500750c201 Mon Sep 17 00:00:00 2001
From: Sateesh Peri <perisateesh@gmail.com>
Date: Sun, 6 Aug 2023 19:54:56 -0400
Subject: [PATCH 372/852] update test_data config to fetch urls and update
 snapshots

---
 conf/test_data.config                         |  27 +++-
 .../local/sra_fastq_ftp/sra_fastq_ftp.nf.test |   6 +-
 .../sra_fastq_ftp/sra_fastq_ftp.nf.test.snap  | 140 ++++++++++++++++++
 .../sra_ids_to_runinfo.nf.test                |   4 +-
 .../sra_ids_to_runinfo.nf.test.snap           |   6 +-
 .../sra_merge_samplesheet.nf.test             |   4 +-
 .../sra_runinfo_to_ftp.nf.test.snap           |   2 +-
 .../sra_to_samplesheet.nf.test                |   9 +-
 workflows/sra/tests/skip_fastq.nf.test.snap   |  16 +-
 workflows/sra/tests/sra.nf.test.snap          |  18 +--
 .../with_atacseq_samplesheet.nf.test.snap     |  18 +--
 .../with_rnaseq_samplesheet.nf.test.snap      |  18 +--
 .../sra/tests/with_sratools.nf.test.snap      |  18 +--
 .../with_taxprofiler_samplesheet.nf.test.snap |  18 +--
 .../with_viralrecon_samplesheet.nf.test.snap  |  18 +--
 15 files changed, 241 insertions(+), 81 deletions(-)
 create mode 100644 modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test.snap

diff --git a/conf/test_data.config b/conf/test_data.config
index 16acdabf..42d3d818 100644
--- a/conf/test_data.config
+++ b/conf/test_data.config
@@ -2,13 +2,34 @@ params {
     // Base directory for test data
     test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs"
 
+    merge_samplesheet_ids = [ "DRX024467_DRR026872", "SRX11047067_SRR14709033", "SRX9504942_SRR13055517", "DRX026011_DRR028935", "SRX17709227_SRR21711856", "SRX9504942_SRR13055518", "ERX1188904_ERR1109373", "SRX17709228_SRR21711855", "SRX9504942_SRR13055519", "ERX1234253_ERR1160846", "SRX6725035_SRR9984183", "SRX9504942_SRR13055520", "SRX10940790_SRR14593545", "SRX9315476_SRR12848126", "SRX9626017_SRR13191702" ]
+
+    def merge_samplesheet_url  = "${params.test_data_base}/modules/local/sra_merge_samplesheet/samplesheets/"
+    def merge_mappings_url     = "${params.test_data_base}/modules/local/sra_merge_samplesheet/mappings/"
+    def merge_samplesheet_urls = []
+    def merge_mappings_urls    = []
+
+    merge_samplesheet_ids.each { id ->
+        merge_samplesheet_urls += "${merge_samplesheet_url}${id}.samplesheet.csv"
+        merge_mappings_urls    += "${merge_mappings_url}/${id}.mappings.csv"
+    }
+
+    fastq_ftp_ids      = ["SRR13191702"]
+    def fastq_ftp_url  = "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/"
+    def fastq_ftp_urls = []
+
+    fastq_ftp_ids.each { id ->
+        fastq_ftp_urls += "${fastq_ftp_url}${id}_1.fastq.gz"
+        fastq_ftp_urls += "${fastq_ftp_url}${id}_2.fastq.gz"
+    }
+
     test_data {
         'modules_local' {
                 multiqc_mappings_config             = "${params.test_data_base}/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv"
-                sra_merge_samplesheet_samplesheets  = "${params.test_data_base}/modules/local/sra_merge_samplesheet/samplesheets/"
-                sra_merge_samplesheet_mappings      = "${params.test_data_base}/modules/local/sra_merge_samplesheet/mappings/"
+                sra_merge_samplesheet_samplesheets  = merge_samplesheet_urls
+                sra_merge_samplesheet_mappings      = merge_mappings_urls
                 sra_to_samplesheet                  = "${params.test_data_base}/modules/local/sra_to_samplesheet/SRX9626017_SRR13191702.mappings.csv"
-                sra_fastq_ftp                       = "${params.test_data_base}/modules/local/sra_fastq_ftp/"
+                sra_fastq_ftp                       = fastq_ftp_urls
                 sra_runinfo_to_ftp                  = "${params.test_data_base}/modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv"
         }
     }
diff --git a/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test b/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test
index 7ba37846..5fa043ab 100644
--- a/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test
+++ b/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test
@@ -6,7 +6,7 @@ nextflow_process {
     tag "sra_fastq_ftp"
     tag "modules_local"
 
-    test("Should run without failures") {
+    test("SRX9626017_SRR13191702") {
 
         when {
             params {
@@ -15,8 +15,8 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                            [ id:'SRX9626017_SRR13191702', single_end:false ], // meta map
-                            [ SRR13191702 ]
+                            [ id:'SRX9626017_SRR13191702', single_end:false, md5_1: '89c5be920021a035084d8aeb74f32df7', md5_2: '56271be38a80db78ef3bdfc5d9909b98' ], // meta map
+                            params.test_data['modules_local']['sra_fastq_ftp']
                         ]
                 """
             }
diff --git a/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test.snap b/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test.snap
new file mode 100644
index 00000000..c0d5ffdc
--- /dev/null
+++ b/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test.snap
@@ -0,0 +1,140 @@
+{
+    "SRX9626017_SRR13191702": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
+                            "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
+                        ]
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b"
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
+                        ]
+                    ]
+                ],
+                "md5": [
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
+                            "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b"
+                ]
+            }
+        ],
+        "timestamp": "2023-08-06T23:31:57+0000"
+    },
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
+                            "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
+                        ]
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b"
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
+                        ]
+                    ]
+                ],
+                "md5": [
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
+                            "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b"
+                ]
+            }
+        ],
+        "timestamp": "2023-08-06T23:31:57+0000"
+    }
+}
\ No newline at end of file
diff --git a/modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test b/modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test
index 36699bb4..a89e21fa 100644
--- a/modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test
+++ b/modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test
@@ -1,7 +1,7 @@
 nextflow_process {
 
     name "Test Process SRA_IDS_TO_RUNINFO"
-    script "modules/local/sra_ids_to_runinfo.nf"
+    script "modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf"
     process "SRA_IDS_TO_RUNINFO"
     tag "sra_ids_to_runinfo"
     tag "modules_local"
@@ -14,7 +14,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = 'SRR9984183'
+                input[0] = 'SRR13191702'
                 input[1] = ''
                 """
             }
diff --git a/modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test.snap b/modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test.snap
index d4e1e05d..dbca931f 100644
--- a/modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test.snap
+++ b/modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test.snap
@@ -3,19 +3,19 @@
         "content": [
             {
                 "0": [
-                    "SRR9984183.runinfo.tsv:md5,51cba5fab4d6f0c0386e4397672240b9"
+                    "SRR13191702.runinfo.tsv:md5,3a1be35781ca6e8a28d8fd4d2f3bbe85"
                 ],
                 "1": [
                     "versions.yml:md5,1c14442e9b494b586eafe41e77300fae"
                 ],
                 "tsv": [
-                    "SRR9984183.runinfo.tsv:md5,51cba5fab4d6f0c0386e4397672240b9"
+                    "SRR13191702.runinfo.tsv:md5,3a1be35781ca6e8a28d8fd4d2f3bbe85"
                 ],
                 "versions": [
                     "versions.yml:md5,1c14442e9b494b586eafe41e77300fae"
                 ]
             }
         ],
-        "timestamp": "2023-07-06T13:16:51+0000"
+        "timestamp": "2023-08-06T23:30:51+0000"
     }
 }
\ No newline at end of file
diff --git a/modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test b/modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test
index fae3fdf1..9385dab8 100644
--- a/modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test
+++ b/modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test
@@ -14,8 +14,8 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = file(params.test_data['modules_local']['sra_merge_samplesheet_samplesheets'], checkIfExists: true)
-                input[1] = file(params.test_data['modules_local']['sra_merge_samplesheet_mappings'], checkIfExists: true)
+                input[0] = params.test_data['modules_local']['sra_merge_samplesheet_samplesheets'].collect { file(it, checkIfExists: true) }
+                input[1] = params.test_data['modules_local']['sra_merge_samplesheet_mappings'].collect { file(it, checkIfExists: true) }
                 """
             }
         }
diff --git a/modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test.snap b/modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test.snap
index 03cf80e8..71a25f99 100644
--- a/modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test.snap
+++ b/modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test.snap
@@ -16,6 +16,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-07-06T02:05:52+0000"
+        "timestamp": "2023-08-06T23:13:20+0000"
     }
 }
\ No newline at end of file
diff --git a/modules/local/sra_to_samplesheet/sra_to_samplesheet.nf.test b/modules/local/sra_to_samplesheet/sra_to_samplesheet.nf.test
index a9e8c1f7..5c7ff7d9 100644
--- a/modules/local/sra_to_samplesheet/sra_to_samplesheet.nf.test
+++ b/modules/local/sra_to_samplesheet/sra_to_samplesheet.nf.test
@@ -4,7 +4,6 @@ nextflow_process {
     script "modules/local/sra_to_samplesheet/sra_to_samplesheet.nf"
     process "SRA_TO_SAMPLESHEET"
     tag "sra_to_samplesheet"
-    tag "modules_local"
 
     test("Should run without failures") {
 
@@ -14,10 +13,10 @@ nextflow_process {
             }
             process {
                 """
-                input[1] =
-                input[2] =
-                input[3] =
-                input[4] = file(params.test_data['modules_local']['sra_to_samplesheet'], checkIfExists: true)
+                input[0] = 'meta'
+                input[1] = 'rnaseq'
+                input[2] = 'strandedness'
+                input[3] = 'mapping_fields'
                 """
             }
         }
diff --git a/workflows/sra/tests/skip_fastq.nf.test.snap b/workflows/sra/tests/skip_fastq.nf.test.snap
index 6d3201e8..7f71a838 100644
--- a/workflows/sra/tests/skip_fastq.nf.test.snap
+++ b/workflows/sra/tests/skip_fastq.nf.test.snap
@@ -1,30 +1,30 @@
 {
     "metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,ef90876b2cbcb3721251b4cdef8cc47b",
+            "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
             "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
             "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
             "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
             "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
-            "SRR14593545.runinfo_ftp.tsv:md5,888eaa19fd0b7fea4dc3e9800c1d26f2",
+            "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54",
             "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
-            "SRR9984183.runinfo_ftp.tsv:md5,911a48308f76387b97842d35abc43c8f"
+            "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
         ],
-        "timestamp": "2023-07-06T14:02:03+0000"
+        "timestamp": "2023-08-06T23:37:00+0000"
     },
     "samplesheet": {
         "content": [
-            "id_mappings.csv:md5,aa5eab8068e59a3866fd6d1fa8fe1b5a",
-            "multiqc_config.yml:md5,1337fdab76cbca9b78dbf06d7344a3b8"
+            "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
+            "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
         ],
-        "timestamp": "2023-07-06T14:02:03+0000"
+        "timestamp": "2023-08-06T23:37:00+0000"
     },
     "software_versions": {
         "content": [
             "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
-        "timestamp": "2023-07-06T14:02:03+0000"
+        "timestamp": "2023-08-06T23:37:00+0000"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra.nf.test.snap b/workflows/sra/tests/sra.nf.test.snap
index a4276e94..dcdb43b5 100644
--- a/workflows/sra/tests/sra.nf.test.snap
+++ b/workflows/sra/tests/sra.nf.test.snap
@@ -1,31 +1,31 @@
 {
     "metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,ef90876b2cbcb3721251b4cdef8cc47b",
+            "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
             "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
             "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
             "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
             "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
-            "SRR14593545.runinfo_ftp.tsv:md5,888eaa19fd0b7fea4dc3e9800c1d26f2",
+            "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54",
             "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
-            "SRR9984183.runinfo_ftp.tsv:md5,911a48308f76387b97842d35abc43c8f"
+            "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
         ],
-        "timestamp": "2023-07-06T14:10:16+0000"
+        "timestamp": "2023-08-06T23:48:50+0000"
     },
     "samplesheet": {
         "content": [
-            "id_mappings.csv:md5,aa5eab8068e59a3866fd6d1fa8fe1b5a",
-            "multiqc_config.yml:md5,1337fdab76cbca9b78dbf06d7344a3b8"
+            "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
+            "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
         ],
-        "timestamp": "2023-07-06T14:10:16+0000"
+        "timestamp": "2023-08-06T23:48:50+0000"
     },
     "software_versions": {
         "content": [
             "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
-        "timestamp": "2023-07-06T14:10:16+0000"
+        "timestamp": "2023-08-06T23:48:50+0000"
     },
     "fastq": {
         "content": [
@@ -75,6 +75,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-07-06T14:10:16+0000"
+        "timestamp": "2023-08-06T23:48:50+0000"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/with_atacseq_samplesheet.nf.test.snap b/workflows/sra/tests/with_atacseq_samplesheet.nf.test.snap
index e49f6010..a9dd40a0 100644
--- a/workflows/sra/tests/with_atacseq_samplesheet.nf.test.snap
+++ b/workflows/sra/tests/with_atacseq_samplesheet.nf.test.snap
@@ -1,31 +1,31 @@
 {
     "metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,ef90876b2cbcb3721251b4cdef8cc47b",
+            "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
             "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
             "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
             "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
             "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
-            "SRR14593545.runinfo_ftp.tsv:md5,888eaa19fd0b7fea4dc3e9800c1d26f2",
+            "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54",
             "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
-            "SRR9984183.runinfo_ftp.tsv:md5,911a48308f76387b97842d35abc43c8f"
+            "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
         ],
-        "timestamp": "2023-07-06T14:03:45+0000"
+        "timestamp": "2023-08-06T23:38:47+0000"
     },
     "samplesheet": {
         "content": [
-            "id_mappings.csv:md5,aa5eab8068e59a3866fd6d1fa8fe1b5a",
-            "multiqc_config.yml:md5,1337fdab76cbca9b78dbf06d7344a3b8"
+            "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
+            "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
         ],
-        "timestamp": "2023-07-06T14:03:45+0000"
+        "timestamp": "2023-08-06T23:38:47+0000"
     },
     "software_versions": {
         "content": [
             "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
-        "timestamp": "2023-07-06T14:03:45+0000"
+        "timestamp": "2023-08-06T23:38:47+0000"
     },
     "fastq": {
         "content": [
@@ -75,6 +75,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-07-06T14:03:45+0000"
+        "timestamp": "2023-08-06T23:38:47+0000"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/with_rnaseq_samplesheet.nf.test.snap b/workflows/sra/tests/with_rnaseq_samplesheet.nf.test.snap
index 1efae9c1..1e3e8a5b 100644
--- a/workflows/sra/tests/with_rnaseq_samplesheet.nf.test.snap
+++ b/workflows/sra/tests/with_rnaseq_samplesheet.nf.test.snap
@@ -1,31 +1,31 @@
 {
     "metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,ef90876b2cbcb3721251b4cdef8cc47b",
+            "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
             "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
             "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
             "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
             "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
-            "SRR14593545.runinfo_ftp.tsv:md5,888eaa19fd0b7fea4dc3e9800c1d26f2",
+            "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54",
             "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
-            "SRR9984183.runinfo_ftp.tsv:md5,911a48308f76387b97842d35abc43c8f"
+            "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
         ],
-        "timestamp": "2023-07-06T14:12:03+0000"
+        "timestamp": "2023-08-06T23:50:46+0000"
     },
     "samplesheet": {
         "content": [
-            "id_mappings.csv:md5,aa5eab8068e59a3866fd6d1fa8fe1b5a",
-            "multiqc_config.yml:md5,1337fdab76cbca9b78dbf06d7344a3b8"
+            "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
+            "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
         ],
-        "timestamp": "2023-07-06T14:12:03+0000"
+        "timestamp": "2023-08-06T23:50:46+0000"
     },
     "software_versions": {
         "content": [
             "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
-        "timestamp": "2023-07-06T14:12:03+0000"
+        "timestamp": "2023-08-06T23:50:46+0000"
     },
     "fastq": {
         "content": [
@@ -75,6 +75,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-07-06T14:12:03+0000"
+        "timestamp": "2023-08-06T23:50:46+0000"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/with_sratools.nf.test.snap b/workflows/sra/tests/with_sratools.nf.test.snap
index 7d6d007a..bbec9969 100644
--- a/workflows/sra/tests/with_sratools.nf.test.snap
+++ b/workflows/sra/tests/with_sratools.nf.test.snap
@@ -1,31 +1,31 @@
 {
     "metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,ef90876b2cbcb3721251b4cdef8cc47b",
+            "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
             "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
             "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
             "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
             "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
-            "SRR14593545.runinfo_ftp.tsv:md5,888eaa19fd0b7fea4dc3e9800c1d26f2",
+            "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54",
             "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
-            "SRR9984183.runinfo_ftp.tsv:md5,911a48308f76387b97842d35abc43c8f"
+            "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
         ],
-        "timestamp": "2023-07-06T14:08:40+0000"
+        "timestamp": "2023-08-06T23:43:45+0000"
     },
     "samplesheet": {
         "content": [
-            "id_mappings.csv:md5,aa5eab8068e59a3866fd6d1fa8fe1b5a",
-            "multiqc_config.yml:md5,1337fdab76cbca9b78dbf06d7344a3b8"
+            "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
+            "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
         ],
-        "timestamp": "2023-07-06T14:08:40+0000"
+        "timestamp": "2023-08-06T23:43:45+0000"
     },
     "software_versions": {
         "content": [
             "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
-        "timestamp": "2023-07-06T14:08:40+0000"
+        "timestamp": "2023-08-06T23:43:45+0000"
     },
     "fastq": {
         "content": [
@@ -54,6 +54,6 @@
             "SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7",
             "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af"
         ],
-        "timestamp": "2023-07-06T14:08:40+0000"
+        "timestamp": "2023-08-06T23:43:45+0000"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test.snap b/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test.snap
index 1e10d64b..b4fe3748 100644
--- a/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test.snap
+++ b/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test.snap
@@ -1,31 +1,31 @@
 {
     "metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,ef90876b2cbcb3721251b4cdef8cc47b",
+            "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
             "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
             "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
             "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
             "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
-            "SRR14593545.runinfo_ftp.tsv:md5,888eaa19fd0b7fea4dc3e9800c1d26f2",
+            "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54",
             "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
-            "SRR9984183.runinfo_ftp.tsv:md5,911a48308f76387b97842d35abc43c8f"
+            "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
         ],
-        "timestamp": "2023-07-06T14:05:23+0000"
+        "timestamp": "2023-08-06T23:40:33+0000"
     },
     "samplesheet": {
         "content": [
-            "id_mappings.csv:md5,aa5eab8068e59a3866fd6d1fa8fe1b5a",
-            "multiqc_config.yml:md5,1337fdab76cbca9b78dbf06d7344a3b8"
+            "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
+            "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
         ],
-        "timestamp": "2023-07-06T14:05:23+0000"
+        "timestamp": "2023-08-06T23:40:33+0000"
     },
     "software_versions": {
         "content": [
             "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
-        "timestamp": "2023-07-06T14:05:23+0000"
+        "timestamp": "2023-08-06T23:40:33+0000"
     },
     "fastq": {
         "content": [
@@ -75,6 +75,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-07-06T14:05:23+0000"
+        "timestamp": "2023-08-06T23:40:33+0000"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/with_viralrecon_samplesheet.nf.test.snap b/workflows/sra/tests/with_viralrecon_samplesheet.nf.test.snap
index 34e8a234..51b0ea51 100644
--- a/workflows/sra/tests/with_viralrecon_samplesheet.nf.test.snap
+++ b/workflows/sra/tests/with_viralrecon_samplesheet.nf.test.snap
@@ -1,31 +1,31 @@
 {
     "metadata": {
         "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,ef90876b2cbcb3721251b4cdef8cc47b",
+            "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
             "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
             "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
             "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
             "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
             "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
             "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
-            "SRR14593545.runinfo_ftp.tsv:md5,888eaa19fd0b7fea4dc3e9800c1d26f2",
+            "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54",
             "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
-            "SRR9984183.runinfo_ftp.tsv:md5,911a48308f76387b97842d35abc43c8f"
+            "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
         ],
-        "timestamp": "2023-07-06T13:44:03+0000"
+        "timestamp": "2023-08-06T23:34:45+0000"
     },
     "samplesheet": {
         "content": [
-            "id_mappings.csv:md5,aa5eab8068e59a3866fd6d1fa8fe1b5a",
-            "multiqc_config.yml:md5,1337fdab76cbca9b78dbf06d7344a3b8"
+            "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
+            "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
         ],
-        "timestamp": "2023-07-06T13:44:03+0000"
+        "timestamp": "2023-08-06T23:34:45+0000"
     },
     "software_versions": {
         "content": [
             "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
-        "timestamp": "2023-07-06T13:44:03+0000"
+        "timestamp": "2023-08-06T23:34:45+0000"
     },
     "fastq": {
         "content": [
@@ -75,6 +75,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-07-06T13:44:03+0000"
+        "timestamp": "2023-08-06T23:34:45+0000"
     }
 }
\ No newline at end of file

From 4cf72b43e4d7668e9efbd6784a2ed8afb013bf00 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 16 Aug 2023 18:55:23 +0100
Subject: [PATCH 373/852] Restructure local modules and main script names

---
 .../{multiqc_mappings_config.nf => main.nf}                       | 0
 .../{multiqc_mappings_config.nf.test => tests/main.nf.test}       | 0
 .../main.nf.test.snap}                                            | 0
 modules/local/sra_fastq_ftp/{sra_fastq_ftp.nf => main.nf}         | 0
 .../sra_fastq_ftp/{sra_fastq_ftp.nf.test => tests/main.nf.test}   | 0
 .../{sra_fastq_ftp.nf.test.snap => tests/main.nf.test.snap}       | 0
 .../local/sra_ids_to_runinfo/{sra_ids_to_runinfo.nf => main.nf}   | 0
 .../{sra_ids_to_runinfo.nf.test => tests/main.nf.test}            | 0
 .../{sra_ids_to_runinfo.nf.test.snap => tests/main.nf.test.snap}  | 0
 .../sra_merge_samplesheet/{sra_merge_samplesheet.nf => main.nf}   | 0
 .../{sra_merge_samplesheet.nf.test => tests/main.nf.test}         | 0
 .../main.nf.test.snap}                                            | 0
 .../local/sra_runinfo_to_ftp/{sra_runinfo_to_ftp.nf => main.nf}   | 0
 .../{sra_runinfo_to_ftp.nf.test => tests/main.nf.test}            | 0
 .../{sra_runinfo_to_ftp.nf.test.snap => tests/main.nf.test.snap}  | 0
 .../local/sra_to_samplesheet/{sra_to_samplesheet.nf => main.nf}   | 0
 .../{sra_to_samplesheet.nf.test => tests/main.nf.test}            | 0
 modules/local/synapse_get/{synapse_get.nf => main.nf}             | 0
 modules/local/synapse_list/{synapse_list.nf => main.nf}           | 0
 .../{synapse_merge_samplesheet.nf => main.nf}                     | 0
 modules/local/synapse_show/{synapse_show.nf => main.nf}           | 0
 .../synapse_to_samplesheet.nf => synapse_to_samplesheet/main.nf}  | 0
 workflows/sra/tests/{sra.nf.test => main.nf.test}                 | 0
 workflows/sra/tests/{sra.nf.test.snap => main.nf.test.snap}       | 0
 workflows/synapse/tests/{synapse.test => main.nf.test}            | 0
 25 files changed, 0 insertions(+), 0 deletions(-)
 rename modules/local/multiqc_mappings_config/{multiqc_mappings_config.nf => main.nf} (100%)
 rename modules/local/multiqc_mappings_config/{multiqc_mappings_config.nf.test => tests/main.nf.test} (100%)
 rename modules/local/multiqc_mappings_config/{multiqc_mappings_config.nf.test.snap => tests/main.nf.test.snap} (100%)
 rename modules/local/sra_fastq_ftp/{sra_fastq_ftp.nf => main.nf} (100%)
 rename modules/local/sra_fastq_ftp/{sra_fastq_ftp.nf.test => tests/main.nf.test} (100%)
 rename modules/local/sra_fastq_ftp/{sra_fastq_ftp.nf.test.snap => tests/main.nf.test.snap} (100%)
 rename modules/local/sra_ids_to_runinfo/{sra_ids_to_runinfo.nf => main.nf} (100%)
 rename modules/local/sra_ids_to_runinfo/{sra_ids_to_runinfo.nf.test => tests/main.nf.test} (100%)
 rename modules/local/sra_ids_to_runinfo/{sra_ids_to_runinfo.nf.test.snap => tests/main.nf.test.snap} (100%)
 rename modules/local/sra_merge_samplesheet/{sra_merge_samplesheet.nf => main.nf} (100%)
 rename modules/local/sra_merge_samplesheet/{sra_merge_samplesheet.nf.test => tests/main.nf.test} (100%)
 rename modules/local/sra_merge_samplesheet/{sra_merge_samplesheet.nf.test.snap => tests/main.nf.test.snap} (100%)
 rename modules/local/sra_runinfo_to_ftp/{sra_runinfo_to_ftp.nf => main.nf} (100%)
 rename modules/local/sra_runinfo_to_ftp/{sra_runinfo_to_ftp.nf.test => tests/main.nf.test} (100%)
 rename modules/local/sra_runinfo_to_ftp/{sra_runinfo_to_ftp.nf.test.snap => tests/main.nf.test.snap} (100%)
 rename modules/local/sra_to_samplesheet/{sra_to_samplesheet.nf => main.nf} (100%)
 rename modules/local/sra_to_samplesheet/{sra_to_samplesheet.nf.test => tests/main.nf.test} (100%)
 rename modules/local/synapse_get/{synapse_get.nf => main.nf} (100%)
 rename modules/local/synapse_list/{synapse_list.nf => main.nf} (100%)
 rename modules/local/synapse_merge_samplesheet/{synapse_merge_samplesheet.nf => main.nf} (100%)
 rename modules/local/synapse_show/{synapse_show.nf => main.nf} (100%)
 rename modules/local/{synapse_to_sampleshee/synapse_to_samplesheet.nf => synapse_to_samplesheet/main.nf} (100%)
 rename workflows/sra/tests/{sra.nf.test => main.nf.test} (100%)
 rename workflows/sra/tests/{sra.nf.test.snap => main.nf.test.snap} (100%)
 rename workflows/synapse/tests/{synapse.test => main.nf.test} (100%)

diff --git a/modules/local/multiqc_mappings_config/multiqc_mappings_config.nf b/modules/local/multiqc_mappings_config/main.nf
similarity index 100%
rename from modules/local/multiqc_mappings_config/multiqc_mappings_config.nf
rename to modules/local/multiqc_mappings_config/main.nf
diff --git a/modules/local/multiqc_mappings_config/multiqc_mappings_config.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test
similarity index 100%
rename from modules/local/multiqc_mappings_config/multiqc_mappings_config.nf.test
rename to modules/local/multiqc_mappings_config/tests/main.nf.test
diff --git a/modules/local/multiqc_mappings_config/multiqc_mappings_config.nf.test.snap b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap
similarity index 100%
rename from modules/local/multiqc_mappings_config/multiqc_mappings_config.nf.test.snap
rename to modules/local/multiqc_mappings_config/tests/main.nf.test.snap
diff --git a/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf b/modules/local/sra_fastq_ftp/main.nf
similarity index 100%
rename from modules/local/sra_fastq_ftp/sra_fastq_ftp.nf
rename to modules/local/sra_fastq_ftp/main.nf
diff --git a/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test
similarity index 100%
rename from modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test
rename to modules/local/sra_fastq_ftp/tests/main.nf.test
diff --git a/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test.snap b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap
similarity index 100%
rename from modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test.snap
rename to modules/local/sra_fastq_ftp/tests/main.nf.test.snap
diff --git a/modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf b/modules/local/sra_ids_to_runinfo/main.nf
similarity index 100%
rename from modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf
rename to modules/local/sra_ids_to_runinfo/main.nf
diff --git a/modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test
similarity index 100%
rename from modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test
rename to modules/local/sra_ids_to_runinfo/tests/main.nf.test
diff --git a/modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test.snap b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap
similarity index 100%
rename from modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test.snap
rename to modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap
diff --git a/modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf b/modules/local/sra_merge_samplesheet/main.nf
similarity index 100%
rename from modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf
rename to modules/local/sra_merge_samplesheet/main.nf
diff --git a/modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test b/modules/local/sra_merge_samplesheet/tests/main.nf.test
similarity index 100%
rename from modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test
rename to modules/local/sra_merge_samplesheet/tests/main.nf.test
diff --git a/modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test.snap b/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap
similarity index 100%
rename from modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test.snap
rename to modules/local/sra_merge_samplesheet/tests/main.nf.test.snap
diff --git a/modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf b/modules/local/sra_runinfo_to_ftp/main.nf
similarity index 100%
rename from modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf
rename to modules/local/sra_runinfo_to_ftp/main.nf
diff --git a/modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
similarity index 100%
rename from modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test
rename to modules/local/sra_runinfo_to_ftp/tests/main.nf.test
diff --git a/modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test.snap b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap
similarity index 100%
rename from modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test.snap
rename to modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap
diff --git a/modules/local/sra_to_samplesheet/sra_to_samplesheet.nf b/modules/local/sra_to_samplesheet/main.nf
similarity index 100%
rename from modules/local/sra_to_samplesheet/sra_to_samplesheet.nf
rename to modules/local/sra_to_samplesheet/main.nf
diff --git a/modules/local/sra_to_samplesheet/sra_to_samplesheet.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test
similarity index 100%
rename from modules/local/sra_to_samplesheet/sra_to_samplesheet.nf.test
rename to modules/local/sra_to_samplesheet/tests/main.nf.test
diff --git a/modules/local/synapse_get/synapse_get.nf b/modules/local/synapse_get/main.nf
similarity index 100%
rename from modules/local/synapse_get/synapse_get.nf
rename to modules/local/synapse_get/main.nf
diff --git a/modules/local/synapse_list/synapse_list.nf b/modules/local/synapse_list/main.nf
similarity index 100%
rename from modules/local/synapse_list/synapse_list.nf
rename to modules/local/synapse_list/main.nf
diff --git a/modules/local/synapse_merge_samplesheet/synapse_merge_samplesheet.nf b/modules/local/synapse_merge_samplesheet/main.nf
similarity index 100%
rename from modules/local/synapse_merge_samplesheet/synapse_merge_samplesheet.nf
rename to modules/local/synapse_merge_samplesheet/main.nf
diff --git a/modules/local/synapse_show/synapse_show.nf b/modules/local/synapse_show/main.nf
similarity index 100%
rename from modules/local/synapse_show/synapse_show.nf
rename to modules/local/synapse_show/main.nf
diff --git a/modules/local/synapse_to_sampleshee/synapse_to_samplesheet.nf b/modules/local/synapse_to_samplesheet/main.nf
similarity index 100%
rename from modules/local/synapse_to_sampleshee/synapse_to_samplesheet.nf
rename to modules/local/synapse_to_samplesheet/main.nf
diff --git a/workflows/sra/tests/sra.nf.test b/workflows/sra/tests/main.nf.test
similarity index 100%
rename from workflows/sra/tests/sra.nf.test
rename to workflows/sra/tests/main.nf.test
diff --git a/workflows/sra/tests/sra.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
similarity index 100%
rename from workflows/sra/tests/sra.nf.test.snap
rename to workflows/sra/tests/main.nf.test.snap
diff --git a/workflows/synapse/tests/synapse.test b/workflows/synapse/tests/main.nf.test
similarity index 100%
rename from workflows/synapse/tests/synapse.test
rename to workflows/synapse/tests/main.nf.test

From 168a6812bf84e1044520b2907b79c987ba2bb892 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 17 Aug 2023 11:31:36 +0100
Subject: [PATCH 374/852] Fix tests and standardise tags

---
 main.nf                                          |  4 ++--
 .../multiqc_mappings_config/tests/main.nf.test   |  5 +++--
 modules/local/sra_fastq_ftp/tests/main.nf.test   |  5 +++--
 .../local/sra_ids_to_runinfo/tests/main.nf.test  |  5 +++--
 .../sra_merge_samplesheet/tests/main.nf.test     |  5 +++--
 .../local/sra_runinfo_to_ftp/tests/main.nf.test  |  5 +++--
 .../local/sra_to_samplesheet/tests/main.nf.test  |  4 +++-
 workflows/sra/main.nf                            | 16 ++++++++--------
 workflows/sra/tests/main.nf.test                 |  3 ++-
 workflows/sra/tests/skip_fastq.nf.test           |  3 ++-
 .../sra/tests/with_atacseq_samplesheet.nf.test   |  3 ++-
 .../sra/tests/with_rnaseq_samplesheet.nf.test    |  3 ++-
 .../with_rnaseq_specific_ena_metadata.nf.test    |  3 ++-
 workflows/sra/tests/with_sratools.nf.test        |  3 ++-
 .../tests/with_taxprofiler_samplesheet.nf.test   |  3 ++-
 .../tests/with_viralrecon_samplesheet.nf.test    |  3 ++-
 workflows/synapse/main.nf                        |  2 +-
 workflows/synapse/tests/main.nf.test             |  4 +++-
 18 files changed, 48 insertions(+), 31 deletions(-)

diff --git a/main.nf b/main.nf
index f856a93c..6da732be 100644
--- a/main.nf
+++ b/main.nf
@@ -49,9 +49,9 @@ if (WorkflowMain.isSraId(ch_input)) {
 
 if (params.input_type == input_type) {
     if (params.input_type == 'sra') {
-        include { SRA } from './workflows/sra/main'
+        include { SRA } from './workflows/sra'
     } else if (params.input_type == 'synapse') {
-        include { SYNAPSE } from './workflows/synapse/main'
+        include { SYNAPSE } from './workflows/synapse'
     }
 } else {
     exit 1, "Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!"
diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test
index a5c148dc..26dbe22f 100644
--- a/modules/local/multiqc_mappings_config/tests/main.nf.test
+++ b/modules/local/multiqc_mappings_config/tests/main.nf.test
@@ -1,10 +1,11 @@
 nextflow_process {
 
     name "Test Process MULTIQC_MAPPINGS_CONFIG"
-    script "modules/local/multiqc_mappings_config/multiqc_mappings_config.nf"
+    script "modules/local/multiqc_mappings_config/main.nf"
     process "MULTIQC_MAPPINGS_CONFIG"
-    tag "multiqc_mappings_config"
+    tag "modules"
     tag "modules_local"
+    tag "multiqc_mappings_config"
 
     test("SRX9626017_SRR13191702") {
 
diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test
index 5fa043ab..e8b0d406 100644
--- a/modules/local/sra_fastq_ftp/tests/main.nf.test
+++ b/modules/local/sra_fastq_ftp/tests/main.nf.test
@@ -1,10 +1,11 @@
 nextflow_process {
 
     name "Test Process SRA_FASTQ_FTP"
-    script "modules/local/sra_fastq_ftp/sra_fastq_ftp.nf"
+    script "modules/local/sra_fastq_ftp/main.nf"
     process "SRA_FASTQ_FTP"
-    tag "sra_fastq_ftp"
+    tag "modules"
     tag "modules_local"
+    tag "sra_fastq_ftp"
 
     test("SRX9626017_SRR13191702") {
 
diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test
index a89e21fa..a140efdc 100644
--- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test
+++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test
@@ -1,10 +1,11 @@
 nextflow_process {
 
     name "Test Process SRA_IDS_TO_RUNINFO"
-    script "modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf"
+    script "modules/local/sra_ids_to_runinfo/main.nf"
     process "SRA_IDS_TO_RUNINFO"
-    tag "sra_ids_to_runinfo"
+    tag "modules"
     tag "modules_local"
+    tag "sra_ids_to_runinfo"
 
     test("Should run without failures") {
 
diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test b/modules/local/sra_merge_samplesheet/tests/main.nf.test
index 9385dab8..6ff471e8 100644
--- a/modules/local/sra_merge_samplesheet/tests/main.nf.test
+++ b/modules/local/sra_merge_samplesheet/tests/main.nf.test
@@ -1,10 +1,11 @@
 nextflow_process {
 
     name "Test Process SRA_MERGE_SAMPLESHEET"
-    script "modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf"
+    script "modules/local/sra_merge_samplesheet/main.nf"
     process "SRA_MERGE_SAMPLESHEET"
-    tag "sra_merge_samplesheet"
+    tag "modules"
     tag "modules_local"
+    tag "sra_merge_samplesheet"
 
     test("Should run without failures") {
 
diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
index dfff36fe..154ae4eb 100644
--- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
+++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
@@ -1,10 +1,11 @@
 nextflow_process {
 
     name "Test Process SRA_RUNINFO_TO_FTP"
-    script "modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf"
+    script "modules/local/sra_runinfo_to_ftp/main.nf"
     process "SRA_RUNINFO_TO_FTP"
-    tag "sra_runinfo_to_ftp"
+    tag "modules"
     tag "modules_local"
+    tag "sra_runinfo_to_ftp"
 
     test("Should run without failures") {
 
diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test
index 5c7ff7d9..7448fe1d 100644
--- a/modules/local/sra_to_samplesheet/tests/main.nf.test
+++ b/modules/local/sra_to_samplesheet/tests/main.nf.test
@@ -1,8 +1,10 @@
 nextflow_process {
 
     name "Test Process SRA_TO_SAMPLESHEET"
-    script "modules/local/sra_to_samplesheet/sra_to_samplesheet.nf"
+    script "modules/local/sra_to_samplesheet/main.nf"
     process "SRA_TO_SAMPLESHEET"
+    tag "modules"
+    tag "modules_local"
     tag "sra_to_samplesheet"
 
     test("Should run without failures") {
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 05b9a80d..512a73d4 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -19,12 +19,12 @@ WorkflowSra.initialise(params, valid_params)
 ========================================================================================
 */
 
-include { SRA_IDS_TO_RUNINFO      } from '../../modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo'
-include { SRA_RUNINFO_TO_FTP      } from '../../modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp'
-include { SRA_FASTQ_FTP           } from '../../modules/local/sra_fastq_ftp/sra_fastq_ftp'
-include { SRA_TO_SAMPLESHEET      } from '../../modules/local/sra_to_samplesheet/sra_to_samplesheet'
-include { SRA_MERGE_SAMPLESHEET   } from '../../modules/local/sra_merge_samplesheet/sra_merge_samplesheet'
-include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_config/multiqc_mappings_config'
+include { SRA_IDS_TO_RUNINFO      } from '../../modules/local/sra_ids_to_runinfo'
+include { SRA_RUNINFO_TO_FTP      } from '../../modules/local/sra_runinfo_to_ftp'
+include { SRA_FASTQ_FTP           } from '../../modules/local/sra_fastq_ftp'
+include { SRA_TO_SAMPLESHEET      } from '../../modules/local/sra_to_samplesheet'
+include { SRA_MERGE_SAMPLESHEET   } from '../../modules/local/sra_merge_samplesheet'
+include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_config'
 
 /*
 ========================================================================================
@@ -32,9 +32,9 @@ include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_c
 ========================================================================================
 */
 
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions/main'
+include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions'
 
-include { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS } from '../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main'
+include { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS } from '../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools'
 
 /*
 ========================================================================================
diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 16074b64..4fa13985 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -2,8 +2,9 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
+    tag "workflows"
     tag "sra"
-    tag "workflow"
+    tag "sra_default"
 
     test("SRA FASTQ & Metadata") {
 
diff --git a/workflows/sra/tests/skip_fastq.nf.test b/workflows/sra/tests/skip_fastq.nf.test
index 38814a77..188f0652 100644
--- a/workflows/sra/tests/skip_fastq.nf.test
+++ b/workflows/sra/tests/skip_fastq.nf.test
@@ -2,8 +2,9 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
+    tag "workflows"
+    tag "sra"
     tag "sra_skip_fastq"
-    tag "workflow"
 
     test("SRA Skip FASTQ") {
 
diff --git a/workflows/sra/tests/with_atacseq_samplesheet.nf.test b/workflows/sra/tests/with_atacseq_samplesheet.nf.test
index 4ebc9352..13f41868 100644
--- a/workflows/sra/tests/with_atacseq_samplesheet.nf.test
+++ b/workflows/sra/tests/with_atacseq_samplesheet.nf.test
@@ -2,8 +2,9 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
+    tag "workflows"
+    tag "sra"
     tag "sra_with_atacseq"
-    tag "workflow"
 
     test("SRA NF-CORE/ATACSEQ Samplesheet") {
 
diff --git a/workflows/sra/tests/with_rnaseq_samplesheet.nf.test b/workflows/sra/tests/with_rnaseq_samplesheet.nf.test
index ca77778c..fce8853c 100644
--- a/workflows/sra/tests/with_rnaseq_samplesheet.nf.test
+++ b/workflows/sra/tests/with_rnaseq_samplesheet.nf.test
@@ -2,8 +2,9 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
+    tag "workflows"
+    tag "sra"
     tag "sra_with_rnaseq"
-    tag "workflow"
 
     test("SRA NF-CORE/RNASEQ Samplesheet") {
 
diff --git a/workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test b/workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test
index 2fc12241..b9956366 100644
--- a/workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test
+++ b/workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test
@@ -2,8 +2,9 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
+    tag "workflows"
+    tag "sra"
     tag "sra_with_rnaseq_specific_ena"
-    tag "workflow"
 
     test("SRA NF-CORE/RNASEQ Samplesheet With Specific ENA metadata") {
 
diff --git a/workflows/sra/tests/with_sratools.nf.test b/workflows/sra/tests/with_sratools.nf.test
index 839e3089..e3239a18 100644
--- a/workflows/sra/tests/with_sratools.nf.test
+++ b/workflows/sra/tests/with_sratools.nf.test
@@ -2,8 +2,9 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
+    tag "workflows"
+    tag "sra"
     tag "sra_force_sratools_download"
-    tag "workflow"
 
     test("Force SRA-Tools Download") {
 
diff --git a/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test b/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test
index 7ffbca59..9d6e5f1f 100644
--- a/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test
+++ b/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test
@@ -2,8 +2,9 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
+    tag "workflows"
+    tag "sra"
     tag "sra_with_taxprofiler"
-    tag "workflow"
 
     test("SRA NF-CORE/TAXPROFILER Samplesheet") {
 
diff --git a/workflows/sra/tests/with_viralrecon_samplesheet.nf.test b/workflows/sra/tests/with_viralrecon_samplesheet.nf.test
index e10e2db8..429a114a 100644
--- a/workflows/sra/tests/with_viralrecon_samplesheet.nf.test
+++ b/workflows/sra/tests/with_viralrecon_samplesheet.nf.test
@@ -2,8 +2,9 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
+    tag "workflows"
+    tag "sra"
     tag "sra_with_viralrecon"
-    tag "workflow"
 
     test("SRA NF-CORE/VIRALRECON Samplesheet") {
 
diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf
index 7d871659..f8cbeba1 100644
--- a/workflows/synapse/main.nf
+++ b/workflows/synapse/main.nf
@@ -31,7 +31,7 @@ include { SYNAPSE_MERGE_SAMPLESHEET } from '../../modules/local/synapse_merge_sa
 ========================================================================================
 */
 
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions/main'
+include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions'
 
 /*
 ========================================================================================
diff --git a/workflows/synapse/tests/main.nf.test b/workflows/synapse/tests/main.nf.test
index 464ad226..efb7d793 100644
--- a/workflows/synapse/tests/main.nf.test
+++ b/workflows/synapse/tests/main.nf.test
@@ -2,8 +2,10 @@ nextflow_pipeline {
 
     name "Test Workflow main.nf"
     script "main.nf"
+    tag "workflows"
+    tag "synapse"
+    tag "synapse_default"
     profile "test_synapse"
-    tag "pipeline"
 
     test("Synapse Input Type") {
 

From 53f75ecc1e9e8e7ea57fce3d494c282f45edd90d Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 17 Aug 2023 11:31:55 +0100
Subject: [PATCH 375/852] Use generic tags in CI tests

---
 .github/workflows/ci.yml | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 0abe1037..5f329342 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -44,15 +44,8 @@ jobs:
       matrix:
         NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
         test_tags:
-          - "sra"
-          - "sra_force_sratools_download"
-          - "sra_skip_fastq"
-          - "sra_with_atacseq"
-          - "sra_with_rnaseq"
-          - "sra_with_rnaseq_specific_ena"
-          - "sra_with_taxprofiler"
-          - "sra_with_viralrecon"
           - "modules_local"
+          - "sra"
         profile:
           - "docker"
 

From e49ad85996f27286b1e0971063bbb1f7e683af42 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 17 Aug 2023 12:51:05 +0100
Subject: [PATCH 376/852] Fix tests for sra_to_samplesheet module

---
 .../tests/main.nf.test.snap                   | 113 ++++++++++++++++++
 1 file changed, 113 insertions(+)
 create mode 100644 modules/local/sra_to_samplesheet/tests/main.nf.test.snap

diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap
new file mode 100644
index 00000000..8b5f4947
--- /dev/null
+++ b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap
@@ -0,0 +1,113 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "ERX1188904_ERR1109373",
+                            "run_accession": "ERR1109373",
+                            "experiment_accession": "ERX1188904",
+                            "sample_accession": "SAMEA3643867",
+                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
+                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
+                            "sample_alias": "sample_56",
+                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
+                            "library_layout": "PAIRED",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
+                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
+                            "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
+                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
+                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
+                            "single_end": false
+                        },
+                        "ERX1188904_ERR1109373.samplesheet.csv:md5,e7898191d57258e049ee7129d36f5c08"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "ERX1188904_ERR1109373",
+                            "run_accession": "ERR1109373",
+                            "experiment_accession": "ERX1188904",
+                            "sample_accession": "SAMEA3643867",
+                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
+                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
+                            "sample_alias": "sample_56",
+                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
+                            "library_layout": "PAIRED",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
+                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
+                            "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
+                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
+                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
+                            "single_end": false
+                        },
+                        "ERX1188904_ERR1109373.mappings.csv:md5,d09ddb4f0709675e5dfe1eadf12c608f"
+                    ]
+                ],
+                "mappings": [
+                    [
+                        {
+                            "id": "ERX1188904_ERR1109373",
+                            "run_accession": "ERR1109373",
+                            "experiment_accession": "ERX1188904",
+                            "sample_accession": "SAMEA3643867",
+                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
+                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
+                            "sample_alias": "sample_56",
+                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
+                            "library_layout": "PAIRED",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
+                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
+                            "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
+                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
+                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
+                            "single_end": false
+                        },
+                        "ERX1188904_ERR1109373.mappings.csv:md5,d09ddb4f0709675e5dfe1eadf12c608f"
+                    ]
+                ],
+                "samplesheet": [
+                    [
+                        {
+                            "id": "ERX1188904_ERR1109373",
+                            "run_accession": "ERR1109373",
+                            "experiment_accession": "ERX1188904",
+                            "sample_accession": "SAMEA3643867",
+                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
+                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
+                            "sample_alias": "sample_56",
+                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
+                            "library_layout": "PAIRED",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
+                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
+                            "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
+                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
+                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
+                            "single_end": false
+                        },
+                        "ERX1188904_ERR1109373.samplesheet.csv:md5,e7898191d57258e049ee7129d36f5c08"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2023-08-17T10:55:52+0000"
+    }
+}
\ No newline at end of file

From 885ba0f30cc0c6925b081d14eb2720e6299e9136 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 17 Aug 2023 12:51:32 +0100
Subject: [PATCH 377/852] Rename workflows and standardise tags

---
 .github/workflows/ci.yml                      |  9 ++++-
 .../tests/main.nf.test                        |  9 ++---
 .../local/sra_fastq_ftp/tests/main.nf.test    | 15 ++++----
 .../sra_ids_to_runinfo/tests/main.nf.test     |  7 ++--
 .../sra_merge_samplesheet/tests/main.nf.test  |  7 ++--
 .../sra_runinfo_to_ftp/tests/main.nf.test     |  7 ++--
 .../sra_to_samplesheet/tests/main.nf.test     | 13 +++----
 workflows/sra/tests/main.nf.test              | 38 ++++++++++---------
 ...=> sra_custom_ena_metadata_fields.nf.test} | 14 +++----
 ...a_custom_ena_metadata_fields.nf.test.snap} |  0
 ...st => sra_force_sratools_download.nf.test} | 10 ++---
 ... sra_force_sratools_download.nf.test.snap} |  0
 ...t => sra_nf_core_pipeline_atacseq.nf.test} | 10 ++---
 ...sra_nf_core_pipeline_atacseq.nf.test.snap} |  0
 ...st => sra_nf_core_pipeline_rnaseq.nf.test} | 10 ++---
 ... sra_nf_core_pipeline_rnaseq.nf.test.snap} |  0
 ... sra_nf_core_pipeline_taxprofiler.nf.test} | 11 +++---
 ...nf_core_pipeline_taxprofiler.nf.test.snap} |  0
 ...> sra_nf_core_pipeline_viralrecon.nf.test} | 10 ++---
 ..._nf_core_pipeline_viralrecon.nf.test.snap} |  0
 ...f.test => sra_skip_fastq_download.nf.test} | 12 +++---
 ...p => sra_skip_fastq_download.nf.test.snap} |  0
 workflows/synapse/tests/main.nf.test          |  2 +-
 23 files changed, 91 insertions(+), 93 deletions(-)
 rename workflows/sra/tests/{with_rnaseq_specific_ena_metadata.nf.test => sra_custom_ena_metadata_fields.nf.test} (81%)
 rename workflows/sra/tests/{with_rnaseq_specific_ena_metadata.nf.test.snap => sra_custom_ena_metadata_fields.nf.test.snap} (100%)
 rename workflows/sra/tests/{with_sratools.nf.test => sra_force_sratools_download.nf.test} (92%)
 rename workflows/sra/tests/{with_sratools.nf.test.snap => sra_force_sratools_download.nf.test.snap} (100%)
 rename workflows/sra/tests/{with_atacseq_samplesheet.nf.test => sra_nf_core_pipeline_atacseq.nf.test} (90%)
 rename workflows/sra/tests/{with_atacseq_samplesheet.nf.test.snap => sra_nf_core_pipeline_atacseq.nf.test.snap} (100%)
 rename workflows/sra/tests/{with_rnaseq_samplesheet.nf.test => sra_nf_core_pipeline_rnaseq.nf.test} (90%)
 rename workflows/sra/tests/{with_rnaseq_samplesheet.nf.test.snap => sra_nf_core_pipeline_rnaseq.nf.test.snap} (100%)
 rename workflows/sra/tests/{with_taxprofiler_samplesheet.nf.test => sra_nf_core_pipeline_taxprofiler.nf.test} (89%)
 rename workflows/sra/tests/{with_taxprofiler_samplesheet.nf.test.snap => sra_nf_core_pipeline_taxprofiler.nf.test.snap} (100%)
 rename workflows/sra/tests/{with_viralrecon_samplesheet.nf.test => sra_nf_core_pipeline_viralrecon.nf.test} (90%)
 rename workflows/sra/tests/{with_viralrecon_samplesheet.nf.test.snap => sra_nf_core_pipeline_viralrecon.nf.test.snap} (100%)
 rename workflows/sra/tests/{skip_fastq.nf.test => sra_skip_fastq_download.nf.test} (94%)
 rename workflows/sra/tests/{skip_fastq.nf.test.snap => sra_skip_fastq_download.nf.test.snap} (100%)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 5f329342..451613fb 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -45,7 +45,14 @@ jobs:
         NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
         test_tags:
           - "modules_local"
-          - "sra"
+          - "sra_default_parameters"
+          - "sra_custom_ena_metadata_fields"
+          - "sra_force_sratools_download"
+          - "sra_nf_core_pipeline_atacseq"
+          - "sra_nf_core_pipeline_rnaseq"
+          - "sra_nf_core_pipeline_taxprofiler"
+          - "sra_nf_core_pipeline_viralrecon"
+          - "sra_skip_fastq_download"
         profile:
           - "docker"
 
diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test
index 26dbe22f..5f08ceca 100644
--- a/modules/local/multiqc_mappings_config/tests/main.nf.test
+++ b/modules/local/multiqc_mappings_config/tests/main.nf.test
@@ -1,18 +1,19 @@
 nextflow_process {
 
-    name "Test Process MULTIQC_MAPPINGS_CONFIG"
+    name "Test process: MULTIQC_MAPPINGS_CONFIG"
     script "modules/local/multiqc_mappings_config/main.nf"
     process "MULTIQC_MAPPINGS_CONFIG"
     tag "modules"
     tag "modules_local"
     tag "multiqc_mappings_config"
 
-    test("SRX9626017_SRR13191702") {
+    test("Should run without failures") {
 
         when {
             params {
-                outdir   = "$outputDir"
+                outdir = "$outputDir"
             }
+
             process {
                 """
                 input[0] = file(params.test_data['modules_local']['multiqc_mappings_config'], checkIfExists: true)
@@ -26,7 +27,5 @@ nextflow_process {
                 { assert snapshot(process.out).match() },
             )
         }
-
     }
-
 }
diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test
index e8b0d406..33b9b185 100644
--- a/modules/local/sra_fastq_ftp/tests/main.nf.test
+++ b/modules/local/sra_fastq_ftp/tests/main.nf.test
@@ -1,24 +1,25 @@
 nextflow_process {
 
-    name "Test Process SRA_FASTQ_FTP"
+    name "Test process: SRA_FASTQ_FTP"
     script "modules/local/sra_fastq_ftp/main.nf"
     process "SRA_FASTQ_FTP"
     tag "modules"
     tag "modules_local"
     tag "sra_fastq_ftp"
 
-    test("SRX9626017_SRR13191702") {
+    test("Should run without failures") {
 
         when {
             params {
-                outdir   = "$outputDir"
+                outdir = "$outputDir"
             }
+
             process {
                 """
                 input[0] = [
-                            [ id:'SRX9626017_SRR13191702', single_end:false, md5_1: '89c5be920021a035084d8aeb74f32df7', md5_2: '56271be38a80db78ef3bdfc5d9909b98' ], // meta map
-                            params.test_data['modules_local']['sra_fastq_ftp']
-                        ]
+                    [ id:'SRX9626017_SRR13191702', single_end:false, md5_1: '89c5be920021a035084d8aeb74f32df7', md5_2: '56271be38a80db78ef3bdfc5d9909b98' ], // meta map
+                    params.test_data['modules_local']['sra_fastq_ftp']
+                ]
                 """
             }
         }
@@ -29,7 +30,5 @@ nextflow_process {
                 { assert snapshot(process.out).match() },
             )
         }
-
     }
-
 }
diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test
index a140efdc..3953f008 100644
--- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test
+++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test
@@ -1,6 +1,6 @@
 nextflow_process {
 
-    name "Test Process SRA_IDS_TO_RUNINFO"
+    name "Test process: SRA_IDS_TO_RUNINFO"
     script "modules/local/sra_ids_to_runinfo/main.nf"
     process "SRA_IDS_TO_RUNINFO"
     tag "modules"
@@ -11,8 +11,9 @@ nextflow_process {
 
         when {
             params {
-                outdir   = "$outputDir"
+                outdir = "$outputDir"
             }
+
             process {
                 """
                 input[0] = 'SRR13191702'
@@ -27,7 +28,5 @@ nextflow_process {
                 { assert snapshot(process.out).match() },
             )
         }
-
     }
-
 }
diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test b/modules/local/sra_merge_samplesheet/tests/main.nf.test
index 6ff471e8..6012103e 100644
--- a/modules/local/sra_merge_samplesheet/tests/main.nf.test
+++ b/modules/local/sra_merge_samplesheet/tests/main.nf.test
@@ -1,6 +1,6 @@
 nextflow_process {
 
-    name "Test Process SRA_MERGE_SAMPLESHEET"
+    name "Test process: SRA_MERGE_SAMPLESHEET"
     script "modules/local/sra_merge_samplesheet/main.nf"
     process "SRA_MERGE_SAMPLESHEET"
     tag "modules"
@@ -11,8 +11,9 @@ nextflow_process {
 
         when {
             params {
-                outdir   = "$outputDir"
+                outdir = "$outputDir"
             }
+
             process {
                 """
                 input[0] = params.test_data['modules_local']['sra_merge_samplesheet_samplesheets'].collect { file(it, checkIfExists: true) }
@@ -27,7 +28,5 @@ nextflow_process {
                 { assert snapshot(process.out).match() },
             )
         }
-
     }
-
 }
diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
index 154ae4eb..7311f847 100644
--- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
+++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
@@ -1,6 +1,6 @@
 nextflow_process {
 
-    name "Test Process SRA_RUNINFO_TO_FTP"
+    name "Test process: SRA_RUNINFO_TO_FTP"
     script "modules/local/sra_runinfo_to_ftp/main.nf"
     process "SRA_RUNINFO_TO_FTP"
     tag "modules"
@@ -11,8 +11,9 @@ nextflow_process {
 
         when {
             params {
-                outdir   = "$outputDir"
+                outdir = "$outputDir"
             }
+
             process {
                 """
                 input[0] = file(params.test_data['modules_local']['sra_runinfo_to_ftp'], checkIfExists: true)
@@ -26,7 +27,5 @@ nextflow_process {
                 { assert snapshot(process.out).match() },
             )
         }
-
     }
-
 }
diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test
index 7448fe1d..163312c7 100644
--- a/modules/local/sra_to_samplesheet/tests/main.nf.test
+++ b/modules/local/sra_to_samplesheet/tests/main.nf.test
@@ -1,6 +1,6 @@
 nextflow_process {
 
-    name "Test Process SRA_TO_SAMPLESHEET"
+    name "Test process: SRA_TO_SAMPLESHEET"
     script "modules/local/sra_to_samplesheet/main.nf"
     process "SRA_TO_SAMPLESHEET"
     tag "modules"
@@ -11,14 +11,15 @@ nextflow_process {
 
         when {
             params {
-                outdir   = "$outputDir"
+                outdir = "$outputDir"
             }
+
             process {
                 """
-                input[0] = 'meta'
+                input[0] = [id:'ERX1188904_ERR1109373', run_accession:'ERR1109373', experiment_accession:'ERX1188904', sample_accession:'SAMEA3643867',  experiment_alias:'ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7', run_alias:'ena-RUN-CAM-03-11-2015-17:01:52:847-7',  sample_alias:'sample_56', study_alias:'ena-STUDY-CAM-02-11-2015-17:42:24:189-13', library_layout:'PAIRED', experiment_title:'Illumina HiSeq 2500 paired end sequencing', sample_title:'RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome', sample_description:'RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome', fastq_md5:'8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9', fastq_ftp:'ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz', fastq_1:'./results/fastq/ERX1188904_ERR1109373_1.fastq.gz', fastq_2:'./results/fastq/ERX1188904_ERR1109373_2.fastq.gz', md5_1:'9fd57225d6c07a31843276d6df9b15c0', md5_2:'5a62e8f785687dce890cfb4fe3e607f9', single_end:false]
                 input[1] = 'rnaseq'
-                input[2] = 'strandedness'
-                input[3] = 'mapping_fields'
+                input[2] = 'auto'
+                input[3] = 'experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description'
                 """
             }
         }
@@ -29,7 +30,5 @@ nextflow_process {
                 { assert snapshot(process.out).match() },
             )
         }
-
     }
-
 }
diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 4fa13985..0d6aa1a1 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -1,12 +1,12 @@
 nextflow_pipeline {
 
-    name "Test Workflow main.nf"
+    name "Test workflow: sra.nf"
     script "main.nf"
     tag "workflows"
-    tag "sra"
-    tag "sra_default"
+    tag "workflows_sra"
+    tag "sra_default_parameters"
 
-    test("SRA FASTQ & Metadata") {
+    test("Parameters: default") {
 
         when {
             params {
@@ -19,23 +19,25 @@ nextflow_pipeline {
                 { assert workflow.success },
                 { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") },
                 { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
-                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") },
+                { assert snapshot(
+                    path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
+                    path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
+                    path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
+                    path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
+                    path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
+                    path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
+                    path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
+                    path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
+                    path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
+                    path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") 
+                },
                 { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
-                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
-                                path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
+                { assert snapshot(
+                    path("$outputDir/samplesheet/id_mappings.csv"),
+                    path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet")
+                },
                 { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
             )
         }
-
     }
-
 }
diff --git a/workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
similarity index 81%
rename from workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test
rename to workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index b9956366..173b9fbd 100644
--- a/workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -1,18 +1,18 @@
 nextflow_pipeline {
 
-    name "Test Workflow main.nf"
+    name "Test workflow: sra.nf"
     script "main.nf"
     tag "workflows"
-    tag "sra"
-    tag "sra_with_rnaseq_specific_ena"
+    tag "workflows_sra"
+    tag "sra_custom_ena_metadata_fields"
 
-    test("SRA NF-CORE/RNASEQ Samplesheet With Specific ENA metadata") {
+    test("Parameters: '--nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...'") {
 
         when {
             params {
-                outdir                = "$outputDir"
-                nf_core_pipeline      = "rnaseq"
-                ena_metadata_fields   = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5"
+                outdir = "$outputDir"
+                nf_core_pipeline = "rnaseq"
+                ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5"
                 sample_mapping_fields = "run_accession,library_layout"
             }
         }
diff --git a/workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
similarity index 100%
rename from workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test.snap
rename to workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
diff --git a/workflows/sra/tests/with_sratools.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
similarity index 92%
rename from workflows/sra/tests/with_sratools.nf.test
rename to workflows/sra/tests/sra_force_sratools_download.nf.test
index e3239a18..a5c6afa6 100644
--- a/workflows/sra/tests/with_sratools.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -1,16 +1,16 @@
 nextflow_pipeline {
 
-    name "Test Workflow main.nf"
+    name "Test workflow: sra.nf"
     script "main.nf"
     tag "workflows"
-    tag "sra"
+    tag "workflows_sra"
     tag "sra_force_sratools_download"
 
-    test("Force SRA-Tools Download") {
+    test("Parameters: '--force_sratools_download'") {
 
         when {
             params {
-                outdir                  = "$outputDir"
+                outdir = "$outputDir"
                 force_sratools_download = true
             }
         }
@@ -36,7 +36,5 @@ nextflow_pipeline {
                 { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
             )
         }
-
     }
-
 }
diff --git a/workflows/sra/tests/with_sratools.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
similarity index 100%
rename from workflows/sra/tests/with_sratools.nf.test.snap
rename to workflows/sra/tests/sra_force_sratools_download.nf.test.snap
diff --git a/workflows/sra/tests/with_atacseq_samplesheet.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
similarity index 90%
rename from workflows/sra/tests/with_atacseq_samplesheet.nf.test
rename to workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index 13f41868..4286327f 100644
--- a/workflows/sra/tests/with_atacseq_samplesheet.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -1,16 +1,16 @@
 nextflow_pipeline {
 
-    name "Test Workflow main.nf"
+    name "Test workflow: sra.nf"
     script "main.nf"
     tag "workflows"
-    tag "sra"
-    tag "sra_with_atacseq"
+    tag "workflows_sra"
+    tag "sra_nf_core_pipeline_atacseq"
 
-    test("SRA NF-CORE/ATACSEQ Samplesheet") {
+    test("Parameters: '--nf_core_pipeline atacseq'") {
 
         when {
             params {
-                outdir           = "$outputDir"
+                outdir = "$outputDir"
                 nf_core_pipeline = "atacseq"
             }
         }
diff --git a/workflows/sra/tests/with_atacseq_samplesheet.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
similarity index 100%
rename from workflows/sra/tests/with_atacseq_samplesheet.nf.test.snap
rename to workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
diff --git a/workflows/sra/tests/with_rnaseq_samplesheet.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
similarity index 90%
rename from workflows/sra/tests/with_rnaseq_samplesheet.nf.test
rename to workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index fce8853c..c948e7dc 100644
--- a/workflows/sra/tests/with_rnaseq_samplesheet.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -1,16 +1,16 @@
 nextflow_pipeline {
 
-    name "Test Workflow main.nf"
+    name "Test workflow: sra.nf"
     script "main.nf"
     tag "workflows"
-    tag "sra"
-    tag "sra_with_rnaseq"
+    tag "workflows_sra"
+    tag "sra_nf_core_pipeline_rnaseq"
 
-    test("SRA NF-CORE/RNASEQ Samplesheet") {
+    test("Parameters: '--nf_core_pipeline rnaseq'") {
 
         when {
             params {
-                outdir           = "$outputDir"
+                outdir = "$outputDir"
                 nf_core_pipeline = "rnaseq"
             }
         }
diff --git a/workflows/sra/tests/with_rnaseq_samplesheet.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
similarity index 100%
rename from workflows/sra/tests/with_rnaseq_samplesheet.nf.test.snap
rename to workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
diff --git a/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
similarity index 89%
rename from workflows/sra/tests/with_taxprofiler_samplesheet.nf.test
rename to workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index 9d6e5f1f..ab39f52f 100644
--- a/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -1,16 +1,16 @@
 nextflow_pipeline {
 
-    name "Test Workflow main.nf"
+    name "Test workflow: sra.nf"
     script "main.nf"
     tag "workflows"
-    tag "sra"
-    tag "sra_with_taxprofiler"
+    tag "workflows_sra"
+    tag "sra_nf_core_pipeline_taxprofiler"
 
-    test("SRA NF-CORE/TAXPROFILER Samplesheet") {
+    test("Parameters: '--nf_core_pipeline taxprofiler'") {
 
         when {
             params {
-                outdir           = "$outputDir"
+                outdir = "$outputDir"
                 nf_core_pipeline = "taxprofiler"
             }
         }
@@ -37,5 +37,4 @@ nextflow_pipeline {
             )
         }
     }
-
 }
diff --git a/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
similarity index 100%
rename from workflows/sra/tests/with_taxprofiler_samplesheet.nf.test.snap
rename to workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
diff --git a/workflows/sra/tests/with_viralrecon_samplesheet.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
similarity index 90%
rename from workflows/sra/tests/with_viralrecon_samplesheet.nf.test
rename to workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index 429a114a..c80a092a 100644
--- a/workflows/sra/tests/with_viralrecon_samplesheet.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -1,16 +1,16 @@
 nextflow_pipeline {
 
-    name "Test Workflow main.nf"
+    name "Test workflow: sra.nf"
     script "main.nf"
     tag "workflows"
-    tag "sra"
-    tag "sra_with_viralrecon"
+    tag "workflows_sra"
+    tag "sra_nf_core_pipeline_viralrecon"
 
-    test("SRA NF-CORE/VIRALRECON Samplesheet") {
+    test("Parameters: '--nf_core_pipeline viralrecon'") {
 
         when {
             params {
-                outdir           = "$outputDir"
+                outdir = "$outputDir"
                 nf_core_pipeline = "viralrecon"
             }
         }
diff --git a/workflows/sra/tests/with_viralrecon_samplesheet.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
similarity index 100%
rename from workflows/sra/tests/with_viralrecon_samplesheet.nf.test.snap
rename to workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
diff --git a/workflows/sra/tests/skip_fastq.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
similarity index 94%
rename from workflows/sra/tests/skip_fastq.nf.test
rename to workflows/sra/tests/sra_skip_fastq_download.nf.test
index 188f0652..9a274731 100644
--- a/workflows/sra/tests/skip_fastq.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -1,16 +1,16 @@
 nextflow_pipeline {
 
-    name "Test Workflow main.nf"
+    name "Test workflow: sra.nf"
     script "main.nf"
     tag "workflows"
-    tag "sra"
-    tag "sra_skip_fastq"
+    tag "workflows_sra"
+    tag "sra_skip_fastq_download"
 
-    test("SRA Skip FASTQ") {
+    test("Parameters: '--skip_fastq_download'") {
 
         when {
             params {
-                outdir              = "$outputDir"
+                outdir = "$outputDir"
                 skip_fastq_download = true
             }
         }
@@ -49,7 +49,5 @@ nextflow_pipeline {
                 { assert !new File("$outputDir/fastq/SRX9626017_SRR13191702_2.fastq.gz").exists() }
             )
         }
-
     }
-
 }
diff --git a/workflows/sra/tests/skip_fastq.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
similarity index 100%
rename from workflows/sra/tests/skip_fastq.nf.test.snap
rename to workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
diff --git a/workflows/synapse/tests/main.nf.test b/workflows/synapse/tests/main.nf.test
index efb7d793..7cbfed11 100644
--- a/workflows/synapse/tests/main.nf.test
+++ b/workflows/synapse/tests/main.nf.test
@@ -1,6 +1,6 @@
 nextflow_pipeline {
 
-    name "Test Workflow main.nf"
+    name "Test workflow: synapse.nf"
     script "main.nf"
     tag "workflows"
     tag "synapse"

From 73ea3ca585f027ae73bd9003f0f5480389ab5528 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 17 Aug 2023 13:06:34 +0100
Subject: [PATCH 378/852] Patch custom/dumpsoftwareversions module to remove NF
 version dump

---
 modules.json                                        |  3 ++-
 .../custom-dumpsoftwareversions.diff                | 13 +++++++++++++
 .../templates/dumpsoftwareversions.py               |  1 -
 3 files changed, 15 insertions(+), 2 deletions(-)
 create mode 100644 modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff

diff --git a/modules.json b/modules.json
index 3137b88b..2244addd 100644
--- a/modules.json
+++ b/modules.json
@@ -8,7 +8,8 @@
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff"
                     },
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
diff --git a/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff b/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff
new file mode 100644
index 00000000..a7893b24
--- /dev/null
+++ b/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff
@@ -0,0 +1,13 @@
+Changes in module 'nf-core/custom/dumpsoftwareversions'
+--- modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
++++ modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+@@ -75,7 +75,6 @@
+             versions_by_module[module] = process_versions
+ 
+     versions_by_module["Workflow"] = {
+-        "Nextflow": "$workflow.nextflow.version",
+         "$workflow.manifest.name": "$workflow.manifest.version",
+     }
+ 
+
+************************************************************
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
index da033408..33d127f8 100755
--- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
@@ -75,7 +75,6 @@ def main():
             versions_by_module[module] = process_versions
 
     versions_by_module["Workflow"] = {
-        "Nextflow": "$workflow.nextflow.version",
         "$workflow.manifest.name": "$workflow.manifest.version",
     }
 

From de464567cb187f5eddecaa9b0e3c5f8ef3bedd69 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 17 Aug 2023 13:27:34 +0100
Subject: [PATCH 379/852] Use default snapshot for all workflows

---
 .../tests/main.nf.test                        |  2 +-
 .../tests/main.nf.test.snap                   | 27 +++++++++++++++-
 .../local/sra_fastq_ftp/tests/main.nf.test    |  2 +-
 .../sra_ids_to_runinfo/tests/main.nf.test     |  2 +-
 .../sra_merge_samplesheet/tests/main.nf.test  |  2 +-
 .../sra_runinfo_to_ftp/tests/main.nf.test     |  2 +-
 .../sra_to_samplesheet/tests/main.nf.test     |  2 +-
 workflows/sra/tests/main.nf.test              | 21 +-----------
 workflows/sra/tests/main.nf.test.snap         | 16 +++++++---
 .../sra_custom_ena_metadata_fields.nf.test    | 19 ++---------
 ...ra_custom_ena_metadata_fields.nf.test.snap | 16 +++++++---
 .../tests/sra_force_sratools_download.nf.test | 19 ++---------
 .../sra_force_sratools_download.nf.test.snap  | 16 +++++++---
 .../sra_nf_core_pipeline_atacseq.nf.test      | 19 ++---------
 .../sra_nf_core_pipeline_atacseq.nf.test.snap | 16 +++++++---
 .../tests/sra_nf_core_pipeline_rnaseq.nf.test | 19 ++---------
 .../sra_nf_core_pipeline_rnaseq.nf.test.snap  | 16 +++++++---
 .../sra_nf_core_pipeline_taxprofiler.nf.test  | 19 ++---------
 ..._nf_core_pipeline_taxprofiler.nf.test.snap | 16 +++++++---
 .../sra_nf_core_pipeline_viralrecon.nf.test   | 19 ++---------
 ...a_nf_core_pipeline_viralrecon.nf.test.snap | 16 +++++++---
 .../sra/tests/sra_skip_fastq_download.nf.test | 32 ++-----------------
 .../sra_skip_fastq_download.nf.test.snap      | 22 +++++++++++--
 23 files changed, 150 insertions(+), 190 deletions(-)

diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test
index 5f08ceca..3bf79537 100644
--- a/modules/local/multiqc_mappings_config/tests/main.nf.test
+++ b/modules/local/multiqc_mappings_config/tests/main.nf.test
@@ -24,7 +24,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
+                { assert snapshot(process.out).match() }
             )
         }
     }
diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap
index e8914aea..9cf7fb38 100644
--- a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap
+++ b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap
@@ -22,6 +22,31 @@
                 ]
             }
         ],
-        "timestamp": "2023-07-05T15:01:18+0000"
+        "timestamp": "2023-08-17T12:02:35+0000"
+    },
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
+                        "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                ],
+                "versions": [
+                    "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                ],
+                "yml": [
+                    [
+                        "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
+                        "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2023-08-17T12:02:35+0000"
     }
 }
\ No newline at end of file
diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test
index 33b9b185..7892d156 100644
--- a/modules/local/sra_fastq_ftp/tests/main.nf.test
+++ b/modules/local/sra_fastq_ftp/tests/main.nf.test
@@ -27,7 +27,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
+                { assert snapshot(process.out).match() }
             )
         }
     }
diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test
index 3953f008..f8a44086 100644
--- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test
+++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test
@@ -25,7 +25,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
+                { assert snapshot(process.out).match() }
             )
         }
     }
diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test b/modules/local/sra_merge_samplesheet/tests/main.nf.test
index 6012103e..e37039bd 100644
--- a/modules/local/sra_merge_samplesheet/tests/main.nf.test
+++ b/modules/local/sra_merge_samplesheet/tests/main.nf.test
@@ -25,7 +25,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
+                { assert snapshot(process.out).match() }
             )
         }
     }
diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
index 7311f847..1558ff39 100644
--- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
+++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
@@ -24,7 +24,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
+                { assert snapshot(process.out).match() }
             )
         }
     }
diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test
index 163312c7..b2ec5b11 100644
--- a/modules/local/sra_to_samplesheet/tests/main.nf.test
+++ b/modules/local/sra_to_samplesheet/tests/main.nf.test
@@ -27,7 +27,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
+                { assert snapshot(process.out).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 0d6aa1a1..39a5cc3f 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -17,26 +17,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") },
-                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
-                { assert snapshot(
-                    path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
-                    path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
-                    path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
-                    path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
-                    path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
-                    path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
-                    path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
-                    path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
-                    path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
-                    path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") 
-                },
-                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
-                { assert snapshot(
-                    path("$outputDir/samplesheet/id_mappings.csv"),
-                    path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet")
-                },
-                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
+                { assert snapshot(process.out).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
index dcdb43b5..88ea9654 100644
--- a/workflows/sra/tests/main.nf.test.snap
+++ b/workflows/sra/tests/main.nf.test.snap
@@ -1,4 +1,12 @@
 {
+    "Parameters: default": {
+        "content": [
+            {
+                
+            }
+        ],
+        "timestamp": "2023-08-17T12:09:45+0000"
+    },
     "metadata": {
         "content": [
             "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
@@ -12,20 +20,20 @@
             "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
             "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
         ],
-        "timestamp": "2023-08-06T23:48:50+0000"
+        "timestamp": "2023-08-17T12:09:45+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
             "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
         ],
-        "timestamp": "2023-08-06T23:48:50+0000"
+        "timestamp": "2023-08-17T12:09:45+0000"
     },
     "software_versions": {
         "content": [
             "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
-        "timestamp": "2023-08-06T23:48:50+0000"
+        "timestamp": "2023-08-17T12:09:45+0000"
     },
     "fastq": {
         "content": [
@@ -75,6 +83,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-08-06T23:48:50+0000"
+        "timestamp": "2023-08-17T12:09:45+0000"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index 173b9fbd..6e27c4a9 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -6,7 +6,7 @@ nextflow_pipeline {
     tag "workflows_sra"
     tag "sra_custom_ena_metadata_fields"
 
-    test("Parameters: '--nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...'") {
+    test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") {
 
         when {
             params {
@@ -20,22 +20,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") },
-                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
-                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") },
-                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
-                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
-                                path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
-                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
+                { assert snapshot(process.out).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
index bfa3c9cd..55c39d4f 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
@@ -12,20 +12,28 @@
             "SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1",
             "SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236"
         ],
-        "timestamp": "2023-07-03T23:38:27+0000"
+        "timestamp": "2023-08-17T12:11:42+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f",
             "multiqc_config.yml:md5,6f6189ee58855de81eaf82ad86e21040"
         ],
-        "timestamp": "2023-07-03T23:38:27+0000"
+        "timestamp": "2023-08-17T12:11:42+0000"
     },
     "software_versions": {
         "content": [
             "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
-        "timestamp": "2023-07-03T23:38:27+0000"
+        "timestamp": "2023-08-17T12:11:42+0000"
+    },
+    "Parameters: '--nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...'": {
+        "content": [
+            {
+                
+            }
+        ],
+        "timestamp": "2023-08-17T12:11:42+0000"
     },
     "fastq": {
         "content": [
@@ -75,6 +83,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-07-03T23:38:27+0000"
+        "timestamp": "2023-08-17T12:11:42+0000"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index a5c6afa6..1b501975 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -6,7 +6,7 @@ nextflow_pipeline {
     tag "workflows_sra"
     tag "sra_force_sratools_download"
 
-    test("Parameters: '--force_sratools_download'") {
+    test("Parameters: --force_sratools_download") {
 
         when {
             params {
@@ -18,22 +18,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") },
-                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
-                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") },
-                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
-                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
-                                path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
-                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
+                { assert snapshot(process.out).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
index bbec9969..d5d694da 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
@@ -1,4 +1,12 @@
 {
+    "Parameters: '--force_sratools_download'": {
+        "content": [
+            {
+                
+            }
+        ],
+        "timestamp": "2023-08-17T12:15:55+0000"
+    },
     "metadata": {
         "content": [
             "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
@@ -12,20 +20,20 @@
             "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
             "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
         ],
-        "timestamp": "2023-08-06T23:43:45+0000"
+        "timestamp": "2023-08-17T12:15:55+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
             "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
         ],
-        "timestamp": "2023-08-06T23:43:45+0000"
+        "timestamp": "2023-08-17T12:15:55+0000"
     },
     "software_versions": {
         "content": [
             "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
-        "timestamp": "2023-08-06T23:43:45+0000"
+        "timestamp": "2023-08-17T12:15:55+0000"
     },
     "fastq": {
         "content": [
@@ -54,6 +62,6 @@
             "SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7",
             "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af"
         ],
-        "timestamp": "2023-08-06T23:43:45+0000"
+        "timestamp": "2023-08-17T12:15:55+0000"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index 4286327f..bda1d724 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -6,7 +6,7 @@ nextflow_pipeline {
     tag "workflows_sra"
     tag "sra_nf_core_pipeline_atacseq"
 
-    test("Parameters: '--nf_core_pipeline atacseq'") {
+    test("Parameters: --nf_core_pipeline atacseq") {
 
         when {
             params {
@@ -18,22 +18,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") },
-                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
-                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") },
-                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
-                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
-                                path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
-                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
+                { assert snapshot(process.out).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
index a9dd40a0..c99f258e 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
@@ -12,20 +12,28 @@
             "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
             "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
         ],
-        "timestamp": "2023-08-06T23:38:47+0000"
+        "timestamp": "2023-08-17T12:21:36+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
             "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
         ],
-        "timestamp": "2023-08-06T23:38:47+0000"
+        "timestamp": "2023-08-17T12:21:36+0000"
     },
     "software_versions": {
         "content": [
             "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
-        "timestamp": "2023-08-06T23:38:47+0000"
+        "timestamp": "2023-08-17T12:21:36+0000"
+    },
+    "Parameters: '--nf_core_pipeline atacseq'": {
+        "content": [
+            {
+                
+            }
+        ],
+        "timestamp": "2023-08-17T12:21:36+0000"
     },
     "fastq": {
         "content": [
@@ -75,6 +83,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-08-06T23:38:47+0000"
+        "timestamp": "2023-08-17T12:21:36+0000"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index c948e7dc..438b7f55 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -6,7 +6,7 @@ nextflow_pipeline {
     tag "workflows_sra"
     tag "sra_nf_core_pipeline_rnaseq"
 
-    test("Parameters: '--nf_core_pipeline rnaseq'") {
+    test("Parameters: --nf_core_pipeline rnaseq") {
 
         when {
             params {
@@ -18,22 +18,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") },
-                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
-                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") },
-                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
-                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
-                                path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
-                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
+                { assert snapshot(process.out).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
index 1e3e8a5b..1da0381a 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
@@ -12,20 +12,28 @@
             "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
             "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
         ],
-        "timestamp": "2023-08-06T23:50:46+0000"
+        "timestamp": "2023-08-17T12:19:51+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
             "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
         ],
-        "timestamp": "2023-08-06T23:50:46+0000"
+        "timestamp": "2023-08-17T12:19:51+0000"
     },
     "software_versions": {
         "content": [
             "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
-        "timestamp": "2023-08-06T23:50:46+0000"
+        "timestamp": "2023-08-17T12:19:51+0000"
+    },
+    "Parameters: '--nf_core_pipeline rnaseq'": {
+        "content": [
+            {
+                
+            }
+        ],
+        "timestamp": "2023-08-17T12:19:51+0000"
     },
     "fastq": {
         "content": [
@@ -75,6 +83,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-08-06T23:50:46+0000"
+        "timestamp": "2023-08-17T12:19:51+0000"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index ab39f52f..301938c4 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -6,7 +6,7 @@ nextflow_pipeline {
     tag "workflows_sra"
     tag "sra_nf_core_pipeline_taxprofiler"
 
-    test("Parameters: '--nf_core_pipeline taxprofiler'") {
+    test("Parameters: --nf_core_pipeline taxprofiler") {
 
         when {
             params {
@@ -18,22 +18,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") },
-                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
-                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") },
-                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
-                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
-                                path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
-                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
+                { assert snapshot(process.out).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
index b4fe3748..85f3957b 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
@@ -12,20 +12,28 @@
             "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
             "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
         ],
-        "timestamp": "2023-08-06T23:40:33+0000"
+        "timestamp": "2023-08-17T12:24:34+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
             "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
         ],
-        "timestamp": "2023-08-06T23:40:33+0000"
+        "timestamp": "2023-08-17T12:24:34+0000"
     },
     "software_versions": {
         "content": [
             "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
-        "timestamp": "2023-08-06T23:40:33+0000"
+        "timestamp": "2023-08-17T12:24:34+0000"
+    },
+    "Parameters: --nf_core_pipeline taxprofiler": {
+        "content": [
+            {
+                
+            }
+        ],
+        "timestamp": "2023-08-17T12:24:34+0000"
     },
     "fastq": {
         "content": [
@@ -75,6 +83,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-08-06T23:40:33+0000"
+        "timestamp": "2023-08-17T12:24:34+0000"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index c80a092a..892a7c3a 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -6,7 +6,7 @@ nextflow_pipeline {
     tag "workflows_sra"
     tag "sra_nf_core_pipeline_viralrecon"
 
-    test("Parameters: '--nf_core_pipeline viralrecon'") {
+    test("Parameters: --nf_core_pipeline viralrecon") {
 
         when {
             params {
@@ -18,22 +18,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") },
-                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
-                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") },
-                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
-                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
-                                path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
-                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
+                { assert snapshot(process.out).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
index 51b0ea51..13c59b5d 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
@@ -12,20 +12,28 @@
             "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
             "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
         ],
-        "timestamp": "2023-08-06T23:34:45+0000"
+        "timestamp": "2023-08-17T12:26:57+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
             "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
         ],
-        "timestamp": "2023-08-06T23:34:45+0000"
+        "timestamp": "2023-08-17T12:26:57+0000"
+    },
+    "Parameters: --nf_core_pipeline viralrecon": {
+        "content": [
+            {
+                
+            }
+        ],
+        "timestamp": "2023-08-17T12:26:57+0000"
     },
     "software_versions": {
         "content": [
             "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
-        "timestamp": "2023-08-06T23:34:45+0000"
+        "timestamp": "2023-08-17T12:26:57+0000"
     },
     "fastq": {
         "content": [
@@ -75,6 +83,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-08-06T23:34:45+0000"
+        "timestamp": "2023-08-17T12:26:57+0000"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index 9a274731..7d218cf7 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -6,7 +6,7 @@ nextflow_pipeline {
     tag "workflows_sra"
     tag "sra_skip_fastq_download"
 
-    test("Parameters: '--skip_fastq_download'") {
+    test("Parameters: --skip_fastq_download") {
 
         when {
             params {
@@ -18,35 +18,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") },
-                { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
-                                path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") },
-                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
-                { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
-                                path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
-                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() },
-                { assert !new File("$outputDir/fastq/DRX024467_DRR026872.fastq.gz").exists() },
-                { assert !new File("$outputDir/fastq/DRX026011_DRR028935_1.fastq.gz").exists() },
-                { assert !new File("$outputDir/fastq/DRX026011_DRR028935_2.fastq.gz").exists() },
-                { assert !new File("$outputDir/fastq/ERX1188904_ERR1109373_1.fastq.gz").exists() },
-                { assert !new File("$outputDir/fastq/ERX1188904_ERR1109373_2.fastq.gz").exists() },
-                { assert !new File("$outputDir/fastq/ERX1234253_ERR1160846.fastq.gz").exists() },
-                { assert !new File("$outputDir/fastq/SRX10940790_SRR14593545_1.fastq.gz").exists() },
-                { assert !new File("$outputDir/fastq/SRX10940790_SRR14593545_2.fastq.gz").exists() },
-                { assert !new File("$outputDir/fastq/SRX11047067_SRR14709033.fastq.gz").exists() },
-                { assert !new File("$outputDir/fastq/SRX6725035_SRR9984183.fastq.gz").exists() },
-                { assert !new File("$outputDir/fastq/SRX9315476_SRR12848126_1.fastq.gz").exists() },
-                { assert !new File("$outputDir/fastq/SRX9315476_SRR12848126_2.fastq.gz").exists() },
-                { assert !new File("$outputDir/fastq/SRX9626017_SRR13191702_1.fastq.gz").exists() },
-                { assert !new File("$outputDir/fastq/SRX9626017_SRR13191702_2.fastq.gz").exists() }
+                { assert snapshot(process.out).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
index 7f71a838..d004d5d2 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
@@ -1,4 +1,12 @@
 {
+    "Parameters: '--skip_fastq_download'": {
+        "content": [
+            {
+                
+            }
+        ],
+        "timestamp": "2023-08-17T12:25:19+0000"
+    },
     "metadata": {
         "content": [
             "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
@@ -12,19 +20,27 @@
             "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
             "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
         ],
-        "timestamp": "2023-08-06T23:37:00+0000"
+        "timestamp": "2023-08-17T12:25:19+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
             "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
         ],
-        "timestamp": "2023-08-06T23:37:00+0000"
+        "timestamp": "2023-08-17T12:25:19+0000"
     },
     "software_versions": {
         "content": [
             "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
-        "timestamp": "2023-08-06T23:37:00+0000"
+        "timestamp": "2023-08-17T12:25:19+0000"
+    },
+    "Parameters: --skip_fastq_download": {
+        "content": [
+            {
+                
+            }
+        ],
+        "timestamp": "2023-08-17T12:25:19+0000"
     }
 }
\ No newline at end of file

From dd94d03ece17a14b09f89fe3058213ee9eb666d1 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 23 Aug 2023 14:00:50 +0200
Subject: [PATCH 380/852] remove public aws ecr profile

---
 conf/public_aws_ecr.config | 33 ---------------------------------
 nextflow.config            |  3 ---
 2 files changed, 36 deletions(-)
 delete mode 100644 conf/public_aws_ecr.config

diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config
deleted file mode 100644
index 14b577d7..00000000
--- a/conf/public_aws_ecr.config
+++ /dev/null
@@ -1,33 +0,0 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    AWS ECR Config
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Config to set public AWS ECR images wherever possible
-    This improves speed when running on AWS infrastructure.
-    Use this as an example template when using your own private registry.
-----------------------------------------------------------------------------------------
-*/
-
-docker.registry = 'public.ecr.aws'
-podman.registry = 'public.ecr.aws'
-
-process {
-    withName: '.*:SRA_IDS_TO_RUNINFO' {
-        container = 'quay.io/biocontainers/python:3.9--1'
-    }
-    withName: '.*:SRA_RUNINFO_TO_FTP' {
-        container = 'quay.io/biocontainers/python:3.9--1'
-    }
-    withName: '.*:MULTIQC_MAPPINGS_CONFIG' {
-        container = 'quay.io/biocontainers/python:3.9--1'
-    }
-    withName: '.*:SRATOOLS_FASTERQDUMP' {
-        container = 'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0'
-    }
-    withName: '.*:SRA_MERGE_SAMPLESHEET' {
-        container = 'quay.io/nf-core/ubuntu:20.04'
-    }
-    withName: '.*:SYNAPSE_MERGE_SAMPLESHEET' {
-        container = 'quay.io/nf-core/ubuntu:20.04'
-    }
-}
diff --git a/nextflow.config b/nextflow.config
index 6eb5c18d..7b693a85 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -159,9 +159,6 @@ profiles {
         executor.cpus          = 16
         executor.memory        = 60.GB
     }
-    public_aws_ecr {
-        includeConfig 'conf/public_aws_ecr.config'
-    }
     test         { includeConfig 'conf/test.config'         }
     test_synapse { includeConfig 'conf/test_synapse.config' }
     test_full    { includeConfig 'conf/test_full.config'    }

From 1c5a396d686d53d58833c1be10c9b555ffb0c1e0 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 23 Aug 2023 14:06:42 +0200
Subject: [PATCH 381/852] split up config files to be more modular

---
 conf/modules/base.config                    | 32 +++++++++
 conf/{modules.config => modules/sra.config} | 79 ---------------------
 conf/modules/synapse.config                 | 69 ++++++++++++++++++
 nextflow.config                             |  4 +-
 4 files changed, 104 insertions(+), 80 deletions(-)
 create mode 100644 conf/modules/base.config
 rename conf/{modules.config => modules/sra.config} (58%)
 create mode 100644 conf/modules/synapse.config

diff --git a/conf/modules/base.config b/conf/modules/base.config
new file mode 100644
index 00000000..d7eb6c86
--- /dev/null
+++ b/conf/modules/base.config
@@ -0,0 +1,32 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+//
+// Generic process options for all workflows
+//
+process {
+
+    publishDir = [
+        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+    ]
+
+    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
+        publishDir = [
+            path: { "${params.outdir}/pipeline_info" },
+            mode: params.publish_dir_mode,
+            pattern: '*_versions.yml'
+        ]
+    }
+
+}
diff --git a/conf/modules.config b/conf/modules/sra.config
similarity index 58%
rename from conf/modules.config
rename to conf/modules/sra.config
index f5cb1c77..e6e9d168 100644
--- a/conf/modules.config
+++ b/conf/modules/sra.config
@@ -10,27 +10,6 @@
 ----------------------------------------------------------------------------------------
 */
 
-//
-// Generic process options for all workflows
-//
-process {
-
-    publishDir = [
-        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-    ]
-
-    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            pattern: '*_versions.yml'
-        ]
-    }
-
-}
-
 //
 //  Process options for the SRA workflow
 //
@@ -111,61 +90,3 @@ if (params.input_type == 'sra') {
     }
 
 }
-
-//
-//  Process options for the Synapse workflow
-//
-if (params.input_type == 'synapse') {
-
-    process {
-
-        withName: SYNAPSE_LIST {
-            ext.args = '--long'
-            publishDir = [
-                path: { "${params.outdir}/metadata" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
-        withName: SYNAPSE_GET {
-            publishDir = [
-                [
-                    path: { "${params.outdir}/fastq" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.fastq.gz"
-                ],
-                [
-                    path: { "${params.outdir}/fastq/md5" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.md5"
-                ]
-            ]
-        }
-
-        withName: SYNAPSE_SHOW {
-            publishDir = [
-                path: { "${params.outdir}/metadata" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
-        withName: SYNAPSE_TO_SAMPLESHEET {
-            publishDir = [
-                path: { "${params.outdir}/samplesheet" },
-                enabled: false
-            ]
-        }
-
-        withName: SYNAPSE_MERGE_SAMPLESHEET {
-            publishDir = [
-                path: { "${params.outdir}/samplesheet" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
-    }
-
-}
diff --git a/conf/modules/synapse.config b/conf/modules/synapse.config
new file mode 100644
index 00000000..bcca94db
--- /dev/null
+++ b/conf/modules/synapse.config
@@ -0,0 +1,69 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+//
+//  Process options for the Synapse workflow
+//
+if (params.input_type == 'synapse') {
+
+    process {
+
+        withName: SYNAPSE_LIST {
+            ext.args = '--long'
+            publishDir = [
+                path: { "${params.outdir}/metadata" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+        withName: SYNAPSE_GET {
+            publishDir = [
+                [
+                    path: { "${params.outdir}/fastq" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.fastq.gz"
+                ],
+                [
+                    path: { "${params.outdir}/fastq/md5" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.md5"
+                ]
+            ]
+        }
+
+        withName: SYNAPSE_SHOW {
+            publishDir = [
+                path: { "${params.outdir}/metadata" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+        withName: SYNAPSE_TO_SAMPLESHEET {
+            publishDir = [
+                path: { "${params.outdir}/samplesheet" },
+                enabled: false
+            ]
+        }
+
+        withName: SYNAPSE_MERGE_SAMPLESHEET {
+            publishDir = [
+                path: { "${params.outdir}/samplesheet" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+    }
+
+}
diff --git a/nextflow.config b/nextflow.config
index 6eb5c18d..486c058c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -217,7 +217,9 @@ manifest {
 }
 
 // Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
+includeConfig 'conf/modules/base.config'
+includeConfig 'conf/modules/sra.config'
+includeConfig 'conf/modules/synapse.config'
 
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit

From 9c5fadbd335d3f84064516d3bc1b93a06dc4baa9 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 23 Aug 2023 15:33:13 +0200
Subject: [PATCH 382/852] no cascade inclusion of config files

---
 conf/test.config | 3 ---
 nextflow.config  | 5 ++++-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/conf/test.config b/conf/test.config
index 0bc98595..3c58e9cf 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -22,6 +22,3 @@ params {
     // Input data
     input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv'
 }
-
-// Load test_data.config for nf-tests
-includeConfig 'test_data.config'
diff --git a/nextflow.config b/nextflow.config
index 7b693a85..578b233d 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -159,7 +159,10 @@ profiles {
         executor.cpus          = 16
         executor.memory        = 60.GB
     }
-    test         { includeConfig 'conf/test.config'         }
+    test         {
+        includeConfig 'conf/test.config'
+        includeConfig 'conf/test_data.config'
+    }
     test_synapse { includeConfig 'conf/test_synapse.config' }
     test_full    { includeConfig 'conf/test_full.config'    }
 }

From 5073409171943f07d0248f8bc15dc2db52e13bef Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 23 Aug 2023 15:33:46 +0200
Subject: [PATCH 383/852] use schema_ignore_params to remove warnings

---
 conf/test.config | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/conf/test.config b/conf/test.config
index 3c58e9cf..6a9d5d38 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -21,4 +21,6 @@ params {
 
     // Input data
     input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv'
+
+    schema_ignore_params = 'fastq_ftp_ids,genomes,merge_samplesheet_ids,test_data,test_data_base'
 }

From bc7fd25c21e1a058d00870513d1eb742847d3b0f Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 23 Aug 2023 16:21:07 +0200
Subject: [PATCH 384/852] fix lint

---
 .nf-core.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index 253f86e2..269ee3ed 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,5 +1,8 @@
 repository_type: pipeline
 lint:
+  actions_ci: false
+  files_exist:
+    - conf/modules.config
   files_unchanged:
     - .github/CONTRIBUTING.md
     - .github/ISSUE_TEMPLATE/bug_report.yml
@@ -7,7 +10,6 @@ lint:
     - assets/sendmail_template.txt
     - lib/NfcoreTemplate.groovy
     - .gitattributes
-  actions_ci: false
   multiqc_config: false
   nextflow_config:
     - "params.validationShowHiddenParams"

From 81324d23467f153484ffbb4f65f465f118d071c7 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 21 Aug 2023 18:05:36 +0100
Subject: [PATCH 385/852] Adds emit statement for FASTQs and metadata to SRA
 workflow

---
 CHANGELOG.md                                   |  1 +
 .../sra_to_samplesheet/tests/main.nf.test.snap | 18 +++++++++---------
 workflows/sra/main.nf                          | 18 ++++++++++++++----
 3 files changed, 24 insertions(+), 13 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 146b93b6..8573dea7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -18,6 +18,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 ### Enhancements & fixes
 
 - [#166](https://github.com/nf-core/fetchngs/issues/175) - Add NF-TEST pipeline end-to-end tests for existing CI tests
+- Emits all files in workflow for testing and enabling workflow to be imported when supported by Nextflow
 
 ## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-16
 
diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap
index 8b5f4947..e60c646a 100644
--- a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap
+++ b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap
@@ -19,8 +19,8 @@
                             "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
                             "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
                             "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
+                            "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz",
+                            "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz",
                             "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
                             "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
                             "single_end": false
@@ -45,8 +45,8 @@
                             "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
                             "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
                             "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
+                            "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz",
+                            "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz",
                             "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
                             "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
                             "single_end": false
@@ -71,8 +71,8 @@
                             "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
                             "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
                             "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
+                            "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz",
+                            "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz",
                             "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
                             "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
                             "single_end": false
@@ -97,8 +97,8 @@
                             "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
                             "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
                             "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
+                            "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz",
+                            "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz",
                             "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
                             "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
                             "single_end": false
@@ -108,6 +108,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-08-17T10:55:52+0000"
+        "timestamp": "2023-08-23T09:38:15+0000"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 512a73d4..3ca9b33e 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -81,6 +81,8 @@ workflow SRA {
         .set { ch_sra_metadata }
     ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first())
 
+    fastq_files = Channel.empty()
+
     if (!params.skip_fastq_download) {
 
         ch_sra_metadata
@@ -111,10 +113,13 @@ workflow SRA {
         )
         ch_versions = ch_versions.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.versions.first())
 
-        SRA_FASTQ_FTP
-            .out
-            .fastq
-            .mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads)
+        // Isolate FASTQ channel which will be added to emit block
+        fastq_files = fastq_files.mix(
+            SRA_FASTQ_FTP.out.fastq,
+            FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads
+        )
+
+        fastq_files
             .map { 
                 meta, fastq ->
                     def reads = fastq instanceof List ? fastq.flatten() : [ fastq ]
@@ -161,6 +166,11 @@ workflow SRA {
     CUSTOM_DUMPSOFTWAREVERSIONS (
         ch_versions.unique().collectFile(name: 'collated_versions.yml')
     )
+
+    emit:
+        fastq       = fastq_files
+        samplesheet = SRA_MERGE_SAMPLESHEET.out.samplesheet
+        mapping     = SRA_MERGE_SAMPLESHEET.out.mappings
 }
 
 /*

From 82fa5000fe8a468a4e202f5765d78b12a93c7e0f Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Thu, 24 Aug 2023 15:50:52 +0200
Subject: [PATCH 386/852] Update nextflow.config

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
---
 nextflow.config | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 486c058c..6b7463d3 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -218,8 +218,12 @@ manifest {
 
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules/base.config'
-includeConfig 'conf/modules/sra.config'
-includeConfig 'conf/modules/synapse.config'
+if ( params.input_type == 'sra' ) {
+    includeConfig 'conf/modules/sra.config'
+}
+if ( params.input_type == 'synapse' ) {
+    includeConfig 'conf/modules/synapse.config'
+}
 
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit

From 011addc3cf5d6ad036adc435cd30eaf88df2582d Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Aug 2023 15:52:05 +0200
Subject: [PATCH 387/852] remove if statement

---
 conf/modules/sra.config     | 122 +++++++++++++++++-------------------
 conf/modules/synapse.config |  83 ++++++++++++------------
 2 files changed, 99 insertions(+), 106 deletions(-)

diff --git a/conf/modules/sra.config b/conf/modules/sra.config
index e6e9d168..15802b41 100644
--- a/conf/modules/sra.config
+++ b/conf/modules/sra.config
@@ -13,80 +13,76 @@
 //
 //  Process options for the SRA workflow
 //
-if (params.input_type == 'sra') {
+process {
 
-    process {
-
-        withName: SRA_IDS_TO_RUNINFO {
-            publishDir = [
-                path: { "${params.outdir}/metadata" },
-                enabled: false
-            ]
-        }
-
-        withName: SRA_RUNINFO_TO_FTP {
-            publishDir = [
-                path: { "${params.outdir}/metadata" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
-        withName: SRA_FASTQ_FTP {
-            ext.args = '--retry 5 --continue-at - --max-time 1200'
-            publishDir = [
-                [
-                    path: { "${params.outdir}/fastq" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.fastq.gz"
-                ],
-                [
-                    path: { "${params.outdir}/fastq/md5" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.md5"
-                ]
-            ]
-        }
+    withName: SRA_IDS_TO_RUNINFO {
+        publishDir = [
+            path: { "${params.outdir}/metadata" },
+            enabled: false
+        ]
+    }
 
-        withName: SRATOOLS_PREFETCH {
-            publishDir = [
-                path: { "${params.outdir}/sra" },
-                enabled: false
-            ]
-        }
+    withName: SRA_RUNINFO_TO_FTP {
+        publishDir = [
+            path: { "${params.outdir}/metadata" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 
-        withName: SRATOOLS_FASTERQDUMP {
-            ext.args = '--split-files --include-technical'
-            publishDir = [
+    withName: SRA_FASTQ_FTP {
+        ext.args = '--retry 5 --continue-at - --max-time 1200'
+        publishDir = [
+            [
                 path: { "${params.outdir}/fastq" },
                 mode: params.publish_dir_mode,
                 pattern: "*.fastq.gz"
+            ],
+            [
+                path: { "${params.outdir}/fastq/md5" },
+                mode: params.publish_dir_mode,
+                pattern: "*.md5"
             ]
-        }
+        ]
+    }
 
-        withName: SRA_TO_SAMPLESHEET {
-            publishDir = [
-                path: { "${params.outdir}/samplesheet" },
-                enabled: false
-            ]
-        }
+    withName: SRATOOLS_PREFETCH {
+        publishDir = [
+            path: { "${params.outdir}/sra" },
+            enabled: false
+        ]
+    }
 
-        withName: SRA_MERGE_SAMPLESHEET {
-            publishDir = [
-                path: { "${params.outdir}/samplesheet" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
+    withName: SRATOOLS_FASTERQDUMP {
+        ext.args = '--split-files --include-technical'
+        publishDir = [
+            path: { "${params.outdir}/fastq" },
+            mode: params.publish_dir_mode,
+            pattern: "*.fastq.gz"
+        ]
+    }
 
-        withName: MULTIQC_MAPPINGS_CONFIG {
-            publishDir = [
-                path: { "${params.outdir}/samplesheet" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
+    withName: SRA_TO_SAMPLESHEET {
+        publishDir = [
+            path: { "${params.outdir}/samplesheet" },
+            enabled: false
+        ]
+    }
+
+    withName: SRA_MERGE_SAMPLESHEET {
+        publishDir = [
+            path: { "${params.outdir}/samplesheet" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 
+    withName: MULTIQC_MAPPINGS_CONFIG {
+        publishDir = [
+            path: { "${params.outdir}/samplesheet" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
     }
 
 }
diff --git a/conf/modules/synapse.config b/conf/modules/synapse.config
index bcca94db..2f52aa6f 100644
--- a/conf/modules/synapse.config
+++ b/conf/modules/synapse.config
@@ -13,57 +13,54 @@
 //
 //  Process options for the Synapse workflow
 //
-if (params.input_type == 'synapse') {
 
-    process {
+process {
 
-        withName: SYNAPSE_LIST {
-            ext.args = '--long'
-            publishDir = [
-                path: { "${params.outdir}/metadata" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
-        withName: SYNAPSE_GET {
-            publishDir = [
-                [
-                    path: { "${params.outdir}/fastq" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.fastq.gz"
-                ],
-                [
-                    path: { "${params.outdir}/fastq/md5" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.md5"
-                ]
-            ]
-        }
+    withName: SYNAPSE_LIST {
+        ext.args = '--long'
+        publishDir = [
+            path: { "${params.outdir}/metadata" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 
-        withName: SYNAPSE_SHOW {
-            publishDir = [
-                path: { "${params.outdir}/metadata" },
+    withName: SYNAPSE_GET {
+        publishDir = [
+            [
+                path: { "${params.outdir}/fastq" },
+                mode: params.publish_dir_mode,
+                pattern: "*.fastq.gz"
+            ],
+            [
+                path: { "${params.outdir}/fastq/md5" },
                 mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                pattern: "*.md5"
             ]
-        }
+        ]
+    }
 
-        withName: SYNAPSE_TO_SAMPLESHEET {
-            publishDir = [
-                path: { "${params.outdir}/samplesheet" },
-                enabled: false
-            ]
-        }
+    withName: SYNAPSE_SHOW {
+        publishDir = [
+            path: { "${params.outdir}/metadata" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 
-        withName: SYNAPSE_MERGE_SAMPLESHEET {
-            publishDir = [
-                path: { "${params.outdir}/samplesheet" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
+    withName: SYNAPSE_TO_SAMPLESHEET {
+        publishDir = [
+            path: { "${params.outdir}/samplesheet" },
+            enabled: false
+        ]
+    }
 
+    withName: SYNAPSE_MERGE_SAMPLESHEET {
+        publishDir = [
+            path: { "${params.outdir}/samplesheet" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
     }
 
 }

From 464397c9225cccb293240cfefcf0fded5915a985 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 24 Aug 2023 15:07:04 +0100
Subject: [PATCH 388/852] Add emit statement to synpase workflow

---
 workflows/sra/main.nf                     |  8 +++++---
 workflows/synapse/main.nf                 |  5 +++++
 workflows/synapse/tests/main.nf.test.snap | 16 ++++++++++++++++
 3 files changed, 26 insertions(+), 3 deletions(-)
 create mode 100644 workflows/synapse/tests/main.nf.test.snap

diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 3ca9b33e..e60386f9 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -168,9 +168,11 @@ workflow SRA {
     )
 
     emit:
-        fastq       = fastq_files
-        samplesheet = SRA_MERGE_SAMPLESHEET.out.samplesheet
-        mapping     = SRA_MERGE_SAMPLESHEET.out.mappings
+        fastq         = fastq_files
+        samplesheet   = SRA_MERGE_SAMPLESHEET.out.samplesheet
+        mapping       = SRA_MERGE_SAMPLESHEET.out.mappings
+        multiqc_config = MULTIQC_MAPPINGS_CONFIG.out.yml
+        versions      = ch_versions.unique()
 }
 
 /*
diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf
index f8cbeba1..0753a521 100644
--- a/workflows/synapse/main.nf
+++ b/workflows/synapse/main.nf
@@ -133,6 +133,11 @@ workflow SYNAPSE {
     CUSTOM_DUMPSOFTWAREVERSIONS (
         ch_versions.unique().collectFile(name: 'collated_versions.yml')
     )
+
+    emit:
+        fastq       = ch_fastq
+        samplesheet = SYNAPSE_MERGE_SAMPLESHEET.out.samplesheet
+        versions    = ch_versions.unique()
 }
 
 /*
diff --git a/workflows/synapse/tests/main.nf.test.snap b/workflows/synapse/tests/main.nf.test.snap
new file mode 100644
index 00000000..8528f776
--- /dev/null
+++ b/workflows/synapse/tests/main.nf.test.snap
@@ -0,0 +1,16 @@
+{
+    "samplesheet": {
+        "content": [
+            "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
+            "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548",
+            "samplesheet.csv:md5,9b3c35e8af74e9af194baa2498aaf4d4"
+        ],
+        "timestamp": "2023-08-24T14:05:07+0000"
+    },
+    "software_versions": {
+        "content": [
+            "software_versions.yml:md5,f37983a6b1ce2334fe62fa188b31ca51"
+        ],
+        "timestamp": "2023-08-24T14:05:07+0000"
+    }
+}
\ No newline at end of file

From 97af5cd85d6c20127c16dee4b3f158867943bbbf Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 24 Aug 2023 15:53:28 +0100
Subject: [PATCH 389/852] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8573dea7..20dd21f8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -18,7 +18,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 ### Enhancements & fixes
 
 - [#166](https://github.com/nf-core/fetchngs/issues/175) - Add NF-TEST pipeline end-to-end tests for existing CI tests
-- Emits all files in workflow for testing and enabling workflow to be imported when supported by Nextflow
+- [#184](https://github.com/nf-core/fetchngs/pull/184/files) Emits all files in workflow for testing and enabling workflow to be imported (not supported by Nextflow)
 
 ## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-16
 

From c7ab8b8bb2240d0d27a341e0ea20b4efec3f4913 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Aug 2023 18:07:07 +0200
Subject: [PATCH 390/852] move out multiqc and versions

---
 main.nf                   | 42 ++++++++++++++++++++++++++++++++++++
 workflows/sra/main.nf     | 45 +++++----------------------------------
 workflows/synapse/main.nf | 15 -------------
 3 files changed, 47 insertions(+), 55 deletions(-)

diff --git a/main.nf b/main.nf
index 6da732be..e9bce9cd 100644
--- a/main.nf
+++ b/main.nf
@@ -31,6 +31,15 @@ Channel
     .unique()
     .set { ch_ids }
 
+/*
+========================================================================================
+    IMPORT MODULES/SUBWORKFLOWS
+========================================================================================
+*/
+
+include { CUSTOM_DUMPSOFTWAREVERSIONS } from './modules/nf-core/custom/dumpsoftwareversions'
+include { MULTIQC_MAPPINGS_CONFIG     } from './modules/local/multiqc_mappings_config'
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     NAMED WORKFLOW FOR PIPELINE
@@ -62,18 +71,37 @@ if (params.input_type == input_type) {
 //
 workflow NFCORE_FETCHNGS {
 
+    ch_versions = Channel.empty()
+
     //
     // WORKFLOW: Download FastQ files for SRA / ENA / GEO / DDBJ ids
     //
     if (params.input_type == 'sra') {
         SRA ( ch_ids )
 
+    //
+    // MODULE: Create a MutiQC config file with sample name mappings
+    //
+        if (params.sample_mapping_fields) {
+            MULTIQC_MAPPINGS_CONFIG (SRA.out.mappings)
+            ch_versions = SRA.out.versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions)
+        }
+
+    //
+    // MODULE: Dump software versions for all tools used in the workflow
+    //
+
     //
     // WORKFLOW: Download FastQ files for Synapse ids
     //
     } else if (params.input_type == 'synapse') {
         SYNAPSE ( ch_ids )
+        ch_versions = SYNAPSE.out.versions
     }
+
+    CUSTOM_DUMPSOFTWAREVERSIONS (
+        ch_versions.unique().collectFile(name: 'collated_versions.yml')
+    )
 }
 
 /*
@@ -90,6 +118,20 @@ workflow {
     NFCORE_FETCHNGS ()
 }
 
+/*
+========================================================================================
+    COMPLETION EMAIL AND SUMMARY
+========================================================================================
+*/
+
+workflow.onComplete {
+    if (params.email || params.email_on_fail) {
+        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)
+    }
+    NfcoreTemplate.summary(workflow, params, log)
+    WorkflowSra.curateSamplesheetWarn(log)
+}
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     THE END
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index e60386f9..d4612cd0 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -24,7 +24,6 @@ include { SRA_RUNINFO_TO_FTP      } from '../../modules/local/sra_runinfo_to_ftp
 include { SRA_FASTQ_FTP           } from '../../modules/local/sra_fastq_ftp'
 include { SRA_TO_SAMPLESHEET      } from '../../modules/local/sra_to_samplesheet'
 include { SRA_MERGE_SAMPLESHEET   } from '../../modules/local/sra_merge_samplesheet'
-include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_config'
 
 /*
 ========================================================================================
@@ -32,8 +31,6 @@ include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_c
 ========================================================================================
 */
 
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions'
-
 include { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS } from '../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools'
 
 /*
@@ -86,9 +83,9 @@ workflow SRA {
     if (!params.skip_fastq_download) {
 
         ch_sra_metadata
-            .map { 
-                meta -> 
-                    [ meta, [ meta.fastq_1, meta.fastq_2 ] ] 
+            .map {
+                meta ->
+                    [ meta, [ meta.fastq_1, meta.fastq_2 ] ]
             }
             .branch {
                 ftp: it[0].fastq_1  && !params.force_sratools_download
@@ -120,7 +117,7 @@ workflow SRA {
         )
 
         fastq_files
-            .map { 
+            .map {
                 meta, fastq ->
                     def reads = fastq instanceof List ? fastq.flatten() : [ fastq ]
                     def meta_clone = meta.clone()
@@ -150,45 +147,13 @@ workflow SRA {
     )
     ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions)
 
-    //
-    // MODULE: Create a MutiQC config file with sample name mappings
-    //
-    if (params.sample_mapping_fields) {
-        MULTIQC_MAPPINGS_CONFIG (
-            SRA_MERGE_SAMPLESHEET.out.mappings
-        )
-        ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions)
-    }
-
-    //
-    // MODULE: Dump software versions for all tools used in the workflow
-    //
-    CUSTOM_DUMPSOFTWAREVERSIONS (
-        ch_versions.unique().collectFile(name: 'collated_versions.yml')
-    )
-
     emit:
         fastq         = fastq_files
         samplesheet   = SRA_MERGE_SAMPLESHEET.out.samplesheet
-        mapping       = SRA_MERGE_SAMPLESHEET.out.mappings
-        multiqc_config = MULTIQC_MAPPINGS_CONFIG.out.yml
+        mappings      = SRA_MERGE_SAMPLESHEET.out.mappings
         versions      = ch_versions.unique()
 }
 
-/*
-========================================================================================
-    COMPLETION EMAIL AND SUMMARY
-========================================================================================
-*/
-
-workflow.onComplete {
-    if (params.email || params.email_on_fail) {
-        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)
-    }
-    NfcoreTemplate.summary(workflow, params, log)
-    WorkflowSra.curateSamplesheetWarn(log)
-}
-
 /*
 ========================================================================================
     THE END
diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf
index 0753a521..34c3e315 100644
--- a/workflows/synapse/main.nf
+++ b/workflows/synapse/main.nf
@@ -25,14 +25,6 @@ include { SYNAPSE_GET               } from '../../modules/local/synapse_get'
 include { SYNAPSE_TO_SAMPLESHEET    } from '../../modules/local/synapse_to_samplesheet'
 include { SYNAPSE_MERGE_SAMPLESHEET } from '../../modules/local/synapse_merge_samplesheet'
 
-/*
-========================================================================================
-    IMPORT NF-CORE MODULES/SUBWORKFLOWS
-========================================================================================
-*/
-
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions'
-
 /*
 ========================================================================================
     RUN MAIN WORKFLOW
@@ -127,13 +119,6 @@ workflow SYNAPSE {
     )
     ch_versions = ch_versions.mix(SYNAPSE_MERGE_SAMPLESHEET.out.versions)
 
-    //
-    // MODULE: Dump software versions for all tools used in the workflow
-    //
-    CUSTOM_DUMPSOFTWAREVERSIONS (
-        ch_versions.unique().collectFile(name: 'collated_versions.yml')
-    )
-
     emit:
         fastq       = ch_fastq
         samplesheet = SYNAPSE_MERGE_SAMPLESHEET.out.samplesheet

From 372f9e434af68b1a854e8a68a8bec73510ca8ab9 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Aug 2023 18:10:41 +0200
Subject: [PATCH 391/852] enable tests in refactor

---
 .github/workflows/ci.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 451613fb..2a30309b 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -4,10 +4,12 @@ on:
   push:
     branches:
       - dev
+      - refactor
   pull_request:
     branches:
       - dev
       - master
+      - refactor
   release:
     types:
       - "published"

From 5dab8d0fa3e790ecb7baaced1fe08c9d01e994ec Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Thu, 24 Aug 2023 18:16:24 +0200
Subject: [PATCH 392/852] Apply suggestions from code review

---
 main.nf | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/main.nf b/main.nf
index e9bce9cd..0f48d3c8 100644
--- a/main.nf
+++ b/main.nf
@@ -86,11 +86,6 @@ workflow NFCORE_FETCHNGS {
             MULTIQC_MAPPINGS_CONFIG (SRA.out.mappings)
             ch_versions = SRA.out.versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions)
         }
-
-    //
-    // MODULE: Dump software versions for all tools used in the workflow
-    //
-
     //
     // WORKFLOW: Download FastQ files for Synapse ids
     //
@@ -99,6 +94,9 @@ workflow NFCORE_FETCHNGS {
         ch_versions = SYNAPSE.out.versions
     }
 
+    //
+    // MODULE: Dump software versions for all tools used in the workflow
+    //
     CUSTOM_DUMPSOFTWAREVERSIONS (
         ch_versions.unique().collectFile(name: 'collated_versions.yml')
     )

From aff72b7ecc372162ba88759c2033fe601885c16d Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Thu, 24 Aug 2023 18:43:03 +0200
Subject: [PATCH 393/852] Apply suggestions from code review

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
---
 main.nf | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/main.nf b/main.nf
index 0f48d3c8..2b852884 100644
--- a/main.nf
+++ b/main.nf
@@ -78,20 +78,25 @@ workflow NFCORE_FETCHNGS {
     //
     if (params.input_type == 'sra') {
         SRA ( ch_ids )
+        ch_versions = ch_versions.mix(SRA.out.versions)
+    }
 
     //
-    // MODULE: Create a MutiQC config file with sample name mappings
+    // MODULE: Create a MultiQC config file with sample name mappings
     //
         if (params.sample_mapping_fields) {
             MULTIQC_MAPPINGS_CONFIG (SRA.out.mappings)
-            ch_versions = SRA.out.versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions)
+            ch_versions = ch_versions.mix(
+                SRA.out.versions,
+                MULTIQC_MAPPINGS_CONFIG.out.versions
+            )
         }
     //
     // WORKFLOW: Download FastQ files for Synapse ids
     //
     } else if (params.input_type == 'synapse') {
         SYNAPSE ( ch_ids )
-        ch_versions = SYNAPSE.out.versions
+        ch_versions = ch_versions.mix(SYNAPSE.out.versions)
     }
 
     //

From 7f6439c1e6affd62bc13f76e63fd48ce6e262a75 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Aug 2023 18:46:00 +0200
Subject: [PATCH 394/852] fix syntax

---
 main.nf | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/main.nf b/main.nf
index 2b852884..5311164f 100644
--- a/main.nf
+++ b/main.nf
@@ -79,17 +79,12 @@ workflow NFCORE_FETCHNGS {
     if (params.input_type == 'sra') {
         SRA ( ch_ids )
         ch_versions = ch_versions.mix(SRA.out.versions)
-    }
-
     //
     // MODULE: Create a MultiQC config file with sample name mappings
     //
         if (params.sample_mapping_fields) {
             MULTIQC_MAPPINGS_CONFIG (SRA.out.mappings)
-            ch_versions = ch_versions.mix(
-                SRA.out.versions,
-                MULTIQC_MAPPINGS_CONFIG.out.versions
-            )
+            ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions)
         }
     //
     // WORKFLOW: Download FastQ files for Synapse ids

From 6355a331d97c8f12815926901404760feed3238c Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 25 Aug 2023 10:36:33 +0200
Subject: [PATCH 395/852] small refactor

---
 main.nf                   | 65 ++++++++++++++++++---------------------
 workflows/synapse/main.nf | 14 ---------
 2 files changed, 30 insertions(+), 49 deletions(-)

diff --git a/main.nf b/main.nf
index 5311164f..edb54fd8 100644
--- a/main.nf
+++ b/main.nf
@@ -1,20 +1,20 @@
 #!/usr/bin/env nextflow
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
     nf-core/fetchngs
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
     Github : https://github.com/nf-core/fetchngs
     Website: https://nf-co.re/fetchngs
     Slack  : https://nfcore.slack.com/channels/fetchngs
-----------------------------------------------------------------------------------------
+========================================================================================
 */
 
 nextflow.enable.dsl = 2
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
     VALIDATE & PRINT PARAMETER SUMMARY
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
 */
 
 WorkflowMain.initialise(workflow, params, log)
@@ -24,16 +24,21 @@ ch_input = file(params.input, checkIfExists: true)
 if (ch_input.isEmpty()) {exit 1, "File provided with --input is empty: ${ch_input.getName()}!"}
 
 // Read in ids from --input file
-Channel
-    .from(file(params.input, checkIfExists: true))
+ch_ids = Channel.from(file(params.input, checkIfExists: true))
     .splitCsv(header:false, sep:'', strip:true)
     .map { it[0] }
     .unique()
-    .set { ch_ids }
+
+// Auto-detect input type
+def input_type = ''
+if (WorkflowMain.isSraId(ch_input))          { input_type = 'sra' }
+else if (WorkflowMain.isSynapseId(ch_input)) { input_type = 'synapse' }
+else                                         { exit 1, 'Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!' }
+if (params.input_type != input_type)         { exit 1, "Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!" }
 
 /*
 ========================================================================================
-    IMPORT MODULES/SUBWORKFLOWS
+    IMPORT MODULES
 ========================================================================================
 */
 
@@ -41,30 +46,19 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from './modules/nf-core/custom/dumpsoftw
 include { MULTIQC_MAPPINGS_CONFIG     } from './modules/local/multiqc_mappings_config'
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    NAMED WORKFLOW FOR PIPELINE
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
+    IMPORT WORKFLOWS
+========================================================================================
 */
 
-// Auto-detect input id type
-def input_type = ''
-if (WorkflowMain.isSraId(ch_input)) {
-    input_type = 'sra'
-} else if (WorkflowMain.isSynapseId(ch_input)) {
-    input_type = 'synapse'
-} else {
-    exit 1, 'Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!'
-}
+if (params.input_type == 'sra')     include { SRA     } from './workflows/sra'
+if (params.input_type == 'synapse') include { SYNAPSE } from './workflows/synapse'
 
-if (params.input_type == input_type) {
-    if (params.input_type == 'sra') {
-        include { SRA } from './workflows/sra'
-    } else if (params.input_type == 'synapse') {
-        include { SYNAPSE } from './workflows/synapse'
-    }
-} else {
-    exit 1, "Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!"
-}
+/*
+========================================================================================
+    NAMED WORKFLOW FOR PIPELINE
+========================================================================================
+*/
 
 //
 // WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided
@@ -77,13 +71,13 @@ workflow NFCORE_FETCHNGS {
     // WORKFLOW: Download FastQ files for SRA / ENA / GEO / DDBJ ids
     //
     if (params.input_type == 'sra') {
-        SRA ( ch_ids )
+        SRA(ch_ids)
         ch_versions = ch_versions.mix(SRA.out.versions)
     //
     // MODULE: Create a MultiQC config file with sample name mappings
     //
         if (params.sample_mapping_fields) {
-            MULTIQC_MAPPINGS_CONFIG (SRA.out.mappings)
+            MULTIQC_MAPPINGS_CONFIG(SRA.out.mappings)
             ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions)
         }
     //
@@ -127,11 +121,12 @@ workflow.onComplete {
         NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)
     }
     NfcoreTemplate.summary(workflow, params, log)
-    WorkflowSra.curateSamplesheetWarn(log)
+    if (params.input_type == 'sra')     { WorkflowSra.curateSamplesheetWarn(log) }
+    if (params.input_type == 'synapse') { WorkflowSynapse.curateSamplesheetWarn(log) }
 }
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
     THE END
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
 */
diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf
index 34c3e315..04bb32cb 100644
--- a/workflows/synapse/main.nf
+++ b/workflows/synapse/main.nf
@@ -125,20 +125,6 @@ workflow SYNAPSE {
         versions    = ch_versions.unique()
 }
 
-/*
-========================================================================================
-    COMPLETION EMAIL AND SUMMARY
-========================================================================================
-*/
-
-workflow.onComplete {
-    if (params.email || params.email_on_fail) {
-        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)
-    }
-    NfcoreTemplate.summary(workflow, params, log)
-    WorkflowSynapse.curateSamplesheetWarn(log)
-}
-
 /*
 ========================================================================================
     THE END

From ef03d06a9ec70aecc56d792a754bd900af0eb5d3 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 25 Aug 2023 10:46:38 +0200
Subject: [PATCH 396/852] staging

---
 workflows/sra/tests/main.nf.test | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 39a5cc3f..68ba7b58 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -1,7 +1,8 @@
-nextflow_pipeline {
+nextflow_workflow {
 
-    name "Test workflow: sra.nf"
-    script "main.nf"
+    name "Test workflow: sra/main.nf"
+    script "workflows/sra/main.nf"
+    workflow "SRA"
     tag "workflows"
     tag "workflows_sra"
     tag "sra_default_parameters"

From 1be5ebca09466fe99306fd638dccb9e529652324 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 25 Aug 2023 10:51:52 +0200
Subject: [PATCH 397/852] validate input in main.nf

---
 main.nf                   | 32 +++++++++++++++++++++++++++++++-
 workflows/sra/main.nf     | 15 ---------------
 workflows/synapse/main.nf | 18 ++----------------
 3 files changed, 33 insertions(+), 32 deletions(-)

diff --git a/main.nf b/main.nf
index edb54fd8..ef79d02b 100644
--- a/main.nf
+++ b/main.nf
@@ -36,6 +36,36 @@ else if (WorkflowMain.isSynapseId(ch_input)) { input_type = 'synapse' }
 else                                         { exit 1, 'Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!' }
 if (params.input_type != input_type)         { exit 1, "Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!" }
 
+/*
+========================================================================================
+    VALIDATE INPUTS
+========================================================================================
+*/
+
+if (params.input_type == 'sra') {
+    def valid_params = [
+        ena_metadata_fields : ['run_accession', 'experiment_accession', 'library_layout', 'fastq_ftp', 'fastq_md5']
+    ]
+
+    def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
+
+    // Validate input parameters
+    WorkflowSra.initialise(params, valid_params)
+}
+
+if (params.input_type == 'synapse') {
+
+    def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
+
+    // Create channel for synapse config
+    if (params.synapse_config) {
+        ch_synapse_config = file(params.synapse_config, checkIfExists: true)
+    } else {
+        exit 1, 'Please provide a Synapse config file for download authentication!'
+    }
+
+}
+
 /*
 ========================================================================================
     IMPORT MODULES
@@ -84,7 +114,7 @@ workflow NFCORE_FETCHNGS {
     // WORKFLOW: Download FastQ files for Synapse ids
     //
     } else if (params.input_type == 'synapse') {
-        SYNAPSE ( ch_ids )
+        SYNAPSE(ch_ids, ch_synapse_config)
         ch_versions = ch_versions.mix(SYNAPSE.out.versions)
     }
 
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index d4612cd0..d999d998 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -1,18 +1,3 @@
-/*
-========================================================================================
-    VALIDATE INPUTS
-========================================================================================
-*/
-
-def valid_params = [
-    ena_metadata_fields : ['run_accession', 'experiment_accession', 'library_layout', 'fastq_ftp', 'fastq_md5']
-]
-
-def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
-
-// Validate input parameters
-WorkflowSra.initialise(params, valid_params)
-
 /*
 ========================================================================================
     IMPORT LOCAL MODULES/SUBWORKFLOWS
diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf
index 04bb32cb..30d05f4f 100644
--- a/workflows/synapse/main.nf
+++ b/workflows/synapse/main.nf
@@ -1,18 +1,3 @@
-/*
-========================================================================================
-    VALIDATE INPUTS
-========================================================================================
-*/
-
-def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
-
-// Create channel for synapse config
-if (params.synapse_config) {
-    ch_synapse_config = file(params.synapse_config, checkIfExists: true)
-} else {
-    exit 1, 'Please provide a Synapse config file for download authentication!'
-}
-
 /*
 ========================================================================================
     IMPORT LOCAL MODULES/SUBWORKFLOWS
@@ -34,7 +19,8 @@ include { SYNAPSE_MERGE_SAMPLESHEET } from '../../modules/local/synapse_merge_sa
 workflow SYNAPSE {
 
     take:
-    ids // channel: [ ids ]
+    ids               // channel: [ ids ]
+    ch_synapse_config // channel: [ synapse_config ]
 
     main:
     ch_versions = Channel.empty()

From 698fab108f7638736768cb9a67140ce6801bd3ad Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 25 Aug 2023 11:08:13 +0200
Subject: [PATCH 398/852] use error

---
 main.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/main.nf b/main.nf
index ef79d02b..7575eeb8 100644
--- a/main.nf
+++ b/main.nf
@@ -21,7 +21,7 @@ WorkflowMain.initialise(workflow, params, log)
 
 // Check if --input file is empty
 ch_input = file(params.input, checkIfExists: true)
-if (ch_input.isEmpty()) {exit 1, "File provided with --input is empty: ${ch_input.getName()}!"}
+if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") }
 
 // Read in ids from --input file
 ch_ids = Channel.from(file(params.input, checkIfExists: true))
@@ -33,8 +33,8 @@ ch_ids = Channel.from(file(params.input, checkIfExists: true))
 def input_type = ''
 if (WorkflowMain.isSraId(ch_input))          { input_type = 'sra' }
 else if (WorkflowMain.isSynapseId(ch_input)) { input_type = 'synapse' }
-else                                         { exit 1, 'Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!' }
-if (params.input_type != input_type)         { exit 1, "Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!" }
+else                                         { error('Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!') }
+if (params.input_type != input_type)         { error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!") }
 
 /*
 ========================================================================================
@@ -61,7 +61,7 @@ if (params.input_type == 'synapse') {
     if (params.synapse_config) {
         ch_synapse_config = file(params.synapse_config, checkIfExists: true)
     } else {
-        exit 1, 'Please provide a Synapse config file for download authentication!'
+        error('Please provide a Synapse config file for download authentication!')
     }
 
 }

From e83e909954168129e5f94ddae48493fff505c05d Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 25 Aug 2023 12:14:32 +0200
Subject: [PATCH 399/852] use workflow testing

---
 workflows/sra/tests/main.nf.test      |  6 +-
 workflows/sra/tests/main.nf.test.snap | 80 +--------------------------
 2 files changed, 5 insertions(+), 81 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 68ba7b58..22ed6744 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -10,8 +10,10 @@ nextflow_workflow {
     test("Parameters: default") {
 
         when {
-            params {
-                outdir = "$outputDir"
+            workflow {
+                """
+                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                """
             }
         }
 
diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
index 88ea9654..3261e286 100644
--- a/workflows/sra/tests/main.nf.test.snap
+++ b/workflows/sra/tests/main.nf.test.snap
@@ -5,84 +5,6 @@
                 
             }
         ],
-        "timestamp": "2023-08-17T12:09:45+0000"
-    },
-    "metadata": {
-        "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
-            "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
-            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
-            "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
-            "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
-            "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
-            "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
-            "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54",
-            "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
-            "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
-        ],
-        "timestamp": "2023-08-17T12:09:45+0000"
-    },
-    "samplesheet": {
-        "content": [
-            "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
-            "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
-        ],
-        "timestamp": "2023-08-17T12:09:45+0000"
-    },
-    "software_versions": {
-        "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
-        ],
-        "timestamp": "2023-08-17T12:09:45+0000"
-    },
-    "fastq": {
-        "content": [
-            "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791",
-            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
-            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30",
-            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
-            "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6",
-            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
-            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
-            "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
-            "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64",
-            "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83",
-            "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544",
-            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
-            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
-            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
-            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962",
-            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
-            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76",
-            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
-            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88",
-            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
-            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04",
-            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98",
-            [
-                "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d",
-                "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9",
-                "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f",
-                "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86",
-                "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499",
-                "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff",
-                "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75",
-                "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85",
-                "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4",
-                "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc",
-                "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0",
-                "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368",
-                "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8",
-                "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f",
-                "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3",
-                "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8",
-                "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882",
-                "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
-                "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
-            ]
-        ],
-        "timestamp": "2023-08-17T12:09:45+0000"
+        "timestamp": "2023-08-25T10:11:12+0000"
     }
 }
\ No newline at end of file

From 883a191ec257032a2714ce4683c742a719e33a66 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 25 Aug 2023 13:27:52 +0200
Subject: [PATCH 400/852] update snapshot

---
 workflows/sra/tests/main.nf.test      |    5 +-
 workflows/sra/tests/main.nf.test.snap | 1347 ++++++++++++++++++++++++-
 2 files changed, 1349 insertions(+), 3 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 22ed6744..2652eb80 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -15,12 +15,15 @@ nextflow_workflow {
                 input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
                 """
             }
+            params {
+                outdir = "$outputDir"
+            }
         }
 
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(workflow.out).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
index 3261e286..a0cfc3f8 100644
--- a/workflows/sra/tests/main.nf.test.snap
+++ b/workflows/sra/tests/main.nf.test.snap
@@ -2,9 +2,1352 @@
     "Parameters: default": {
         "content": [
             {
-                
+                "0": [
+                    [
+                        {
+                            "id": "DRX024467_DRR026872",
+                            "run_accession": "DRR026872",
+                            "experiment_accession": "DRX024467",
+                            "sample_accession": "SAMD00023098",
+                            "secondary_sample_accession": "DRS033740",
+                            "study_accession": "PRJDB4356",
+                            "secondary_study_accession": "DRP003256",
+                            "submission_accession": "DRA002758",
+                            "run_alias": "DRR026872",
+                            "experiment_alias": "DRX024467",
+                            "sample_alias": "SAMD00023098",
+                            "study_alias": "DRP003256",
+                            "library_layout": "SINGLE",
+                            "library_selection": "Restriction Digest",
+                            "library_source": "GENOMIC",
+                            "library_strategy": "OTHER",
+                            "library_name": "IpeRAD1_3",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "62550",
+                            "read_count": "417",
+                            "tax_id": "35883",
+                            "scientific_name": "Ipomoea nil",
+                            "sample_title": "F2 plant dreived from a cross between Tokyo Kokei-standard and Africa #21",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Illumina HiSeq 2500 sequencing of SAMD00023098",
+                            "study_title": "The Japanese morning glory genome sequence",
+                            "sample_description": "Keywords: GSC:MIxS MIGS:6.0",
+                            "fastq_md5": "515e5448c55e054113c4a22df5f62791",
+                            "fastq_bytes": "38447",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "515e5448c55e054113c4a22df5f62791",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791"
+                    ],
+                    [
+                        {
+                            "id": "SRX6725035_SRR9984183",
+                            "run_accession": "SRR9984183",
+                            "experiment_accession": "SRX6725035",
+                            "sample_accession": "SAMN12581720",
+                            "secondary_sample_accession": "SRS5277011",
+                            "study_accession": "PRJNA560329",
+                            "secondary_study_accession": "SRP218535",
+                            "submission_accession": "SRA942061",
+                            "run_alias": "Emb289P1_bin131.fastq",
+                            "experiment_alias": "Emb289P1_bin131",
+                            "sample_alias": "Emb289P1_bin131",
+                            "study_alias": "PRJNA560329",
+                            "library_layout": "SINGLE",
+                            "library_selection": "RANDOM",
+                            "library_source": "METAGENOMIC",
+                            "library_strategy": "WGS",
+                            "library_name": "Emb289P1_bin131",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "1996273",
+                            "read_count": "58",
+                            "tax_id": "2660712",
+                            "scientific_name": "Defluviitaleaceae bacterium",
+                            "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
+                            "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
+                            "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
+                            "fastq_md5": "0b512d2dc31685983456bd56fd836544",
+                            "fastq_bytes": "605358",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "0b512d2dc31685983456bd56fd836544",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544"
+                    ],
+                    [
+                        {
+                            "id": "ERX1234253_ERR1160846",
+                            "run_accession": "ERR1160846",
+                            "experiment_accession": "ERX1234253",
+                            "sample_accession": "SAMEA3687214",
+                            "secondary_sample_accession": "ERS994363",
+                            "study_accession": "PRJEB11419",
+                            "secondary_study_accession": "ERP012803",
+                            "submission_accession": "ERA541392",
+                            "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                            "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                            "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                            "study_alias": "qiita_sid_10317",
+                            "library_layout": "SINGLE",
+                            "library_selection": "PCR",
+                            "library_source": "METAGENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "10317.BLANK.93.3E.r22",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "35658",
+                            "read_count": "283",
+                            "tax_id": "256318",
+                            "scientific_name": "metagenome",
+                            "sample_title": "10317.BLANK.93.3E.r22",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                            "study_title": "American Gut Project",
+                            "sample_description": "American Gut control",
+                            "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                            "fastq_bytes": "18077",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6"
+                    ],
+                    [
+                        {
+                            "id": "SRX11047067_SRR14709033",
+                            "run_accession": "SRR14709033",
+                            "experiment_accession": "SRX11047067",
+                            "sample_accession": "SAMN19373034",
+                            "secondary_sample_accession": "SRS9115923",
+                            "study_accession": "PRJNA733285",
+                            "secondary_study_accession": "SRP322267",
+                            "submission_accession": "SRA1239521",
+                            "run_alias": "Sebastes_levis-2.fastq",
+                            "experiment_alias": "Sebastes_macdonaldi-1",
+                            "sample_alias": "S._macdonaldi-1",
+                            "study_alias": "PRJNA733285",
+                            "library_layout": "SINGLE",
+                            "library_selection": "PCR",
+                            "library_source": "GENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "Sebastes_macdonaldi-1",
+                            "instrument_model": "AB 5500 Genetic Analyzer",
+                            "instrument_platform": "ABI_SOLID",
+                            "base_count": "153",
+                            "read_count": "1",
+                            "tax_id": "394693",
+                            "scientific_name": "Sebastes macdonaldi",
+                            "sample_title": "Sebastes_macdonaldi-1",
+                            "experiment_title": "AB 5500 Genetic Analyzer sequencing: Sebastes macdonaldi",
+                            "study_title": "MiSebastes: An eDNA metabarcoding primer set for rockfishes (genus Sebastes)",
+                            "sample_description": "Sebastes_macdonaldi-1",
+                            "fastq_md5": "",
+                            "fastq_bytes": "",
+                            "fastq_ftp": "",
+                            "fastq_galaxy": "",
+                            "fastq_aspera": "",
+                            "fastq_1": "",
+                            "fastq_2": "",
+                            "md5_1": "",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda"
+                    ],
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "run_accession": "SRR13191702",
+                            "experiment_accession": "SRX9626017",
+                            "sample_accession": "SAMN16980141",
+                            "secondary_sample_accession": "SRS7827211",
+                            "study_accession": "PRJNA682076",
+                            "secondary_study_accession": "SRP295653",
+                            "submission_accession": "SRA1166126",
+                            "run_alias": "S.170804.00784_662_L001_R1_001.fastq.gz",
+                            "experiment_alias": "S.170804.00784",
+                            "sample_alias": "S.170804.00784_662",
+                            "study_alias": "PRJNA682076",
+                            "library_layout": "PAIRED",
+                            "library_selection": "PCR",
+                            "library_source": "METAGENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "S.170804.00784",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "45682",
+                            "read_count": "91",
+                            "tax_id": "408170",
+                            "scientific_name": "human gut metagenome",
+                            "sample_title": "Metagenome or environmental sample from human gut metagenome",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
+                            "study_title": "Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
+                            "sample_description": "Metagenome or environmental sample from human gut metagenome",
+                            "fastq_md5": "89c5be920021a035084d8aeb74f32df7;56271be38a80db78ef3bdfc5d9909b98",
+                            "fastq_bytes": "15420;16324",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98",
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+                        },
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+                        ]
+                    ],
+                    [
+                        {
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+                            "run_accession": "ERR1109373",
+                            "experiment_accession": "ERX1188904",
+                            "sample_accession": "SAMEA3643867",
+                            "secondary_sample_accession": "ERS951016",
+                            "study_accession": "PRJEB11633",
+                            "secondary_study_accession": "ERP013030",
+                            "submission_accession": "ERA528939",
+                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
+                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
+                            "sample_alias": "sample_56",
+                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
+                            "library_layout": "PAIRED",
+                            "library_selection": "RT-PCR",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "RNA-Seq",
+                            "library_name": "unspecified",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "29700",
+                            "read_count": "169",
+                            "tax_id": "63433",
+                            "scientific_name": "Leptopilina boulardi",
+                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
+                            "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
+                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
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+                        ]
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+                    [
+                        {
+                            "id": "DRX026011_DRR028935",
+                            "run_accession": "DRR028935",
+                            "experiment_accession": "DRX026011",
+                            "sample_accession": "SAMD00024405",
+                            "secondary_sample_accession": "DRS019431",
+                            "study_accession": "PRJDB3420",
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+                            "submission_accession": "DRA002949",
+                            "run_alias": "DRR028935",
+                            "experiment_alias": "DRX026011",
+                            "sample_alias": "SAMD00024405",
+                            "study_alias": "DRP002616",
+                            "library_layout": "PAIRED",
+                            "library_selection": "cDNA",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "RNA-Seq",
+                            "library_name": "day0_BbSQE-I",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "194930",
+                            "read_count": "965",
+                            "tax_id": "1202541",
+                            "scientific_name": "Botryococcus braunii Showa",
+                            "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
+                            "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
+                            "sample_description": "Liquid culture",
+                            "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
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+                            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
+                            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
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+                    ],
+                    [
+                        {
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+                            "run_accession": "SRR14593545",
+                            "experiment_accession": "SRX10940790",
+                            "sample_accession": "SAMN19097423",
+                            "secondary_sample_accession": "SRS9020442",
+                            "study_accession": "PRJNA728650",
+                            "secondary_study_accession": "SRP319413",
+                            "submission_accession": "SRA1234280",
+                            "run_alias": "577-6_530058_19-037147 Goat_F.ab1",
+                            "experiment_alias": "PRNP_2765",
+                            "sample_alias": "prp_2765",
+                            "study_alias": "PRJNA728650",
+                            "library_layout": "PAIRED",
+                            "library_selection": "PCR",
+                            "library_source": "GENOMIC",
+                            "library_strategy": "AMPLICON",
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+                            "instrument_model": "AB 3500xL Genetic Analyzer",
+                            "instrument_platform": "CAPILLARY",
+                            "base_count": "828",
+                            "read_count": "1",
+                            "tax_id": "9925",
+                            "scientific_name": "Capra hircus",
+                            "sample_title": "MIGS Eukaryotic sample from Capra hircus",
+                            "experiment_title": "AB 3500xL Genetic Analyzer sequencing: prp_2765",
+                            "study_title": "Capra hircus Raw sequence reads",
+                            "sample_description": "Keywords: GSC:MIxS MIGS:5.0",
+                            "fastq_md5": "",
+                            "fastq_bytes": "",
+                            "fastq_ftp": "",
+                            "fastq_galaxy": "",
+                            "fastq_aspera": "",
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+                            "fastq_2": "",
+                            "md5_1": "",
+                            "md5_2": "",
+                            "single_end": false
+                        },
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+                            "study_title": "Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]",
+                            "sample_description": "A20-35 A11A20-35 A11_ROI009PanCK+",
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+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_2.fastq.gz",
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+                            "md5_2": "18dbe96e7f58b63406d9058938df1962",
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+                            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
+                            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX9504942_SRR13055520",
+                            "run_accession": "SRR13055520",
+                            "experiment_accession": "SRX9504942",
+                            "sample_accession": "SAMN16793052",
+                            "secondary_sample_accession": "SRS7713669",
+                            "study_accession": "PRJNA678298",
+                            "secondary_study_accession": "SRP292504",
+                            "submission_accession": "SRA1158402",
+                            "run_alias": "GSM4907283_r4",
+                            "experiment_alias": "GSM4907283",
+                            "sample_alias": "GSM4907283",
+                            "study_alias": "GSE159787",
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+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "OTHER",
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+                            "instrument_model": "NextSeq 550",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "2214488",
+                            "read_count": "29138",
+                            "tax_id": "9606",
+                            "scientific_name": "Homo sapiens",
+                            "sample_title": "A20-35 A11A20-35 A11_ROI009PanCK+",
+                            "experiment_title": "NextSeq 550 sequencing: GSM4907283: A20-35 A11A20-35 A11_ROI009PanCK+ Homo sapiens OTHER",
+                            "study_title": "Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]",
+                            "sample_description": "A20-35 A11A20-35 A11_ROI009PanCK+",
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+                            "fastq_bytes": "709867;716862",
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+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz",
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+                        ]
+                    ],
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+                            "study_accession": "PRJNA678298",
+                            "secondary_study_accession": "SRP292504",
+                            "submission_accession": "SRA1158402",
+                            "run_alias": "GSM4907283_r2",
+                            "experiment_alias": "GSM4907283",
+                            "sample_alias": "GSM4907283",
+                            "study_alias": "GSE159787",
+                            "library_layout": "PAIRED",
+                            "library_selection": "other",
+                            "library_source": "TRANSCRIPTOMIC",
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+                            "instrument_model": "NextSeq 550",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "2235236",
+                            "read_count": "29411",
+                            "tax_id": "9606",
+                            "scientific_name": "Homo sapiens",
+                            "sample_title": "A20-35 A11A20-35 A11_ROI009PanCK+",
+                            "experiment_title": "NextSeq 550 sequencing: GSM4907283: A20-35 A11A20-35 A11_ROI009PanCK+ Homo sapiens OTHER",
+                            "study_title": "Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]",
+                            "sample_description": "A20-35 A11A20-35 A11_ROI009PanCK+",
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+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_2.fastq.gz",
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+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_2.fastq.gz",
+                            "md5_1": "5ec894d863fcefe394470a0925aefde4",
+                            "md5_2": "aead170df9851773d5202b5760c76d76",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
+                            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX9504942_SRR13055519",
+                            "run_accession": "SRR13055519",
+                            "experiment_accession": "SRX9504942",
+                            "sample_accession": "SAMN16793052",
+                            "secondary_sample_accession": "SRS7713669",
+                            "study_accession": "PRJNA678298",
+                            "secondary_study_accession": "SRP292504",
+                            "submission_accession": "SRA1158402",
+                            "run_alias": "GSM4907283_r3",
+                            "experiment_alias": "GSM4907283",
+                            "sample_alias": "GSM4907283",
+                            "study_alias": "GSE159787",
+                            "library_layout": "PAIRED",
+                            "library_selection": "other",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "OTHER",
+                            "library_name": "",
+                            "instrument_model": "NextSeq 550",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "2232728",
+                            "read_count": "29378",
+                            "tax_id": "9606",
+                            "scientific_name": "Homo sapiens",
+                            "sample_title": "A20-35 A11A20-35 A11_ROI009PanCK+",
+                            "experiment_title": "NextSeq 550 sequencing: GSM4907283: A20-35 A11A20-35 A11_ROI009PanCK+ Homo sapiens OTHER",
+                            "study_title": "Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]",
+                            "sample_description": "A20-35 A11A20-35 A11_ROI009PanCK+",
+                            "fastq_md5": "5ad51460c6c4a850dd37a206e2c441c1;a977367bf41dacf4c21bc0c8201b8b88",
+                            "fastq_bytes": "714907;721705",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_2.fastq.gz",
+                            "md5_1": "5ad51460c6c4a850dd37a206e2c441c1",
+                            "md5_2": "a977367bf41dacf4c21bc0c8201b8b88",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
+                            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX9315476_SRR12848126",
+                            "run_accession": "SRR12848126",
+                            "experiment_accession": "SRX9315476",
+                            "sample_accession": "SAMN16455283",
+                            "secondary_sample_accession": "SRS7540262",
+                            "study_accession": "PRJNA670070",
+                            "secondary_study_accession": "SRP287769",
+                            "submission_accession": "SRA1145417",
+                            "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam",
+                            "experiment_alias": "F11-N1-05",
+                            "sample_alias": "F11-N1-05",
+                            "study_alias": "PRJNA670070",
+                            "library_layout": "PAIRED",
+                            "library_selection": "RANDOM PCR",
+                            "library_source": "GENOMIC",
+                            "library_strategy": "Synthetic-Long-Read",
+                            "library_name": "F11-N1-05",
+                            "instrument_model": "Illumina HiSeq 3000",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "431758",
+                            "read_count": "2954",
+                            "tax_id": "10092",
+                            "scientific_name": "Mus musculus domesticus",
+                            "sample_title": "Longshanks_F11-N1-05",
+                            "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                            "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                            "sample_description": "F11-N1-05",
+                            "fastq_md5": "",
+                            "fastq_bytes": "",
+                            "fastq_ftp": "",
+                            "fastq_galaxy": "",
+                            "fastq_aspera": "",
+                            "fastq_1": "",
+                            "fastq_2": "",
+                            "md5_1": "",
+                            "md5_2": "",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
+                            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX17709227_SRR21711856",
+                            "run_accession": "SRR21711856",
+                            "experiment_accession": "SRX17709227",
+                            "sample_accession": "SAMN31021823",
+                            "secondary_sample_accession": "SRS15239723",
+                            "study_accession": "PRJNA884373",
+                            "secondary_study_accession": "SRP399678",
+                            "submission_accession": "SRA1507236",
+                            "run_alias": "GSM6601460_r1",
+                            "experiment_alias": "GSM6601460_r1",
+                            "sample_alias": "GSM6601460",
+                            "study_alias": "GSE214215",
+                            "library_layout": "SINGLE",
+                            "library_selection": "cDNA",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "RNA-Seq",
+                            "library_name": "GSM6601460",
+                            "instrument_model": "Illumina HiSeq 4000",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "573417800",
+                            "read_count": "11468356",
+                            "tax_id": "6239",
+                            "scientific_name": "Caenorhabditis elegans",
+                            "sample_title": "sham-treated worms in day 5",
+                            "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                            "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                            "sample_description": "sham-treated worms in day 5",
+                            "fastq_md5": "7cd1402155befc87be338132d1f31f64",
+                            "fastq_bytes": "447377777",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "7cd1402155befc87be338132d1f31f64",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64"
+                    ],
+                    [
+                        {
+                            "id": "SRX17709228_SRR21711855",
+                            "run_accession": "SRR21711855",
+                            "experiment_accession": "SRX17709228",
+                            "sample_accession": "SAMN31021822",
+                            "secondary_sample_accession": "SRS15239724",
+                            "study_accession": "PRJNA884373",
+                            "secondary_study_accession": "SRP399678",
+                            "submission_accession": "SRA1507236",
+                            "run_alias": "GSM6601461_r1",
+                            "experiment_alias": "GSM6601461_r1",
+                            "sample_alias": "GSM6601461",
+                            "study_alias": "GSE214215",
+                            "library_layout": "SINGLE",
+                            "library_selection": "cDNA",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "RNA-Seq",
+                            "library_name": "GSM6601461",
+                            "instrument_model": "Illumina HiSeq 4000",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "677912850",
+                            "read_count": "13558257",
+                            "tax_id": "6239",
+                            "scientific_name": "Caenorhabditis elegans",
+                            "sample_title": "PM2.5-treated worms in day 5",
+                            "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                            "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                            "sample_description": "PM2.5-treated worms in day 5",
+                            "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                            "fastq_bytes": "529798447",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83"
+                    ]
+                ],
+                "mappings": [
+                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                ],
+                "samplesheet": [
+                    "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341"
+                ],
+                "versions": [
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                ]
             }
         ],
-        "timestamp": "2023-08-25T10:11:12+0000"
+        "timestamp": "2023-08-25T11:27:09+0000"
     }
 }
\ No newline at end of file

From da650afaf646bb4156b81ed0442d0764b7df802c Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 25 Aug 2023 14:22:05 +0200
Subject: [PATCH 401/852] restore versions

---
 modules.json                                        |  3 +--
 .../custom-dumpsoftwareversions.diff                | 13 -------------
 .../templates/dumpsoftwareversions.py               |  1 +
 3 files changed, 2 insertions(+), 15 deletions(-)
 delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff

diff --git a/modules.json b/modules.json
index 2244addd..3137b88b 100644
--- a/modules.json
+++ b/modules.json
@@ -8,8 +8,7 @@
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff"
+                        "installed_by": ["modules"]
                     },
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
diff --git a/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff b/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff
deleted file mode 100644
index a7893b24..00000000
--- a/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff
+++ /dev/null
@@ -1,13 +0,0 @@
-Changes in module 'nf-core/custom/dumpsoftwareversions'
---- modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
-+++ modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
-@@ -75,7 +75,6 @@
-             versions_by_module[module] = process_versions
- 
-     versions_by_module["Workflow"] = {
--        "Nextflow": "$workflow.nextflow.version",
-         "$workflow.manifest.name": "$workflow.manifest.version",
-     }
- 
-
-************************************************************
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
index 33d127f8..da033408 100755
--- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
@@ -75,6 +75,7 @@ def main():
             versions_by_module[module] = process_versions
 
     versions_by_module["Workflow"] = {
+        "Nextflow": "$workflow.nextflow.version",
         "$workflow.manifest.name": "$workflow.manifest.version",
     }
 

From f2d32d25153c9058e1641243849b06fd872316f1 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 25 Aug 2023 14:22:19 +0200
Subject: [PATCH 402/852] update workflow

---
 workflows/sra/main.nf | 42 +++++++++++++++++++++---------------------
 1 file changed, 21 insertions(+), 21 deletions(-)

diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index d999d998..44f6c6f5 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -49,18 +49,17 @@ workflow SRA {
     )
     ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first())
 
-    SRA_RUNINFO_TO_FTP
+    ch_sra_metadata = SRA_RUNINFO_TO_FTP
         .out
         .tsv
         .splitCsv(header:true, sep:'\t')
-        .map {
-            meta ->
-                def meta_clone = meta.clone()
-                meta_clone.single_end = meta_clone.single_end.toBoolean()
-                return meta_clone
+        .map{ meta ->
+            def meta_clone = meta.clone()
+            meta_clone.single_end = meta_clone.single_end.toBoolean()
+            return meta_clone
         }
         .unique()
-        .set { ch_sra_metadata }
+
     ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first())
 
     fastq_files = Channel.empty()
@@ -101,16 +100,17 @@ workflow SRA {
             FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads
         )
 
-        fastq_files
-            .map {
-                meta, fastq ->
-                    def reads = fastq instanceof List ? fastq.flatten() : [ fastq ]
-                    def meta_clone = meta.clone()
-                    meta_clone.fastq_1 = reads[0] ? "${params.outdir}/fastq/${reads[0].getName()}" : ''
-                    meta_clone.fastq_2 = reads[1] && !meta.single_end ? "${params.outdir}/fastq/${reads[1].getName()}" : ''
-                    return meta_clone
-            }
-            .set { ch_sra_metadata }
+        ch_sra_metadata = fastq_files.map { meta, fastq ->
+            def reads = fastq instanceof List ? fastq.flatten() : [ fastq ]
+            def meta_clone = meta.clone()
+
+            meta_clone.fastq_1 = reads[0] ? "${params.outdir}/fastq/${reads[0].getName()}" : ''
+            meta_clone.fastq_2 = reads[1] && !meta.single_end ? "${params.outdir}/fastq/${reads[1].getName()}" : ''
+
+            return meta_clone
+        }
+
+        fastq_only_files = fastq_files.map { meta, fastq -> [fastq] }
     }
 
     //
@@ -133,10 +133,10 @@ workflow SRA {
     ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions)
 
     emit:
-        fastq         = fastq_files
-        samplesheet   = SRA_MERGE_SAMPLESHEET.out.samplesheet
-        mappings      = SRA_MERGE_SAMPLESHEET.out.mappings
-        versions      = ch_versions.unique()
+    fastq         = fastq_only_files
+    samplesheet   = SRA_MERGE_SAMPLESHEET.out.samplesheet
+    mappings      = SRA_MERGE_SAMPLESHEET.out.mappings
+    versions      = ch_versions.unique()
 }
 
 /*

From 3018118620e39e313c4e9c9991981e128fff4bdc Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 25 Aug 2023 14:22:46 +0200
Subject: [PATCH 403/852] update snapshot

---
 workflows/sra/tests/main.nf.test.snap | 1282 ++-----------------------
 1 file changed, 56 insertions(+), 1226 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
index a0cfc3f8..5d4aeaf2 100644
--- a/workflows/sra/tests/main.nf.test.snap
+++ b/workflows/sra/tests/main.nf.test.snap
@@ -4,661 +4,76 @@
             {
                 "0": [
                     [
-                        {
-                            "id": "DRX024467_DRR026872",
-                            "run_accession": "DRR026872",
-                            "experiment_accession": "DRX024467",
-                            "sample_accession": "SAMD00023098",
-                            "secondary_sample_accession": "DRS033740",
-                            "study_accession": "PRJDB4356",
-                            "secondary_study_accession": "DRP003256",
-                            "submission_accession": "DRA002758",
-                            "run_alias": "DRR026872",
-                            "experiment_alias": "DRX024467",
-                            "sample_alias": "SAMD00023098",
-                            "study_alias": "DRP003256",
-                            "library_layout": "SINGLE",
-                            "library_selection": "Restriction Digest",
-                            "library_source": "GENOMIC",
-                            "library_strategy": "OTHER",
-                            "library_name": "IpeRAD1_3",
-                            "instrument_model": "Illumina HiSeq 2500",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "62550",
-                            "read_count": "417",
-                            "tax_id": "35883",
-                            "scientific_name": "Ipomoea nil",
-                            "sample_title": "F2 plant dreived from a cross between Tokyo Kokei-standard and Africa #21",
-                            "experiment_title": "Illumina HiSeq 2500 sequencing: Illumina HiSeq 2500 sequencing of SAMD00023098",
-                            "study_title": "The Japanese morning glory genome sequence",
-                            "sample_description": "Keywords: GSC:MIxS MIGS:6.0",
-                            "fastq_md5": "515e5448c55e054113c4a22df5f62791",
-                            "fastq_bytes": "38447",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
-                            "fastq_2": "",
-                            "md5_1": "515e5448c55e054113c4a22df5f62791",
-                            "md5_2": "",
-                            "single_end": true
-                        },
-                        "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791"
-                    ],
-                    [
-                        {
-                            "id": "SRX6725035_SRR9984183",
-                            "run_accession": "SRR9984183",
-                            "experiment_accession": "SRX6725035",
-                            "sample_accession": "SAMN12581720",
-                            "secondary_sample_accession": "SRS5277011",
-                            "study_accession": "PRJNA560329",
-                            "secondary_study_accession": "SRP218535",
-                            "submission_accession": "SRA942061",
-                            "run_alias": "Emb289P1_bin131.fastq",
-                            "experiment_alias": "Emb289P1_bin131",
-                            "sample_alias": "Emb289P1_bin131",
-                            "study_alias": "PRJNA560329",
-                            "library_layout": "SINGLE",
-                            "library_selection": "RANDOM",
-                            "library_source": "METAGENOMIC",
-                            "library_strategy": "WGS",
-                            "library_name": "Emb289P1_bin131",
-                            "instrument_model": "Illumina HiSeq 2500",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "1996273",
-                            "read_count": "58",
-                            "tax_id": "2660712",
-                            "scientific_name": "Defluviitaleaceae bacterium",
-                            "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
-                            "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
-                            "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
-                            "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
-                            "fastq_md5": "0b512d2dc31685983456bd56fd836544",
-                            "fastq_bytes": "605358",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                            "fastq_2": "",
-                            "md5_1": "0b512d2dc31685983456bd56fd836544",
-                            "md5_2": "",
-                            "single_end": true
-                        },
-                        "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544"
+                        [
+                            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
+                            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
+                        ]
                     ],
                     [
-                        {
-                            "id": "ERX1234253_ERR1160846",
-                            "run_accession": "ERR1160846",
-                            "experiment_accession": "ERX1234253",
-                            "sample_accession": "SAMEA3687214",
-                            "secondary_sample_accession": "ERS994363",
-                            "study_accession": "PRJEB11419",
-                            "secondary_study_accession": "ERP012803",
-                            "submission_accession": "ERA541392",
-                            "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
-                            "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                            "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
-                            "study_alias": "qiita_sid_10317",
-                            "library_layout": "SINGLE",
-                            "library_selection": "PCR",
-                            "library_source": "METAGENOMIC",
-                            "library_strategy": "AMPLICON",
-                            "library_name": "10317.BLANK.93.3E.r22",
-                            "instrument_model": "Illumina HiSeq 2500",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "35658",
-                            "read_count": "283",
-                            "tax_id": "256318",
-                            "scientific_name": "metagenome",
-                            "sample_title": "10317.BLANK.93.3E.r22",
-                            "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                            "study_title": "American Gut Project",
-                            "sample_description": "American Gut control",
-                            "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                            "fastq_bytes": "18077",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                            "fastq_2": "",
-                            "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                            "md5_2": "",
-                            "single_end": true
-                        },
                         "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6"
                     ],
                     [
-                        {
-                            "id": "SRX11047067_SRR14709033",
-                            "run_accession": "SRR14709033",
-                            "experiment_accession": "SRX11047067",
-                            "sample_accession": "SAMN19373034",
-                            "secondary_sample_accession": "SRS9115923",
-                            "study_accession": "PRJNA733285",
-                            "secondary_study_accession": "SRP322267",
-                            "submission_accession": "SRA1239521",
-                            "run_alias": "Sebastes_levis-2.fastq",
-                            "experiment_alias": "Sebastes_macdonaldi-1",
-                            "sample_alias": "S._macdonaldi-1",
-                            "study_alias": "PRJNA733285",
-                            "library_layout": "SINGLE",
-                            "library_selection": "PCR",
-                            "library_source": "GENOMIC",
-                            "library_strategy": "AMPLICON",
-                            "library_name": "Sebastes_macdonaldi-1",
-                            "instrument_model": "AB 5500 Genetic Analyzer",
-                            "instrument_platform": "ABI_SOLID",
-                            "base_count": "153",
-                            "read_count": "1",
-                            "tax_id": "394693",
-                            "scientific_name": "Sebastes macdonaldi",
-                            "sample_title": "Sebastes_macdonaldi-1",
-                            "experiment_title": "AB 5500 Genetic Analyzer sequencing: Sebastes macdonaldi",
-                            "study_title": "MiSebastes: An eDNA metabarcoding primer set for rockfishes (genus Sebastes)",
-                            "sample_description": "Sebastes_macdonaldi-1",
-                            "fastq_md5": "",
-                            "fastq_bytes": "",
-                            "fastq_ftp": "",
-                            "fastq_galaxy": "",
-                            "fastq_aspera": "",
-                            "fastq_1": "",
-                            "fastq_2": "",
-                            "md5_1": "",
-                            "md5_2": "",
-                            "single_end": true
-                        },
-                        "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda"
+                        [
+                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
+                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
+                        ]
                     ],
                     [
-                        {
-                            "id": "SRX9626017_SRR13191702",
-                            "run_accession": "SRR13191702",
-                            "experiment_accession": "SRX9626017",
-                            "sample_accession": "SAMN16980141",
-                            "secondary_sample_accession": "SRS7827211",
-                            "study_accession": "PRJNA682076",
-                            "secondary_study_accession": "SRP295653",
-                            "submission_accession": "SRA1166126",
-                            "run_alias": "S.170804.00784_662_L001_R1_001.fastq.gz",
-                            "experiment_alias": "S.170804.00784",
-                            "sample_alias": "S.170804.00784_662",
-                            "study_alias": "PRJNA682076",
-                            "library_layout": "PAIRED",
-                            "library_selection": "PCR",
-                            "library_source": "METAGENOMIC",
-                            "library_strategy": "AMPLICON",
-                            "library_name": "S.170804.00784",
-                            "instrument_model": "Illumina HiSeq 2500",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "45682",
-                            "read_count": "91",
-                            "tax_id": "408170",
-                            "scientific_name": "human gut metagenome",
-                            "sample_title": "Metagenome or environmental sample from human gut metagenome",
-                            "experiment_title": "Illumina HiSeq 2500 sequencing: Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
-                            "study_title": "Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
-                            "sample_description": "Metagenome or environmental sample from human gut metagenome",
-                            "fastq_md5": "89c5be920021a035084d8aeb74f32df7;56271be38a80db78ef3bdfc5d9909b98",
-                            "fastq_bytes": "15420;16324",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
-                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
-                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98",
-                            "single_end": false
-                        },
                         [
                             "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
                             "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
                         ]
                     ],
                     [
-                        {
-                            "id": "ERX1188904_ERR1109373",
-                            "run_accession": "ERR1109373",
-                            "experiment_accession": "ERX1188904",
-                            "sample_accession": "SAMEA3643867",
-                            "secondary_sample_accession": "ERS951016",
-                            "study_accession": "PRJEB11633",
-                            "secondary_study_accession": "ERP013030",
-                            "submission_accession": "ERA528939",
-                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
-                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
-                            "sample_alias": "sample_56",
-                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
-                            "library_layout": "PAIRED",
-                            "library_selection": "RT-PCR",
-                            "library_source": "TRANSCRIPTOMIC",
-                            "library_strategy": "RNA-Seq",
-                            "library_name": "unspecified",
-                            "instrument_model": "Illumina HiSeq 2500",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "29700",
-                            "read_count": "169",
-                            "tax_id": "63433",
-                            "scientific_name": "Leptopilina boulardi",
-                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
-                            "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
-                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
-                            "fastq_bytes": "3221;8151;8118",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
-                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
-                            "single_end": false
-                        },
-                        [
-                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
-                        ]
+                        "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791"
                     ],
                     [
-                        {
-                            "id": "DRX026011_DRR028935",
-                            "run_accession": "DRR028935",
-                            "experiment_accession": "DRX026011",
-                            "sample_accession": "SAMD00024405",
-                            "secondary_sample_accession": "DRS019431",
-                            "study_accession": "PRJDB3420",
-                            "secondary_study_accession": "DRP002616",
-                            "submission_accession": "DRA002949",
-                            "run_alias": "DRR028935",
-                            "experiment_alias": "DRX026011",
-                            "sample_alias": "SAMD00024405",
-                            "study_alias": "DRP002616",
-                            "library_layout": "PAIRED",
-                            "library_selection": "cDNA",
-                            "library_source": "TRANSCRIPTOMIC",
-                            "library_strategy": "RNA-Seq",
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-                            "library_name": "GSM6601460",
-                            "instrument_model": "Illumina HiSeq 4000",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "573417800",
-                            "read_count": "11468356",
-                            "tax_id": "6239",
-                            "scientific_name": "Caenorhabditis elegans",
-                            "sample_title": "sham-treated worms in day 5",
-                            "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
-                            "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
-                            "sample_description": "sham-treated worms in day 5",
-                            "fastq_md5": "7cd1402155befc87be338132d1f31f64",
-                            "fastq_bytes": "447377777",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                            "fastq_2": "",
-                            "md5_1": "7cd1402155befc87be338132d1f31f64",
-                            "md5_2": "",
-                            "single_end": true
-                        },
-                        "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64"
+                        [
+                            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
+                            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04"
+                        ]
                     ],
                     [
-                        {
-                            "id": "SRX17709228_SRR21711855",
-                            "run_accession": "SRR21711855",
-                            "experiment_accession": "SRX17709228",
-                            "sample_accession": "SAMN31021822",
-                            "secondary_sample_accession": "SRS15239724",
-                            "study_accession": "PRJNA884373",
-                            "secondary_study_accession": "SRP399678",
-                            "submission_accession": "SRA1507236",
-                            "run_alias": "GSM6601461_r1",
-                            "experiment_alias": "GSM6601461_r1",
-                            "sample_alias": "GSM6601461",
-                            "study_alias": "GSE214215",
-                            "library_layout": "SINGLE",
-                            "library_selection": "cDNA",
-                            "library_source": "TRANSCRIPTOMIC",
-                            "library_strategy": "RNA-Seq",
-                            "library_name": "GSM6601461",
-                            "instrument_model": "Illumina HiSeq 4000",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "677912850",
-                            "read_count": "13558257",
-                            "tax_id": "6239",
-                            "scientific_name": "Caenorhabditis elegans",
-                            "sample_title": "PM2.5-treated worms in day 5",
-                            "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
-                            "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
-                            "sample_description": "PM2.5-treated worms in day 5",
-                            "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
-                            "fastq_bytes": "529798447",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                            "fastq_2": "",
-                            "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
-                            "md5_2": "",
-                            "single_end": true
-                        },
-                        "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83"
+                        [
+                            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
+                            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79"
+                        ]
                     ]
                 ],
                 "mappings": [
@@ -1348,6 +178,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-08-25T11:27:09+0000"
+        "timestamp": "2023-08-25T12:20:20+0000"
     }
-}
\ No newline at end of file
+}

From 2010d7f2c5661ce0b1b64f3c0a47ef0f31a39945 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 25 Aug 2023 14:56:39 +0200
Subject: [PATCH 404/852] just one id to test

---
 workflows/sra/tests/main.nf.test      |   2 +-
 workflows/sra/tests/main.nf.test.snap | 154 ++------------------------
 2 files changed, 9 insertions(+), 147 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 2652eb80..6c4ecf17 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -12,7 +12,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                input[0] = Channel.from('DRR026872')
                 """
             }
             params {
diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
index 5d4aeaf2..0d94075c 100644
--- a/workflows/sra/tests/main.nf.test.snap
+++ b/workflows/sra/tests/main.nf.test.snap
@@ -3,181 +3,43 @@
         "content": [
             {
                 "0": [
-                    [
-                        [
-                            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
-                            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
-                        ]
-                    ],
-                    [
-                        "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6"
-                    ],
-                    [
-                        [
-                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
-                        ]
-                    ],
-                    [
-                        [
-                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
-                        ]
-                    ],
                     [
                         "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791"
-                    ],
-                    [
-                        "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda"
-                    ],
-                    [
-                        "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64"
-                    ],
-                    [
-                        "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83"
-                    ],
-                    [
-                        "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544"
-                    ],
-                    [
-                        [
-                            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
-                            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2"
-                        ]
-                    ],
-                    [
-                        [
-                            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
-                            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76"
-                        ]
-                    ],
-                    [
-                        [
-                            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
-                            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88"
-                        ]
-                    ],
-                    [
-                        [
-                            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
-                            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962"
-                        ]
-                    ],
-                    [
-                        [
-                            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
-                            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04"
-                        ]
-                    ],
-                    [
-                        [
-                            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
-                            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79"
-                        ]
                     ]
                 ],
                 "1": [
-                    "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341"
+                    "samplesheet.csv:md5,0f35f9485a633d9c581903abd611b646"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                    "id_mappings.csv:md5,71ebb4334e4a319a1a007370e36c98f7"
                 ],
                 "3": [
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
                     "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
                     "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
                 ],
                 "fastq": [
-                    [
-                        [
-                            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
-                            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
-                        ]
-                    ],
-                    [
-                        "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6"
-                    ],
-                    [
-                        [
-                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
-                        ]
-                    ],
-                    [
-                        [
-                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
-                        ]
-                    ],
                     [
                         "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791"
-                    ],
-                    [
-                        "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda"
-                    ],
-                    [
-                        "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64"
-                    ],
-                    [
-                        "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83"
-                    ],
-                    [
-                        "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544"
-                    ],
-                    [
-                        [
-                            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
-                            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2"
-                        ]
-                    ],
-                    [
-                        [
-                            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
-                            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76"
-                        ]
-                    ],
-                    [
-                        [
-                            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
-                            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88"
-                        ]
-                    ],
-                    [
-                        [
-                            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
-                            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962"
-                        ]
-                    ],
-                    [
-                        [
-                            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
-                            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04"
-                        ]
-                    ],
-                    [
-                        [
-                            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
-                            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79"
-                        ]
                     ]
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                    "id_mappings.csv:md5,71ebb4334e4a319a1a007370e36c98f7"
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341"
+                    "samplesheet.csv:md5,0f35f9485a633d9c581903abd611b646"
                 ],
                 "versions": [
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
                     "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
                     "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
                 ]
             }
         ],
-        "timestamp": "2023-08-25T12:20:20+0000"
+        "timestamp": "2023-08-25T12:56:07+0000"
     }
-}
+}
\ No newline at end of file

From f5d904030a96166699cef738438f17922afebbf3 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 25 Aug 2023 15:17:43 +0200
Subject: [PATCH 405/852] one emit statement at a time

---
 workflows/sra/main.nf                 |  3 ---
 workflows/sra/tests/main.nf.test      |  2 +-
 workflows/sra/tests/main.nf.test.snap | 22 ++++++----------------
 3 files changed, 7 insertions(+), 20 deletions(-)

diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 44f6c6f5..8acb3da6 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -109,8 +109,6 @@ workflow SRA {
 
             return meta_clone
         }
-
-        fastq_only_files = fastq_files.map { meta, fastq -> [fastq] }
     }
 
     //
@@ -133,7 +131,6 @@ workflow SRA {
     ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions)
 
     emit:
-    fastq         = fastq_only_files
     samplesheet   = SRA_MERGE_SAMPLESHEET.out.samplesheet
     mappings      = SRA_MERGE_SAMPLESHEET.out.mappings
     versions      = ch_versions.unique()
diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 6c4ecf17..2652eb80 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -12,7 +12,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('DRR026872')
+                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
                 """
             }
             params {
diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
index 0d94075c..a552d171 100644
--- a/workflows/sra/tests/main.nf.test.snap
+++ b/workflows/sra/tests/main.nf.test.snap
@@ -3,33 +3,23 @@
         "content": [
             {
                 "0": [
-                    [
-                        "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791"
-                    ]
+                    "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341"
                 ],
                 "1": [
-                    "samplesheet.csv:md5,0f35f9485a633d9c581903abd611b646"
+                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,71ebb4334e4a319a1a007370e36c98f7"
-                ],
-                "3": [
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
                     "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
                     "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
                 ],
-                "fastq": [
-                    [
-                        "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791"
-                    ]
-                ],
                 "mappings": [
-                    "id_mappings.csv:md5,71ebb4334e4a319a1a007370e36c98f7"
+                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,0f35f9485a633d9c581903abd611b646"
+                    "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341"
                 ],
                 "versions": [
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
@@ -40,6 +30,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-08-25T12:56:07+0000"
+        "timestamp": "2023-08-25T13:15:46+0000"
     }
-}
\ No newline at end of file
+}

From ac35bc092fcbbf57e95abf1112567fb272ca2b12 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 25 Aug 2023 16:47:43 +0200
Subject: [PATCH 406/852] polish

---
 main.nf                               | 16 +++--------
 workflows/sra/main.nf                 |  3 ++-
 workflows/sra/tests/main.nf.test      |  2 +-
 workflows/sra/tests/main.nf.test.snap | 38 ++++++---------------------
 4 files changed, 15 insertions(+), 44 deletions(-)

diff --git a/main.nf b/main.nf
index 7575eeb8..ad72ea4a 100644
--- a/main.nf
+++ b/main.nf
@@ -97,33 +97,25 @@ workflow NFCORE_FETCHNGS {
 
     ch_versions = Channel.empty()
 
-    //
     // WORKFLOW: Download FastQ files for SRA / ENA / GEO / DDBJ ids
-    //
     if (params.input_type == 'sra') {
         SRA(ch_ids)
         ch_versions = ch_versions.mix(SRA.out.versions)
-    //
-    // MODULE: Create a MultiQC config file with sample name mappings
-    //
+
+        // MODULE: Create a MultiQC config file with sample name mappings
         if (params.sample_mapping_fields) {
             MULTIQC_MAPPINGS_CONFIG(SRA.out.mappings)
             ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions)
         }
-    //
+
     // WORKFLOW: Download FastQ files for Synapse ids
-    //
     } else if (params.input_type == 'synapse') {
         SYNAPSE(ch_ids, ch_synapse_config)
         ch_versions = ch_versions.mix(SYNAPSE.out.versions)
     }
 
-    //
     // MODULE: Dump software versions for all tools used in the workflow
-    //
-    CUSTOM_DUMPSOFTWAREVERSIONS (
-        ch_versions.unique().collectFile(name: 'collated_versions.yml')
-    )
+    CUSTOM_DUMPSOFTWAREVERSIONS(ch_versions.unique().collectFile(name: 'collated_versions.yml'))
 }
 
 /*
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 8acb3da6..c1583956 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -12,7 +12,7 @@ include { SRA_MERGE_SAMPLESHEET   } from '../../modules/local/sra_merge_samplesh
 
 /*
 ========================================================================================
-    IMPORT NF-CORE MODULES/SUBWORKFLOWS
+    IMPORT NF-CORE SUBWORKFLOWS
 ========================================================================================
 */
 
@@ -131,6 +131,7 @@ workflow SRA {
     ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions)
 
     emit:
+    fastq         = fastq_files
     samplesheet   = SRA_MERGE_SAMPLESHEET.out.samplesheet
     mappings      = SRA_MERGE_SAMPLESHEET.out.mappings
     versions      = ch_versions.unique()
diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 2652eb80..92b482bd 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -23,7 +23,7 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(workflow.out).match() }
+                { assert snapshot(workflow.out.mappings, workflow.out.samplesheet).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
index a552d171..8f577ef1 100644
--- a/workflows/sra/tests/main.nf.test.snap
+++ b/workflows/sra/tests/main.nf.test.snap
@@ -1,35 +1,13 @@
 {
     "Parameters: default": {
         "content": [
-            {
-                "0": [
-                    "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341"
-                ],
-                "1": [
-                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
-                ],
-                "2": [
-                    "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
-                ],
-                "mappings": [
-                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
-                ],
-                "samplesheet": [
-                    "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341"
-                ],
-                "versions": [
-                    "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
-                ]
-            }
+            [
+                "id_mappings.csv:md5,71ebb4334e4a319a1a007370e36c98f7"
+            ],
+            [
+                "samplesheet.csv:md5,0f35f9485a633d9c581903abd611b646"
+            ]
         ],
-        "timestamp": "2023-08-25T13:15:46+0000"
+        "timestamp": "2023-08-25T14:23:33+0000"
     }
-}
+}
\ No newline at end of file

From 2efa57f90ccd4f42c5cb298e3c638493d2d03fb9 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 25 Aug 2023 17:07:44 +0200
Subject: [PATCH 407/852] update snapshot

---
 workflows/sra/main.nf                 |    3 +-
 workflows/sra/tests/main.nf.test      |    2 +-
 workflows/sra/tests/main.nf.test.snap | 1374 ++++++++++++++++++++++++-
 3 files changed, 1369 insertions(+), 10 deletions(-)

diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index c1583956..8d5149d2 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -66,7 +66,7 @@ workflow SRA {
 
     if (!params.skip_fastq_download) {
 
-        ch_sra_metadata
+        ch_sra_reads = ch_sra_metadata
             .map {
                 meta ->
                     [ meta, [ meta.fastq_1, meta.fastq_2 ] ]
@@ -75,7 +75,6 @@ workflow SRA {
                 ftp: it[0].fastq_1  && !params.force_sratools_download
                 sra: !it[0].fastq_1 || params.force_sratools_download
             }
-            .set { ch_sra_reads }
 
         //
         // MODULE: If FTP link is provided in run information then download FastQ directly via FTP and validate with md5sums
diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 92b482bd..2652eb80 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -23,7 +23,7 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(workflow.out.mappings, workflow.out.samplesheet).match() }
+                { assert snapshot(workflow.out).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
index 8f577ef1..3db02451 100644
--- a/workflows/sra/tests/main.nf.test.snap
+++ b/workflows/sra/tests/main.nf.test.snap
@@ -1,13 +1,1373 @@
 {
     "Parameters: default": {
         "content": [
-            [
-                "id_mappings.csv:md5,71ebb4334e4a319a1a007370e36c98f7"
-            ],
-            [
-                "samplesheet.csv:md5,0f35f9485a633d9c581903abd611b646"
-            ]
+            {
+                "stderr": [
+                    
+                ],
+                "errorReport": null,
+                "exitStatus": 0,
+                "out": {
+                    "0": [
+                        [
+                            {
+                                "id": "ERX1188904_ERR1109373",
+                                "run_accession": "ERR1109373",
+                                "experiment_accession": "ERX1188904",
+                                "sample_accession": "SAMEA3643867",
+                                "secondary_sample_accession": "ERS951016",
+                                "study_accession": "PRJEB11633",
+                                "secondary_study_accession": "ERP013030",
+                                "submission_accession": "ERA528939",
+                                "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
+                                "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
+                                "sample_alias": "sample_56",
+                                "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
+                                "library_layout": "PAIRED",
+                                "library_selection": "RT-PCR",
+                                "library_source": "TRANSCRIPTOMIC",
+                                "library_strategy": "RNA-Seq",
+                                "library_name": "unspecified",
+                                "instrument_model": "Illumina HiSeq 2500",
+                                "instrument_platform": "ILLUMINA",
+                                "base_count": "29700",
+                                "read_count": "169",
+                                "tax_id": "63433",
+                                "scientific_name": "Leptopilina boulardi",
+                                "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                                "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
+                                "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
+                                "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                                "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
+                                "fastq_bytes": "3221;8151;8118",
+                                "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                                "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                                "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                                "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
+                                "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                                "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
+                                "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
+                                "single_end": false
+                            },
+                            [
+                                "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
+                                "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
+                            ]
+                        ],
+                        [
+                            {
+                                "id": "SRX9504942_SRR13055517",
+                                "run_accession": "SRR13055517",
+                                "experiment_accession": "SRX9504942",
+                                "sample_accession": "SAMN16793052",
+                                "secondary_sample_accession": "SRS7713669",
+                                "study_accession": "PRJNA678298",
+                                "secondary_study_accession": "SRP292504",
+                                "submission_accession": "SRA1158402",
+                                "run_alias": "GSM4907283_r1",
+                                "experiment_alias": "GSM4907283",
+                                "sample_alias": "GSM4907283",
+                                "study_alias": "GSE159787",
+                                "library_layout": "PAIRED",
+                                "library_selection": "other",
+                                "library_source": "TRANSCRIPTOMIC",
+                                "library_strategy": "OTHER",
+                                "library_name": "",
+                                "instrument_model": "NextSeq 550",
+                                "instrument_platform": "ILLUMINA",
+                                "base_count": "2246028",
+                                "read_count": "29553",
+                                "tax_id": "9606",
+                                "scientific_name": "Homo sapiens",
+                                "sample_title": "A20-35 A11A20-35 A11_ROI009PanCK+",
+                                "experiment_title": "NextSeq 550 sequencing: GSM4907283: A20-35 A11A20-35 A11_ROI009PanCK+ Homo sapiens OTHER",
+                                "study_title": "Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]",
+                                "sample_description": "A20-35 A11A20-35 A11_ROI009PanCK+",
+                                "fastq_md5": "dcf4438c0b682242ee90c5f3a803fb40;18dbe96e7f58b63406d9058938df1962",
+                                "fastq_bytes": "721167;723753",
+                                "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_2.fastq.gz",
+                                "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_2.fastq.gz",
+                                "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_2.fastq.gz",
+                                "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_1.fastq.gz",
+                                "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_2.fastq.gz",
+                                "md5_1": "dcf4438c0b682242ee90c5f3a803fb40",
+                                "md5_2": "18dbe96e7f58b63406d9058938df1962",
+                                "single_end": false
+                            },
+                            [
+                                "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
+                                "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962"
+                            ]
+                        ],
+                        [
+                            {
+                                "id": "SRX9504942_SRR13055518",
+                                "run_accession": "SRR13055518",
+                                "experiment_accession": "SRX9504942",
+                                "sample_accession": "SAMN16793052",
+                                "secondary_sample_accession": "SRS7713669",
+                                "study_accession": "PRJNA678298",
+                                "secondary_study_accession": "SRP292504",
+                                "submission_accession": "SRA1158402",
+                                "run_alias": "GSM4907283_r2",
+                                "experiment_alias": "GSM4907283",
+                                "sample_alias": "GSM4907283",
+                                "study_alias": "GSE159787",
+                                "library_layout": "PAIRED",
+                                "library_selection": "other",
+                                "library_source": "TRANSCRIPTOMIC",
+                                "library_strategy": "OTHER",
+                                "library_name": "",
+                                "instrument_model": "NextSeq 550",
+                                "instrument_platform": "ILLUMINA",
+                                "base_count": "2235236",
+                                "read_count": "29411",
+                                "tax_id": "9606",
+                                "scientific_name": "Homo sapiens",
+                                "sample_title": "A20-35 A11A20-35 A11_ROI009PanCK+",
+                                "experiment_title": "NextSeq 550 sequencing: GSM4907283: A20-35 A11A20-35 A11_ROI009PanCK+ Homo sapiens OTHER",
+                                "study_title": "Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]",
+                                "sample_description": "A20-35 A11A20-35 A11_ROI009PanCK+",
+                                "fastq_md5": "5ec894d863fcefe394470a0925aefde4;aead170df9851773d5202b5760c76d76",
+                                "fastq_bytes": "717693;723429",
+                                "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_2.fastq.gz",
+                                "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_2.fastq.gz",
+                                "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_2.fastq.gz",
+                                "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_1.fastq.gz",
+                                "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_2.fastq.gz",
+                                "md5_1": "5ec894d863fcefe394470a0925aefde4",
+                                "md5_2": "aead170df9851773d5202b5760c76d76",
+                                "single_end": false
+                            },
+                            [
+                                "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
+                                "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76"
+                            ]
+                        ],
+                        [
+                            {
+                                "id": "SRX9504942_SRR13055519",
+                                "run_accession": "SRR13055519",
+                                "experiment_accession": "SRX9504942",
+                                "sample_accession": "SAMN16793052",
+                                "secondary_sample_accession": "SRS7713669",
+                                "study_accession": "PRJNA678298",
+                                "secondary_study_accession": "SRP292504",
+                                "submission_accession": "SRA1158402",
+                                "run_alias": "GSM4907283_r3",
+                                "experiment_alias": "GSM4907283",
+                                "sample_alias": "GSM4907283",
+                                "study_alias": "GSE159787",
+                                "library_layout": "PAIRED",
+                                "library_selection": "other",
+                                "library_source": "TRANSCRIPTOMIC",
+                                "library_strategy": "OTHER",
+                                "library_name": "",
+                                "instrument_model": "NextSeq 550",
+                                "instrument_platform": "ILLUMINA",
+                                "base_count": "2232728",
+                                "read_count": "29378",
+                                "tax_id": "9606",
+                                "scientific_name": "Homo sapiens",
+                                "sample_title": "A20-35 A11A20-35 A11_ROI009PanCK+",
+                                "experiment_title": "NextSeq 550 sequencing: GSM4907283: A20-35 A11A20-35 A11_ROI009PanCK+ Homo sapiens OTHER",
+                                "study_title": "Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]",
+                                "sample_description": "A20-35 A11A20-35 A11_ROI009PanCK+",
+                                "fastq_md5": "5ad51460c6c4a850dd37a206e2c441c1;a977367bf41dacf4c21bc0c8201b8b88",
+                                "fastq_bytes": "714907;721705",
+                                "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_2.fastq.gz",
+                                "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_2.fastq.gz",
+                                "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_2.fastq.gz",
+                                "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_1.fastq.gz",
+                                "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_2.fastq.gz",
+                                "md5_1": "5ad51460c6c4a850dd37a206e2c441c1",
+                                "md5_2": "a977367bf41dacf4c21bc0c8201b8b88",
+                                "single_end": false
+                            },
+                            [
+                                "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
+                                "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88"
+                            ]
+                        ],
+                        [
+                            {
+                                "id": "DRX024467_DRR026872",
+                                "run_accession": "DRR026872",
+                                "experiment_accession": "DRX024467",
+                                "sample_accession": "SAMD00023098",
+                                "secondary_sample_accession": "DRS033740",
+                                "study_accession": "PRJDB4356",
+                                "secondary_study_accession": "DRP003256",
+                                "submission_accession": "DRA002758",
+                                "run_alias": "DRR026872",
+                                "experiment_alias": "DRX024467",
+                                "sample_alias": "SAMD00023098",
+                                "study_alias": "DRP003256",
+                                "library_layout": "SINGLE",
+                                "library_selection": "Restriction Digest",
+                                "library_source": "GENOMIC",
+                                "library_strategy": "OTHER",
+                                "library_name": "IpeRAD1_3",
+                                "instrument_model": "Illumina HiSeq 2500",
+                                "instrument_platform": "ILLUMINA",
+                                "base_count": "62550",
+                                "read_count": "417",
+                                "tax_id": "35883",
+                                "scientific_name": "Ipomoea nil",
+                                "sample_title": "F2 plant dreived from a cross between Tokyo Kokei-standard and Africa #21",
+                                "experiment_title": "Illumina HiSeq 2500 sequencing: Illumina HiSeq 2500 sequencing of SAMD00023098",
+                                "study_title": "The Japanese morning glory genome sequence",
+                                "sample_description": "Keywords: GSC:MIxS MIGS:6.0",
+                                "fastq_md5": "515e5448c55e054113c4a22df5f62791",
+                                "fastq_bytes": "38447",
+                                "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                                "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                                "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                                "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                                "fastq_2": "",
+                                "md5_1": "515e5448c55e054113c4a22df5f62791",
+                                "md5_2": "",
+                                "single_end": true
+                            },
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+                                "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                                "fastq_2": "",
+                                "md5_1": "7cd1402155befc87be338132d1f31f64",
+                                "md5_2": "",
+                                "single_end": true
+                            },
+                            "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64"
+                        ],
+                        [
+                            {
+                                "id": "SRX17709228_SRR21711855",
+                                "run_accession": "SRR21711855",
+                                "experiment_accession": "SRX17709228",
+                                "sample_accession": "SAMN31021822",
+                                "secondary_sample_accession": "SRS15239724",
+                                "study_accession": "PRJNA884373",
+                                "secondary_study_accession": "SRP399678",
+                                "submission_accession": "SRA1507236",
+                                "run_alias": "GSM6601461_r1",
+                                "experiment_alias": "GSM6601461_r1",
+                                "sample_alias": "GSM6601461",
+                                "study_alias": "GSE214215",
+                                "library_layout": "SINGLE",
+                                "library_selection": "cDNA",
+                                "library_source": "TRANSCRIPTOMIC",
+                                "library_strategy": "RNA-Seq",
+                                "library_name": "GSM6601461",
+                                "instrument_model": "Illumina HiSeq 4000",
+                                "instrument_platform": "ILLUMINA",
+                                "base_count": "677912850",
+                                "read_count": "13558257",
+                                "tax_id": "6239",
+                                "scientific_name": "Caenorhabditis elegans",
+                                "sample_title": "PM2.5-treated worms in day 5",
+                                "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                                "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                                "sample_description": "PM2.5-treated worms in day 5",
+                                "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                                "fastq_bytes": "529798447",
+                                "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                                "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                                "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                                "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                                "fastq_2": "",
+                                "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                                "md5_2": "",
+                                "single_end": true
+                            },
+                            "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83"
+                        ]
+                    ],
+                    "mappings": [
+                        "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                    ],
+                    "samplesheet": [
+                        "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341"
+                    ],
+                    "versions": [
+                        "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                        "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                        "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                        "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
+                        "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                    ]
+                },
+                "failed": false,
+                "stdout": [
+                    "WARN: There's no process matching config selector: CUSTOM_DUMPSOFTWAREVERSIONS",
+                    "WARN: There's no process matching config selector: MULTIQC_MAPPINGS_CONFIG"
+                ],
+                "errorMessage": null,
+                "trace": {
+                    "tasksFailed": 0,
+                    "tasksCount": 57,
+                    "tasksSucceeded": 57
+                },
+                "name": "workflow",
+                "success": true
+            }
         ],
-        "timestamp": "2023-08-25T14:23:33+0000"
+        "timestamp": "2023-08-25T15:06:56+0000"
     }
 }
\ No newline at end of file

From 20af64e3a871b01c3d97b7f04b0676cf378fd66c Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 25 Aug 2023 17:11:24 +0200
Subject: [PATCH 408/852] disable autosort channel

---
 nf-test.config | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/nf-test.config b/nf-test.config
index 0799cb40..217a5138 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -13,4 +13,7 @@ config {
 
     // run all test with the defined docker profile from the main nextflow.config
     profile ""
+
+    // Disable autosort Channels
+    autoSort false
 }

From 3c2e8fee5b0cdd3db4d862bc03c866a2437fd41a Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 25 Aug 2023 17:14:35 +0200
Subject: [PATCH 409/852] update snapshot

---
 workflows/sra/tests/main.nf.test.snap | 2654 ++++++++++++-------------
 1 file changed, 1317 insertions(+), 1337 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
index 3db02451..3eab5807 100644
--- a/workflows/sra/tests/main.nf.test.snap
+++ b/workflows/sra/tests/main.nf.test.snap
@@ -2,1372 +2,1352 @@
     "Parameters: default": {
         "content": [
             {
-                "stderr": [
-                    
-                ],
-                "errorReport": null,
-                "exitStatus": 0,
-                "out": {
-                    "0": [
-                        [
-                            {
-                                "id": "ERX1188904_ERR1109373",
-                                "run_accession": "ERR1109373",
-                                "experiment_accession": "ERX1188904",
-                                "sample_accession": "SAMEA3643867",
-                                "secondary_sample_accession": "ERS951016",
-                                "study_accession": "PRJEB11633",
-                                "secondary_study_accession": "ERP013030",
-                                "submission_accession": "ERA528939",
-                                "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
-                                "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
-                                "sample_alias": "sample_56",
-                                "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
-                                "library_layout": "PAIRED",
-                                "library_selection": "RT-PCR",
-                                "library_source": "TRANSCRIPTOMIC",
-                                "library_strategy": "RNA-Seq",
-                                "library_name": "unspecified",
-                                "instrument_model": "Illumina HiSeq 2500",
-                                "instrument_platform": "ILLUMINA",
-                                "base_count": "29700",
-                                "read_count": "169",
-                                "tax_id": "63433",
-                                "scientific_name": "Leptopilina boulardi",
-                                "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                                "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
-                                "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
-                                "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                                "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
-                                "fastq_bytes": "3221;8151;8118",
-                                "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                                "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                                "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                                "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
-                                "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                                "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
-                                "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
-                                "single_end": false
-                            },
-                            [
-                                "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                                "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
-                            ]
-                        ],
-                        [
-                            {
-                                "id": "SRX9504942_SRR13055517",
-                                "run_accession": "SRR13055517",
-                                "experiment_accession": "SRX9504942",
-                                "sample_accession": "SAMN16793052",
-                                "secondary_sample_accession": "SRS7713669",
-                                "study_accession": "PRJNA678298",
-                                "secondary_study_accession": "SRP292504",
-                                "submission_accession": "SRA1158402",
-                                "run_alias": "GSM4907283_r1",
-                                "experiment_alias": "GSM4907283",
-                                "sample_alias": "GSM4907283",
-                                "study_alias": "GSE159787",
-                                "library_layout": "PAIRED",
-                                "library_selection": "other",
-                                "library_source": "TRANSCRIPTOMIC",
-                                "library_strategy": "OTHER",
-                                "library_name": "",
-                                "instrument_model": "NextSeq 550",
-                                "instrument_platform": "ILLUMINA",
-                                "base_count": "2246028",
-                                "read_count": "29553",
-                                "tax_id": "9606",
-                                "scientific_name": "Homo sapiens",
-                                "sample_title": "A20-35 A11A20-35 A11_ROI009PanCK+",
-                                "experiment_title": "NextSeq 550 sequencing: GSM4907283: A20-35 A11A20-35 A11_ROI009PanCK+ Homo sapiens OTHER",
-                                "study_title": "Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]",
-                                "sample_description": "A20-35 A11A20-35 A11_ROI009PanCK+",
-                                "fastq_md5": "dcf4438c0b682242ee90c5f3a803fb40;18dbe96e7f58b63406d9058938df1962",
-                                "fastq_bytes": "721167;723753",
-                                "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_2.fastq.gz",
-                                "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_2.fastq.gz",
-                                "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_2.fastq.gz",
-                                "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_1.fastq.gz",
-                                "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_2.fastq.gz",
-                                "md5_1": "dcf4438c0b682242ee90c5f3a803fb40",
-                                "md5_2": "18dbe96e7f58b63406d9058938df1962",
-                                "single_end": false
-                            },
-                            [
-                                "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
-                                "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962"
-                            ]
-                        ],
-                        [
-                            {
-                                "id": "SRX9504942_SRR13055518",
-                                "run_accession": "SRR13055518",
-                                "experiment_accession": "SRX9504942",
-                                "sample_accession": "SAMN16793052",
-                                "secondary_sample_accession": "SRS7713669",
-                                "study_accession": "PRJNA678298",
-                                "secondary_study_accession": "SRP292504",
-                                "submission_accession": "SRA1158402",
-                                "run_alias": "GSM4907283_r2",
-                                "experiment_alias": "GSM4907283",
-                                "sample_alias": "GSM4907283",
-                                "study_alias": "GSE159787",
-                                "library_layout": "PAIRED",
-                                "library_selection": "other",
-                                "library_source": "TRANSCRIPTOMIC",
-                                "library_strategy": "OTHER",
-                                "library_name": "",
-                                "instrument_model": "NextSeq 550",
-                                "instrument_platform": "ILLUMINA",
-                                "base_count": "2235236",
-                                "read_count": "29411",
-                                "tax_id": "9606",
-                                "scientific_name": "Homo sapiens",
-                                "sample_title": "A20-35 A11A20-35 A11_ROI009PanCK+",
-                                "experiment_title": "NextSeq 550 sequencing: GSM4907283: A20-35 A11A20-35 A11_ROI009PanCK+ Homo sapiens OTHER",
-                                "study_title": "Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]",
-                                "sample_description": "A20-35 A11A20-35 A11_ROI009PanCK+",
-                                "fastq_md5": "5ec894d863fcefe394470a0925aefde4;aead170df9851773d5202b5760c76d76",
-                                "fastq_bytes": "717693;723429",
-                                "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_2.fastq.gz",
-                                "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_2.fastq.gz",
-                                "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_2.fastq.gz",
-                                "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_1.fastq.gz",
-                                "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_2.fastq.gz",
-                                "md5_1": "5ec894d863fcefe394470a0925aefde4",
-                                "md5_2": "aead170df9851773d5202b5760c76d76",
-                                "single_end": false
-                            },
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-                                "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76"
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-                        ],
-                        [
-                            {
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-                                "run_accession": "SRR13055519",
-                                "experiment_accession": "SRX9504942",
-                                "sample_accession": "SAMN16793052",
-                                "secondary_sample_accession": "SRS7713669",
-                                "study_accession": "PRJNA678298",
-                                "secondary_study_accession": "SRP292504",
-                                "submission_accession": "SRA1158402",
-                                "run_alias": "GSM4907283_r3",
-                                "experiment_alias": "GSM4907283",
-                                "sample_alias": "GSM4907283",
-                                "study_alias": "GSE159787",
-                                "library_layout": "PAIRED",
-                                "library_selection": "other",
-                                "library_source": "TRANSCRIPTOMIC",
-                                "library_strategy": "OTHER",
-                                "library_name": "",
-                                "instrument_model": "NextSeq 550",
-                                "instrument_platform": "ILLUMINA",
-                                "base_count": "2232728",
-                                "read_count": "29378",
-                                "tax_id": "9606",
-                                "scientific_name": "Homo sapiens",
-                                "sample_title": "A20-35 A11A20-35 A11_ROI009PanCK+",
-                                "experiment_title": "NextSeq 550 sequencing: GSM4907283: A20-35 A11A20-35 A11_ROI009PanCK+ Homo sapiens OTHER",
-                                "study_title": "Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]",
-                                "sample_description": "A20-35 A11A20-35 A11_ROI009PanCK+",
-                                "fastq_md5": "5ad51460c6c4a850dd37a206e2c441c1;a977367bf41dacf4c21bc0c8201b8b88",
-                                "fastq_bytes": "714907;721705",
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-                                "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_2.fastq.gz",
-                                "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_2.fastq.gz",
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-                                "run_accession": "DRR026872",
-                                "experiment_accession": "DRX024467",
-                                "sample_accession": "SAMD00023098",
-                                "secondary_sample_accession": "DRS033740",
-                                "study_accession": "PRJDB4356",
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-                                "submission_accession": "DRA002758",
-                                "run_alias": "DRR026872",
-                                "experiment_alias": "DRX024467",
-                                "sample_alias": "SAMD00023098",
-                                "study_alias": "DRP003256",
-                                "library_layout": "SINGLE",
-                                "library_selection": "Restriction Digest",
-                                "library_source": "GENOMIC",
-                                "library_strategy": "OTHER",
-                                "library_name": "IpeRAD1_3",
-                                "instrument_model": "Illumina HiSeq 2500",
-                                "instrument_platform": "ILLUMINA",
-                                "base_count": "62550",
-                                "read_count": "417",
-                                "tax_id": "35883",
-                                "scientific_name": "Ipomoea nil",
-                                "sample_title": "F2 plant dreived from a cross between Tokyo Kokei-standard and Africa #21",
-                                "experiment_title": "Illumina HiSeq 2500 sequencing: Illumina HiSeq 2500 sequencing of SAMD00023098",
-                                "study_title": "The Japanese morning glory genome sequence",
-                                "sample_description": "Keywords: GSC:MIxS MIGS:6.0",
-                                "fastq_md5": "515e5448c55e054113c4a22df5f62791",
-                                "fastq_bytes": "38447",
-                                "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
-                                "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
-                                "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
-                                "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
-                                "fastq_2": "",
-                                "md5_1": "515e5448c55e054113c4a22df5f62791",
-                                "md5_2": "",
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+                            "single_end": true
+                        },
+                        "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83"
                     ]
-                },
-                "failed": false,
-                "stdout": [
-                    "WARN: There's no process matching config selector: CUSTOM_DUMPSOFTWAREVERSIONS",
-                    "WARN: There's no process matching config selector: MULTIQC_MAPPINGS_CONFIG"
                 ],
-                "errorMessage": null,
-                "trace": {
-                    "tasksFailed": 0,
-                    "tasksCount": 57,
-                    "tasksSucceeded": 57
-                },
-                "name": "workflow",
-                "success": true
+                "mappings": [
+                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                ],
+                "samplesheet": [
+                    "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341"
+                ],
+                "versions": [
+                    "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                ]
             }
         ],
-        "timestamp": "2023-08-25T15:06:56+0000"
+        "timestamp": "2023-08-25T15:13:41+0000"
     }
 }
\ No newline at end of file

From e8258ba4d77dae0e963c63558099c781f36c2435 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 28 Aug 2023 11:17:16 +0200
Subject: [PATCH 410/852] order

---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index ad72ea4a..0535bb57 100644
--- a/main.nf
+++ b/main.nf
@@ -72,8 +72,8 @@ if (params.input_type == 'synapse') {
 ========================================================================================
 */
 
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from './modules/nf-core/custom/dumpsoftwareversions'
 include { MULTIQC_MAPPINGS_CONFIG     } from './modules/local/multiqc_mappings_config'
+include { CUSTOM_DUMPSOFTWAREVERSIONS } from './modules/nf-core/custom/dumpsoftwareversions'
 
 /*
 ========================================================================================

From f8322343c09fd45f30c503002d6542f1459f5d67 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 28 Aug 2023 11:17:32 +0200
Subject: [PATCH 411/852] update test and snapshots

---
 workflows/sra/tests/main.nf.test      |    7 +-
 workflows/sra/tests/main.nf.test.snap | 1043 ++++++++++++++-----------
 2 files changed, 571 insertions(+), 479 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 2652eb80..4822da3d 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -23,7 +23,12 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(workflow.out).match() }
+//                { assert snapshot(workflow.out).match() }
+                { assert new File("$outputDir/custom").exists() },
+                { assert new File("$outputDir/metadata").exists() },
+                { assert new File("$outputDir/pipeline_info").exists() },
+                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
+                { assert snapshot(path("$outputDir/samplesheet/").list()).match("samplesheet") }
             )
         }
     }
diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
index 3eab5807..62d0d976 100644
--- a/workflows/sra/tests/main.nf.test.snap
+++ b/workflows/sra/tests/main.nf.test.snap
@@ -45,6 +45,48 @@
                         },
                         "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791"
                     ],
+                    [
+                        {
+                            "id": "SRX6725035_SRR9984183",
+                            "run_accession": "SRR9984183",
+                            "experiment_accession": "SRX6725035",
+                            "sample_accession": "SAMN12581720",
+                            "secondary_sample_accession": "SRS5277011",
+                            "study_accession": "PRJNA560329",
+                            "secondary_study_accession": "SRP218535",
+                            "submission_accession": "SRA942061",
+                            "run_alias": "Emb289P1_bin131.fastq",
+                            "experiment_alias": "Emb289P1_bin131",
+                            "sample_alias": "Emb289P1_bin131",
+                            "study_alias": "PRJNA560329",
+                            "library_layout": "SINGLE",
+                            "library_selection": "RANDOM",
+                            "library_source": "METAGENOMIC",
+                            "library_strategy": "WGS",
+                            "library_name": "Emb289P1_bin131",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "1996273",
+                            "read_count": "58",
+                            "tax_id": "2660712",
+                            "scientific_name": "Defluviitaleaceae bacterium",
+                            "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
+                            "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
+                            "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
+                            "fastq_md5": "0b512d2dc31685983456bd56fd836544",
+                            "fastq_bytes": "605358",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "0b512d2dc31685983456bd56fd836544",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544"
+                    ],
                     [
                         {
                             "id": "ERX1234253_ERR1160846",
@@ -89,47 +131,47 @@
                     ],
                     [
                         {
-                            "id": "DRX026011_DRR028935",
-                            "run_accession": "DRR028935",
-                            "experiment_accession": "DRX026011",
-                            "sample_accession": "SAMD00024405",
-                            "secondary_sample_accession": "DRS019431",
-                            "study_accession": "PRJDB3420",
-                            "secondary_study_accession": "DRP002616",
-                            "submission_accession": "DRA002949",
-                            "run_alias": "DRR028935",
-                            "experiment_alias": "DRX026011",
-                            "sample_alias": "SAMD00024405",
-                            "study_alias": "DRP002616",
+                            "id": "SRX9626017_SRR13191702",
+                            "run_accession": "SRR13191702",
+                            "experiment_accession": "SRX9626017",
+                            "sample_accession": "SAMN16980141",
+                            "secondary_sample_accession": "SRS7827211",
+                            "study_accession": "PRJNA682076",
+                            "secondary_study_accession": "SRP295653",
+                            "submission_accession": "SRA1166126",
+                            "run_alias": "S.170804.00784_662_L001_R1_001.fastq.gz",
+                            "experiment_alias": "S.170804.00784",
+                            "sample_alias": "S.170804.00784_662",
+                            "study_alias": "PRJNA682076",
                             "library_layout": "PAIRED",
-                            "library_selection": "cDNA",
-                            "library_source": "TRANSCRIPTOMIC",
-                            "library_strategy": "RNA-Seq",
-                            "library_name": "day0_BbSQE-I",
+                            "library_selection": "PCR",
+                            "library_source": "METAGENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "S.170804.00784",
                             "instrument_model": "Illumina HiSeq 2500",
                             "instrument_platform": "ILLUMINA",
-                            "base_count": "194930",
-                            "read_count": "965",
-                            "tax_id": "1202541",
-                            "scientific_name": "Botryococcus braunii Showa",
-                            "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
-                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
-                            "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
-                            "sample_description": "Liquid culture",
-                            "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
-                            "fastq_bytes": "60275;61610",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                            "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
-                            "md5_2": "941c9998d746416dad53c94c480ddf30",
+                            "base_count": "45682",
+                            "read_count": "91",
+                            "tax_id": "408170",
+                            "scientific_name": "human gut metagenome",
+                            "sample_title": "Metagenome or environmental sample from human gut metagenome",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
+                            "study_title": "Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
+                            "sample_description": "Metagenome or environmental sample from human gut metagenome",
+                            "fastq_md5": "89c5be920021a035084d8aeb74f32df7;56271be38a80db78ef3bdfc5d9909b98",
+                            "fastq_bytes": "15420;16324",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98",
                             "single_end": false
                         },
                         [
-                            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
-                            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
                         ]
                     ],
                     [
@@ -179,105 +221,60 @@
                     ],
                     [
                         {
-                            "id": "SRX9504942_SRR13055519",
-                            "run_accession": "SRR13055519",
-                            "experiment_accession": "SRX9504942",
-                            "sample_accession": "SAMN16793052",
-                            "secondary_sample_accession": "SRS7713669",
-                            "study_accession": "PRJNA678298",
-                            "secondary_study_accession": "SRP292504",
-                            "submission_accession": "SRA1158402",
-                            "run_alias": "GSM4907283_r3",
-                            "experiment_alias": "GSM4907283",
-                            "sample_alias": "GSM4907283",
-                            "study_alias": "GSE159787",
-                            "library_layout": "PAIRED",
-                            "library_selection": "other",
-                            "library_source": "TRANSCRIPTOMIC",
-                            "library_strategy": "OTHER",
-                            "library_name": "",
-                            "instrument_model": "NextSeq 550",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "2232728",
-                            "read_count": "29378",
-                            "tax_id": "9606",
-                            "scientific_name": "Homo sapiens",
-                            "sample_title": "A20-35 A11A20-35 A11_ROI009PanCK+",
-                            "experiment_title": "NextSeq 550 sequencing: GSM4907283: A20-35 A11A20-35 A11_ROI009PanCK+ Homo sapiens OTHER",
-                            "study_title": "Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]",
-                            "sample_description": "A20-35 A11A20-35 A11_ROI009PanCK+",
-                            "fastq_md5": "5ad51460c6c4a850dd37a206e2c441c1;a977367bf41dacf4c21bc0c8201b8b88",
-                            "fastq_bytes": "714907;721705",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_2.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_2.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_2.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_2.fastq.gz",
-                            "md5_1": "5ad51460c6c4a850dd37a206e2c441c1",
-                            "md5_2": "a977367bf41dacf4c21bc0c8201b8b88",
-                            "single_end": false
-                        },
-                        [
-                            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
-                            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88"
-                        ]
-                    ],
-                    [
-                        {
-                            "id": "SRX9504942_SRR13055517",
-                            "run_accession": "SRR13055517",
-                            "experiment_accession": "SRX9504942",
-                            "sample_accession": "SAMN16793052",
-                            "secondary_sample_accession": "SRS7713669",
-                            "study_accession": "PRJNA678298",
-                            "secondary_study_accession": "SRP292504",
-                            "submission_accession": "SRA1158402",
-                            "run_alias": "GSM4907283_r1",
-                            "experiment_alias": "GSM4907283",
-                            "sample_alias": "GSM4907283",
-                            "study_alias": "GSE159787",
+                            "id": "DRX026011_DRR028935",
+                            "run_accession": "DRR028935",
+                            "experiment_accession": "DRX026011",
+                            "sample_accession": "SAMD00024405",
+                            "secondary_sample_accession": "DRS019431",
+                            "study_accession": "PRJDB3420",
+                            "secondary_study_accession": "DRP002616",
+                            "submission_accession": "DRA002949",
+                            "run_alias": "DRR028935",
+                            "experiment_alias": "DRX026011",
+                            "sample_alias": "SAMD00024405",
+                            "study_alias": "DRP002616",
                             "library_layout": "PAIRED",
-                            "library_selection": "other",
+                            "library_selection": "cDNA",
                             "library_source": "TRANSCRIPTOMIC",
-                            "library_strategy": "OTHER",
-                            "library_name": "",
-                            "instrument_model": "NextSeq 550",
+                            "library_strategy": "RNA-Seq",
+                            "library_name": "day0_BbSQE-I",
+                            "instrument_model": "Illumina HiSeq 2500",
                             "instrument_platform": "ILLUMINA",
-                            "base_count": "2246028",
-                            "read_count": "29553",
-                            "tax_id": "9606",
-                            "scientific_name": "Homo sapiens",
-                            "sample_title": "A20-35 A11A20-35 A11_ROI009PanCK+",
-                            "experiment_title": "NextSeq 550 sequencing: GSM4907283: A20-35 A11A20-35 A11_ROI009PanCK+ Homo sapiens OTHER",
-                            "study_title": "Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]",
-                            "sample_description": "A20-35 A11A20-35 A11_ROI009PanCK+",
-                            "fastq_md5": "dcf4438c0b682242ee90c5f3a803fb40;18dbe96e7f58b63406d9058938df1962",
-                            "fastq_bytes": "721167;723753",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_2.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_2.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_2.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_2.fastq.gz",
-                            "md5_1": "dcf4438c0b682242ee90c5f3a803fb40",
-                            "md5_2": "18dbe96e7f58b63406d9058938df1962",
+                            "base_count": "194930",
+                            "read_count": "965",
+                            "tax_id": "1202541",
+                            "scientific_name": "Botryococcus braunii Showa",
+                            "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
+                            "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
+                            "sample_description": "Liquid culture",
+                            "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
+                            "fastq_bytes": "60275;61610",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
+                            "md5_2": "941c9998d746416dad53c94c480ddf30",
                             "single_end": false
                         },
                         [
-                            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
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@@ -668,8 +668,8 @@
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+        "timestamp": "2023-08-28T08:57:15+0000"
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+            "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
+            "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54",
+            "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
+            "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
+        ],
+        "timestamp": "2023-08-28T08:57:15+0000"
+    },
+    "samplesheet": {
+        "content": [
+            "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
+            "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341"
+        ],
+        "timestamp": "2023-08-28T08:57:15+0000"
+    },
+    "custom": {
+        "content": [
+            "user-settings.mkfg:md5,a182ee157fbd89040a00b9658f53848d"
+        ],
+        "timestamp": "2023-08-28T08:57:15+0000"
+    },
+    "fastq": {
+        "content": [
+            "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791",
+            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
+            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30",
+            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
+            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
+            "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6",
+            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
+            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
+            "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
+            "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64",
+            "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83",
+            "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544",
+            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
+            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
+            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
+            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962",
+            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
+            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76",
+            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
+            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88",
+            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
+            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04",
+            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98",
+            [
+                "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d",
+                "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9",
+                "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f",
+                "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86",
+                "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499",
+                "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff",
+                "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75",
+                "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85",
+                "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4",
+                "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc",
+                "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0",
+                "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368",
+                "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8",
+                "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f",
+                "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3",
+                "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8",
+                "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882",
+                "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
+                "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
+            ]
+        ],
+        "timestamp": "2023-08-28T08:57:15+0000"
+    },
+    "pipeline_info": {
+        "content": [
+            "execution_report_2023-08-28_10-54-32.html:md5,710a38308b41b4bd86b6d2d8fd4a72b7",
+            "execution_timeline_2023-08-28_10-54-32.html:md5,1583b3c97bc7c97a8550c3d0ce6302c8",
+            "pipeline_dag_2023-08-28_10-54-32.html:md5,63f58c7a48a1b71d3ee7809cb6a92740"
+        ],
+        "timestamp": "2023-08-28T08:57:15+0000"
     }
-}
\ No newline at end of file
+}

From 80892b7ca38100a00b31b5abb2c079694e2729a0 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 28 Aug 2023 13:06:34 +0200
Subject: [PATCH 412/852] update test

---
 workflows/sra/tests/main.nf.test | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 4822da3d..2a1e82a1 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -27,8 +27,8 @@ nextflow_workflow {
                 { assert new File("$outputDir/custom").exists() },
                 { assert new File("$outputDir/metadata").exists() },
                 { assert new File("$outputDir/pipeline_info").exists() },
-                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
-                { assert snapshot(path("$outputDir/samplesheet/").list()).match("samplesheet") }
+                { assert new File("$outputDir/samplesheet").exists() },
+                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }
             )
         }
     }

From 9a70ce9bca6179b6d43f9bb2bb6326de8aa48343 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 28 Aug 2023 14:27:56 +0200
Subject: [PATCH 413/852] update tests and snapshot

---
 .../sra_custom_ena_metadata_fields.nf.test    | 19 +++++++++++++++----
 ...ra_custom_ena_metadata_fields.nf.test.snap | 12 ++++++------
 .../tests/sra_force_sratools_download.nf.test | 19 +++++++++++++++----
 .../sra_nf_core_pipeline_atacseq.nf.test      | 19 +++++++++++++++----
 .../sra_nf_core_pipeline_atacseq.nf.test.snap | 12 ++++++------
 .../tests/sra_nf_core_pipeline_rnaseq.nf.test | 19 +++++++++++++++----
 .../sra_nf_core_pipeline_rnaseq.nf.test.snap  | 12 ++++++------
 .../sra_nf_core_pipeline_taxprofiler.nf.test  | 19 +++++++++++++++----
 ..._nf_core_pipeline_taxprofiler.nf.test.snap | 12 ++++++------
 .../sra_nf_core_pipeline_viralrecon.nf.test   | 19 +++++++++++++++----
 ...a_nf_core_pipeline_viralrecon.nf.test.snap | 12 ++++++------
 11 files changed, 120 insertions(+), 54 deletions(-)

diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index 6e27c4a9..f1f55f02 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -1,7 +1,8 @@
-nextflow_pipeline {
+nextflow_workflow {
 
-    name "Test workflow: sra.nf"
-    script "main.nf"
+    name "Test workflow: sra/main.nf"
+    script "workflows/sra/main.nf"
+    workflow "SRA"
     tag "workflows"
     tag "workflows_sra"
     tag "sra_custom_ena_metadata_fields"
@@ -9,6 +10,11 @@ nextflow_pipeline {
     test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") {
 
         when {
+            workflow {
+                """
+                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                """
+            }
             params {
                 outdir = "$outputDir"
                 nf_core_pipeline = "rnaseq"
@@ -20,7 +26,12 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(process.out).match() }
+//                { assert snapshot(workflow.out).match() }
+                { assert new File("$outputDir/custom").exists() },
+                { assert new File("$outputDir/metadata").exists() },
+                { assert new File("$outputDir/pipeline_info").exists() },
+                { assert new File("$outputDir/samplesheet").exists() },
+                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
index 55c39d4f..ddd8e845 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
@@ -12,20 +12,20 @@
             "SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1",
             "SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236"
         ],
-        "timestamp": "2023-08-17T12:11:42+0000"
+        "timestamp": "2023-08-28T09:29:59+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f",
-            "multiqc_config.yml:md5,6f6189ee58855de81eaf82ad86e21040"
+            "samplesheet.csv:md5,7bca96e409bd9eb6790e0d6737af686c"
         ],
-        "timestamp": "2023-08-17T12:11:42+0000"
+        "timestamp": "2023-08-28T09:29:59+0000"
     },
     "software_versions": {
         "content": [
             "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
-        "timestamp": "2023-08-17T12:11:42+0000"
+        "timestamp": "2023-08-28T09:29:59+0000"
     },
     "Parameters: '--nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...'": {
         "content": [
@@ -33,7 +33,7 @@
                 
             }
         ],
-        "timestamp": "2023-08-17T12:11:42+0000"
+        "timestamp": "2023-08-28T09:29:59+0000"
     },
     "fastq": {
         "content": [
@@ -83,6 +83,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-08-17T12:11:42+0000"
+        "timestamp": "2023-08-28T09:29:59+0000"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index 1b501975..051e4aa5 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -1,7 +1,8 @@
-nextflow_pipeline {
+nextflow_workflow {
 
-    name "Test workflow: sra.nf"
-    script "main.nf"
+    name "Test workflow: sra/main.nf"
+    script "workflows/sra/main.nf"
+    workflow "SRA"
     tag "workflows"
     tag "workflows_sra"
     tag "sra_force_sratools_download"
@@ -9,6 +10,11 @@ nextflow_pipeline {
     test("Parameters: --force_sratools_download") {
 
         when {
+            workflow {
+                """
+                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                """
+            }
             params {
                 outdir = "$outputDir"
                 force_sratools_download = true
@@ -18,7 +24,12 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(process.out).match() }
+//                { assert snapshot(workflow.out).match() }
+                { assert new File("$outputDir/custom").exists() },
+                { assert new File("$outputDir/metadata").exists() },
+                { assert new File("$outputDir/pipeline_info").exists() },
+                { assert new File("$outputDir/samplesheet").exists() },
+                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index bda1d724..6925b971 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -1,7 +1,8 @@
-nextflow_pipeline {
+nextflow_workflow {
 
-    name "Test workflow: sra.nf"
-    script "main.nf"
+    name "Test workflow: sra/main.nf"
+    script "workflows/sra/main.nf"
+    workflow "SRA"
     tag "workflows"
     tag "workflows_sra"
     tag "sra_nf_core_pipeline_atacseq"
@@ -9,6 +10,11 @@ nextflow_pipeline {
     test("Parameters: --nf_core_pipeline atacseq") {
 
         when {
+            workflow {
+                """
+                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                """
+            }
             params {
                 outdir = "$outputDir"
                 nf_core_pipeline = "atacseq"
@@ -18,7 +24,12 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(process.out).match() }
+//                { assert snapshot(workflow.out).match() }
+                { assert new File("$outputDir/custom").exists() },
+                { assert new File("$outputDir/metadata").exists() },
+                { assert new File("$outputDir/pipeline_info").exists() },
+                { assert new File("$outputDir/samplesheet").exists() },
+                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
index c99f258e..0ccec99b 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
@@ -12,20 +12,20 @@
             "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
             "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
         ],
-        "timestamp": "2023-08-17T12:21:36+0000"
+        "timestamp": "2023-08-28T10:05:53+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
-            "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
+            "samplesheet.csv:md5,252449b9f66687af076bb5a9dfea4551"
         ],
-        "timestamp": "2023-08-17T12:21:36+0000"
+        "timestamp": "2023-08-28T10:05:53+0000"
     },
     "software_versions": {
         "content": [
             "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
-        "timestamp": "2023-08-17T12:21:36+0000"
+        "timestamp": "2023-08-28T10:05:53+0000"
     },
     "Parameters: '--nf_core_pipeline atacseq'": {
         "content": [
@@ -33,7 +33,7 @@
                 
             }
         ],
-        "timestamp": "2023-08-17T12:21:36+0000"
+        "timestamp": "2023-08-28T10:05:53+0000"
     },
     "fastq": {
         "content": [
@@ -83,6 +83,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-08-17T12:21:36+0000"
+        "timestamp": "2023-08-28T10:05:57+0000"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index 438b7f55..a84b7c41 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -1,7 +1,8 @@
-nextflow_pipeline {
+nextflow_workflow {
 
-    name "Test workflow: sra.nf"
-    script "main.nf"
+    name "Test workflow: sra/main.nf"
+    script "workflows/sra/main.nf"
+    workflow "SRA"
     tag "workflows"
     tag "workflows_sra"
     tag "sra_nf_core_pipeline_rnaseq"
@@ -9,6 +10,11 @@ nextflow_pipeline {
     test("Parameters: --nf_core_pipeline rnaseq") {
 
         when {
+            workflow {
+                """
+                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                """
+            }
             params {
                 outdir = "$outputDir"
                 nf_core_pipeline = "rnaseq"
@@ -18,7 +24,12 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(process.out).match() }
+//                { assert snapshot(workflow.out).match() }
+                { assert new File("$outputDir/custom").exists() },
+                { assert new File("$outputDir/metadata").exists() },
+                { assert new File("$outputDir/pipeline_info").exists() },
+                { assert new File("$outputDir/samplesheet").exists() },
+                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
index 1da0381a..af68569e 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
@@ -12,20 +12,20 @@
             "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
             "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
         ],
-        "timestamp": "2023-08-17T12:19:51+0000"
+        "timestamp": "2023-08-28T09:32:33+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
-            "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
+            "samplesheet.csv:md5,f0b7e9436c6feb1a31c49c2c8ab761a2"
         ],
-        "timestamp": "2023-08-17T12:19:51+0000"
+        "timestamp": "2023-08-28T09:32:33+0000"
     },
     "software_versions": {
         "content": [
             "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
-        "timestamp": "2023-08-17T12:19:51+0000"
+        "timestamp": "2023-08-28T09:32:33+0000"
     },
     "Parameters: '--nf_core_pipeline rnaseq'": {
         "content": [
@@ -33,7 +33,7 @@
                 
             }
         ],
-        "timestamp": "2023-08-17T12:19:51+0000"
+        "timestamp": "2023-08-28T09:32:33+0000"
     },
     "fastq": {
         "content": [
@@ -83,6 +83,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-08-17T12:19:51+0000"
+        "timestamp": "2023-08-28T09:32:33+0000"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index 301938c4..c2022ce2 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -1,7 +1,8 @@
-nextflow_pipeline {
+nextflow_workflow {
 
-    name "Test workflow: sra.nf"
-    script "main.nf"
+    name "Test workflow: sra/main.nf"
+    script "workflows/sra/main.nf"
+    workflow "SRA"
     tag "workflows"
     tag "workflows_sra"
     tag "sra_nf_core_pipeline_taxprofiler"
@@ -9,6 +10,11 @@ nextflow_pipeline {
     test("Parameters: --nf_core_pipeline taxprofiler") {
 
         when {
+            workflow {
+                """
+                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                """
+            }
             params {
                 outdir = "$outputDir"
                 nf_core_pipeline = "taxprofiler"
@@ -18,7 +24,12 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(process.out).match() }
+//                { assert snapshot(workflow.out).match() }
+                { assert new File("$outputDir/custom").exists() },
+                { assert new File("$outputDir/metadata").exists() },
+                { assert new File("$outputDir/pipeline_info").exists() },
+                { assert new File("$outputDir/samplesheet").exists() },
+                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
index 85f3957b..da686d45 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
@@ -12,20 +12,20 @@
             "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
             "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
         ],
-        "timestamp": "2023-08-17T12:24:34+0000"
+        "timestamp": "2023-08-28T09:27:41+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
-            "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
+            "samplesheet.csv:md5,484efbb550b50f5ac63e4864282edea7"
         ],
-        "timestamp": "2023-08-17T12:24:34+0000"
+        "timestamp": "2023-08-28T09:27:41+0000"
     },
     "software_versions": {
         "content": [
             "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
-        "timestamp": "2023-08-17T12:24:34+0000"
+        "timestamp": "2023-08-28T09:27:41+0000"
     },
     "Parameters: --nf_core_pipeline taxprofiler": {
         "content": [
@@ -33,7 +33,7 @@
                 
             }
         ],
-        "timestamp": "2023-08-17T12:24:34+0000"
+        "timestamp": "2023-08-28T09:27:41+0000"
     },
     "fastq": {
         "content": [
@@ -83,6 +83,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-08-17T12:24:34+0000"
+        "timestamp": "2023-08-28T09:27:41+0000"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index 892a7c3a..e664f0fd 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -1,7 +1,8 @@
-nextflow_pipeline {
+nextflow_workflow {
 
-    name "Test workflow: sra.nf"
-    script "main.nf"
+    name "Test workflow: sra/main.nf"
+    script "workflows/sra/main.nf"
+    workflow "SRA"
     tag "workflows"
     tag "workflows_sra"
     tag "sra_nf_core_pipeline_viralrecon"
@@ -9,6 +10,11 @@ nextflow_pipeline {
     test("Parameters: --nf_core_pipeline viralrecon") {
 
         when {
+            workflow {
+                """
+                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                """
+            }
             params {
                 outdir = "$outputDir"
                 nf_core_pipeline = "viralrecon"
@@ -18,7 +24,12 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(process.out).match() }
+//                { assert snapshot(workflow.out).match() }
+                { assert new File("$outputDir/custom").exists() },
+                { assert new File("$outputDir/metadata").exists() },
+                { assert new File("$outputDir/pipeline_info").exists() },
+                { assert new File("$outputDir/samplesheet").exists() },
+                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
index 13c59b5d..a30d8377 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
@@ -12,14 +12,14 @@
             "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
             "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
         ],
-        "timestamp": "2023-08-17T12:26:57+0000"
+        "timestamp": "2023-08-28T10:03:01+0000"
     },
     "samplesheet": {
         "content": [
             "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
-            "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
+            "samplesheet.csv:md5,3e32e2cfa3c8b23c9cd32d91b885c0de"
         ],
-        "timestamp": "2023-08-17T12:26:57+0000"
+        "timestamp": "2023-08-28T10:03:01+0000"
     },
     "Parameters: --nf_core_pipeline viralrecon": {
         "content": [
@@ -27,13 +27,13 @@
                 
             }
         ],
-        "timestamp": "2023-08-17T12:26:57+0000"
+        "timestamp": "2023-08-28T10:03:01+0000"
     },
     "software_versions": {
         "content": [
             "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
         ],
-        "timestamp": "2023-08-17T12:26:57+0000"
+        "timestamp": "2023-08-28T10:03:01+0000"
     },
     "fastq": {
         "content": [
@@ -83,6 +83,6 @@
                 "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
             ]
         ],
-        "timestamp": "2023-08-17T12:26:57+0000"
+        "timestamp": "2023-08-28T10:03:06+0000"
     }
 }
\ No newline at end of file

From f1c9f4792a212f5d323e4dfd2897ac14ef18da71 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 28 Aug 2023 14:36:24 +0200
Subject: [PATCH 414/852] update snapshot

---
 .../sra_force_sratools_download.nf.test.snap  | 38 +------------------
 1 file changed, 1 insertion(+), 37 deletions(-)

diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
index d5d694da..331943c5 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
@@ -1,40 +1,4 @@
 {
-    "Parameters: '--force_sratools_download'": {
-        "content": [
-            {
-                
-            }
-        ],
-        "timestamp": "2023-08-17T12:15:55+0000"
-    },
-    "metadata": {
-        "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
-            "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
-            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
-            "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
-            "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
-            "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
-            "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
-            "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54",
-            "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
-            "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
-        ],
-        "timestamp": "2023-08-17T12:15:55+0000"
-    },
-    "samplesheet": {
-        "content": [
-            "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
-            "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
-        ],
-        "timestamp": "2023-08-17T12:15:55+0000"
-    },
-    "software_versions": {
-        "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
-        ],
-        "timestamp": "2023-08-17T12:15:55+0000"
-    },
     "fastq": {
         "content": [
             "DRX024467_DRR026872.fastq.gz:md5,bd3f113c3b06cf4499fa0e00c634ec85",
@@ -62,6 +26,6 @@
             "SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7",
             "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af"
         ],
-        "timestamp": "2023-08-17T12:15:55+0000"
+        "timestamp": "2023-08-28T12:35:42+0000"
     }
 }
\ No newline at end of file

From eedee488a9dfaaa1fe43dd60f8647f2152c239ae Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 28 Aug 2023 14:48:35 +0200
Subject: [PATCH 415/852] update test

---
 .../sra/tests/sra_skip_fastq_download.nf.test   | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index 7d218cf7..7180fd6d 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -1,7 +1,8 @@
-nextflow_pipeline {
+nextflow_workflow {
 
-    name "Test workflow: sra.nf"
-    script "main.nf"
+    name "Test workflow: sra/main.nf"
+    script "workflows/sra/main.nf"
+    workflow "SRA"
     tag "workflows"
     tag "workflows_sra"
     tag "sra_skip_fastq_download"
@@ -9,6 +10,11 @@ nextflow_pipeline {
     test("Parameters: --skip_fastq_download") {
 
         when {
+            workflow {
+                """
+                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                """
+            }
             params {
                 outdir = "$outputDir"
                 skip_fastq_download = true
@@ -18,7 +24,10 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(process.out).match() }
+//                { assert snapshot(workflow.out).match() }
+                { assert new File("$outputDir/metadata").exists() },
+                { assert new File("$outputDir/pipeline_info").exists() },
+                { assert new File("$outputDir/samplesheet").exists() }
             )
         }
     }

From db29566dfc71ff5b24d390bb54dfc1fbdce65baf Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 28 Aug 2023 14:51:45 +0200
Subject: [PATCH 416/852] need to update snapshot

---
 .../sra_skip_fastq_download.nf.test.snap      | 46 -------------------
 1 file changed, 46 deletions(-)
 delete mode 100644 workflows/sra/tests/sra_skip_fastq_download.nf.test.snap

diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
deleted file mode 100644
index d004d5d2..00000000
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
+++ /dev/null
@@ -1,46 +0,0 @@
-{
-    "Parameters: '--skip_fastq_download'": {
-        "content": [
-            {
-                
-            }
-        ],
-        "timestamp": "2023-08-17T12:25:19+0000"
-    },
-    "metadata": {
-        "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
-            "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
-            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
-            "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
-            "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
-            "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
-            "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
-            "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54",
-            "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
-            "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
-        ],
-        "timestamp": "2023-08-17T12:25:19+0000"
-    },
-    "samplesheet": {
-        "content": [
-            "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
-            "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
-        ],
-        "timestamp": "2023-08-17T12:25:19+0000"
-    },
-    "software_versions": {
-        "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
-        ],
-        "timestamp": "2023-08-17T12:25:19+0000"
-    },
-    "Parameters: --skip_fastq_download": {
-        "content": [
-            {
-                
-            }
-        ],
-        "timestamp": "2023-08-17T12:25:19+0000"
-    }
-}
\ No newline at end of file

From 57d7ba319a639bc33756df1ff2e8c229cf5b819a Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 28 Aug 2023 15:37:19 +0200
Subject: [PATCH 417/852] add nextflow.log to test output when failures

---
 .github/workflows/ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2a30309b..d652f33e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -81,6 +81,7 @@ jobs:
         run: |
           sudo apt install bat > /dev/null
           batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
 
       - name: Publish Test Report
         uses: mikepenz/action-junit-report@v3

From 57bf16705bf23fe2c7695774e2376f2c709a4d35 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 28 Aug 2023 15:43:35 +0200
Subject: [PATCH 418/852] add nextflow.log to test output when failures

---
 .github/workflows/ci.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d652f33e..aa4b4cf9 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -80,7 +80,6 @@ jobs:
         if: failure()
         run: |
           sudo apt install bat > /dev/null
-          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml
           batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
 
       - name: Publish Test Report

From 43223db40d2c1e26d14763bcd60ce5509adea749 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 11 Sep 2023 15:49:53 +0200
Subject: [PATCH 419/852] test rc

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index aa4b4cf9..5c5df959 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -16,7 +16,7 @@ on:
 
 env:
   NXF_ANSI_LOG: false
-  NFTEST_VER: "0.7.3"
+  NFTEST_VER: "0.8.0-rc1"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"

From b40fe58f06b8f4909754eedddd5864bc614822b7 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 11 Sep 2023 15:50:42 +0200
Subject: [PATCH 420/852] re-able autoSort

---
 nf-test.config | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/nf-test.config b/nf-test.config
index 217a5138..0799cb40 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -13,7 +13,4 @@ config {
 
     // run all test with the defined docker profile from the main nextflow.config
     profile ""
-
-    // Disable autosort Channels
-    autoSort false
 }

From d9168a159281225cbb01336c355b0ede6a752486 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 11 Sep 2023 15:51:21 +0200
Subject: [PATCH 421/852] add .nf-test.log to gitignore

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 935326a7..b1b5890a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,3 +8,4 @@ testing*
 *.pyc
 .nf-test/
 nf-test
+.nf-test.log

From 359462f90f28ea91885685774c9c9d3d0d2870f6 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 11 Sep 2023 16:49:57 +0200
Subject: [PATCH 422/852] simplify tests

---
 workflows/sra/tests/main.nf.test                           | 7 +------
 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test | 7 +------
 workflows/sra/tests/sra_force_sratools_download.nf.test    | 7 +------
 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test   | 7 +------
 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test    | 7 +------
 .../sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test     | 7 +------
 .../sra/tests/sra_nf_core_pipeline_viralrecon.nf.test      | 7 +------
 workflows/sra/tests/sra_skip_fastq_download.nf.test        | 5 +----
 8 files changed, 8 insertions(+), 46 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 2a1e82a1..2652eb80 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -23,12 +23,7 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-//                { assert snapshot(workflow.out).match() }
-                { assert new File("$outputDir/custom").exists() },
-                { assert new File("$outputDir/metadata").exists() },
-                { assert new File("$outputDir/pipeline_info").exists() },
-                { assert new File("$outputDir/samplesheet").exists() },
-                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }
+                { assert snapshot(workflow.out).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index f1f55f02..4dc9ba8b 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -26,12 +26,7 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-//                { assert snapshot(workflow.out).match() }
-                { assert new File("$outputDir/custom").exists() },
-                { assert new File("$outputDir/metadata").exists() },
-                { assert new File("$outputDir/pipeline_info").exists() },
-                { assert new File("$outputDir/samplesheet").exists() },
-                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }
+                { assert snapshot(workflow.out).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index 051e4aa5..2b1b5953 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -24,12 +24,7 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-//                { assert snapshot(workflow.out).match() }
-                { assert new File("$outputDir/custom").exists() },
-                { assert new File("$outputDir/metadata").exists() },
-                { assert new File("$outputDir/pipeline_info").exists() },
-                { assert new File("$outputDir/samplesheet").exists() },
-                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }
+                { assert snapshot(workflow.out).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index 6925b971..3d946fea 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -24,12 +24,7 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-//                { assert snapshot(workflow.out).match() }
-                { assert new File("$outputDir/custom").exists() },
-                { assert new File("$outputDir/metadata").exists() },
-                { assert new File("$outputDir/pipeline_info").exists() },
-                { assert new File("$outputDir/samplesheet").exists() },
-                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }
+                { assert snapshot(workflow.out).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index a84b7c41..f51aa4ca 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -24,12 +24,7 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-//                { assert snapshot(workflow.out).match() }
-                { assert new File("$outputDir/custom").exists() },
-                { assert new File("$outputDir/metadata").exists() },
-                { assert new File("$outputDir/pipeline_info").exists() },
-                { assert new File("$outputDir/samplesheet").exists() },
-                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }
+                { assert snapshot(workflow.out).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index c2022ce2..97cd4a44 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -24,12 +24,7 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-//                { assert snapshot(workflow.out).match() }
-                { assert new File("$outputDir/custom").exists() },
-                { assert new File("$outputDir/metadata").exists() },
-                { assert new File("$outputDir/pipeline_info").exists() },
-                { assert new File("$outputDir/samplesheet").exists() },
-                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }
+                { assert snapshot(workflow.out).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index e664f0fd..434fac63 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -24,12 +24,7 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-//                { assert snapshot(workflow.out).match() }
-                { assert new File("$outputDir/custom").exists() },
-                { assert new File("$outputDir/metadata").exists() },
-                { assert new File("$outputDir/pipeline_info").exists() },
-                { assert new File("$outputDir/samplesheet").exists() },
-                { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }
+                { assert snapshot(workflow.out).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index 7180fd6d..dbe40144 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -24,10 +24,7 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-//                { assert snapshot(workflow.out).match() }
-                { assert new File("$outputDir/metadata").exists() },
-                { assert new File("$outputDir/pipeline_info").exists() },
-                { assert new File("$outputDir/samplesheet").exists() }
+                { assert snapshot(workflow.out).match() }
             )
         }
     }

From b180a636ff039c69cf3bd79060ba8a5a98692fad Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 11 Sep 2023 17:30:07 +0200
Subject: [PATCH 423/852] update snapshot

---
 workflows/sra/tests/main.nf.test.snap         | 1707 ++++++++---------
 ...ra_custom_ena_metadata_fields.nf.test.snap |  647 ++++++-
 .../sra_force_sratools_download.nf.test.snap  | 1372 ++++++++++++-
 .../sra_nf_core_pipeline_atacseq.nf.test.snap | 1427 +++++++++++++-
 .../sra_nf_core_pipeline_rnaseq.nf.test.snap  | 1427 +++++++++++++-
 ..._nf_core_pipeline_taxprofiler.nf.test.snap | 1425 +++++++++++++-
 ...a_nf_core_pipeline_viralrecon.nf.test.snap | 1425 +++++++++++++-
 .../sra_skip_fastq_download.nf.test.snap      |   37 +
 8 files changed, 8141 insertions(+), 1326 deletions(-)
 create mode 100644 workflows/sra/tests/sra_skip_fastq_download.nf.test.snap

diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
index 62d0d976..1c969bc2 100644
--- a/workflows/sra/tests/main.nf.test.snap
+++ b/workflows/sra/tests/main.nf.test.snap
@@ -47,131 +47,47 @@
                     ],
                     [
                         {
-                            "id": "SRX6725035_SRR9984183",
-                            "run_accession": "SRR9984183",
-                            "experiment_accession": "SRX6725035",
-                            "sample_accession": "SAMN12581720",
-                            "secondary_sample_accession": "SRS5277011",
-                            "study_accession": "PRJNA560329",
-                            "secondary_study_accession": "SRP218535",
-                            "submission_accession": "SRA942061",
-                            "run_alias": "Emb289P1_bin131.fastq",
-                            "experiment_alias": "Emb289P1_bin131",
-                            "sample_alias": "Emb289P1_bin131",
-                            "study_alias": "PRJNA560329",
-                            "library_layout": "SINGLE",
-                            "library_selection": "RANDOM",
-                            "library_source": "METAGENOMIC",
-                            "library_strategy": "WGS",
-                            "library_name": "Emb289P1_bin131",
-                            "instrument_model": "Illumina HiSeq 2500",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "1996273",
-                            "read_count": "58",
-                            "tax_id": "2660712",
-                            "scientific_name": "Defluviitaleaceae bacterium",
-                            "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
-                            "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
-                            "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
-                            "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
-                            "fastq_md5": "0b512d2dc31685983456bd56fd836544",
-                            "fastq_bytes": "605358",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                            "fastq_2": "",
-                            "md5_1": "0b512d2dc31685983456bd56fd836544",
-                            "md5_2": "",
-                            "single_end": true
-                        },
-                        "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544"
-                    ],
-                    [
-                        {
-                            "id": "ERX1234253_ERR1160846",
-                            "run_accession": "ERR1160846",
-                            "experiment_accession": "ERX1234253",
-                            "sample_accession": "SAMEA3687214",
-                            "secondary_sample_accession": "ERS994363",
-                            "study_accession": "PRJEB11419",
-                            "secondary_study_accession": "ERP012803",
-                            "submission_accession": "ERA541392",
-                            "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
-                            "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                            "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
-                            "study_alias": "qiita_sid_10317",
-                            "library_layout": "SINGLE",
-                            "library_selection": "PCR",
-                            "library_source": "METAGENOMIC",
-                            "library_strategy": "AMPLICON",
-                            "library_name": "10317.BLANK.93.3E.r22",
-                            "instrument_model": "Illumina HiSeq 2500",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "35658",
-                            "read_count": "283",
-                            "tax_id": "256318",
-                            "scientific_name": "metagenome",
-                            "sample_title": "10317.BLANK.93.3E.r22",
-                            "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                            "study_title": "American Gut Project",
-                            "sample_description": "American Gut control",
-                            "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                            "fastq_bytes": "18077",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                            "fastq_2": "",
-                            "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                            "md5_2": "",
-                            "single_end": true
-                        },
-                        "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6"
-                    ],
-                    [
-                        {
-                            "id": "SRX9626017_SRR13191702",
-                            "run_accession": "SRR13191702",
-                            "experiment_accession": "SRX9626017",
-                            "sample_accession": "SAMN16980141",
-                            "secondary_sample_accession": "SRS7827211",
-                            "study_accession": "PRJNA682076",
-                            "secondary_study_accession": "SRP295653",
-                            "submission_accession": "SRA1166126",
-                            "run_alias": "S.170804.00784_662_L001_R1_001.fastq.gz",
-                            "experiment_alias": "S.170804.00784",
-                            "sample_alias": "S.170804.00784_662",
-                            "study_alias": "PRJNA682076",
+                            "id": "DRX026011_DRR028935",
+                            "run_accession": "DRR028935",
+                            "experiment_accession": "DRX026011",
+                            "sample_accession": "SAMD00024405",
+                            "secondary_sample_accession": "DRS019431",
+                            "study_accession": "PRJDB3420",
+                            "secondary_study_accession": "DRP002616",
+                            "submission_accession": "DRA002949",
+                            "run_alias": "DRR028935",
+                            "experiment_alias": "DRX026011",
+                            "sample_alias": "SAMD00024405",
+                            "study_alias": "DRP002616",
                             "library_layout": "PAIRED",
-                            "library_selection": "PCR",
-                            "library_source": "METAGENOMIC",
-                            "library_strategy": "AMPLICON",
-                            "library_name": "S.170804.00784",
+                            "library_selection": "cDNA",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "RNA-Seq",
+                            "library_name": "day0_BbSQE-I",
                             "instrument_model": "Illumina HiSeq 2500",
                             "instrument_platform": "ILLUMINA",
-                            "base_count": "45682",
-                            "read_count": "91",
-                            "tax_id": "408170",
-                            "scientific_name": "human gut metagenome",
-                            "sample_title": "Metagenome or environmental sample from human gut metagenome",
-                            "experiment_title": "Illumina HiSeq 2500 sequencing: Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
-                            "study_title": "Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
-                            "sample_description": "Metagenome or environmental sample from human gut metagenome",
-                            "fastq_md5": "89c5be920021a035084d8aeb74f32df7;56271be38a80db78ef3bdfc5d9909b98",
-                            "fastq_bytes": "15420;16324",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
-                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
-                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98",
+                            "base_count": "194930",
+                            "read_count": "965",
+                            "tax_id": "1202541",
+                            "scientific_name": "Botryococcus braunii Showa",
+                            "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
+                            "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
+                            "sample_description": "Liquid culture",
+                            "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
+                            "fastq_bytes": "60275;61610",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
+                            "md5_2": "941c9998d746416dad53c94c480ddf30",
                             "single_end": false
                         },
                         [
-                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
+                            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
+                            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
                         ]
                     ],
                     [
@@ -221,137 +137,89 @@
                     ],
                     [
                         {
-                            "id": "DRX026011_DRR028935",
-                            "run_accession": "DRR028935",
-                            "experiment_accession": "DRX026011",
-                            "sample_accession": "SAMD00024405",
-                            "secondary_sample_accession": "DRS019431",
-                            "study_accession": "PRJDB3420",
-                            "secondary_study_accession": "DRP002616",
-                            "submission_accession": "DRA002949",
-                            "run_alias": "DRR028935",
-                            "experiment_alias": "DRX026011",
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-                "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8",
-                "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f",
-                "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3",
-                "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8",
-                "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882",
-                "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
-                "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
-            ]
-        ],
-        "timestamp": "2023-08-28T08:57:15+0000"
-    },
-    "pipeline_info": {
-        "content": [
-            "execution_report_2023-08-28_10-54-32.html:md5,710a38308b41b4bd86b6d2d8fd4a72b7",
-            "execution_timeline_2023-08-28_10-54-32.html:md5,1583b3c97bc7c97a8550c3d0ce6302c8",
-            "pipeline_dag_2023-08-28_10-54-32.html:md5,63f58c7a48a1b71d3ee7809cb6a92740"
-        ],
-        "timestamp": "2023-08-28T08:57:15+0000"
+        "timestamp": "2023-09-11T16:58:15.05829"
     }
-}
+}
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
index ddd8e845..c2782552 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
@@ -1,88 +1,573 @@
 {
-    "metadata": {
-        "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,74a5f7058f27a565ce59db481355ca54",
-            "DRR028935.runinfo_ftp.tsv:md5,07a98fdcec207686a4ea2c9a3997edf3",
-            "ERR1109373.runinfo_ftp.tsv:md5,868897310855c50b1d5fc77d1195a1f9",
-            "ERR1160846.runinfo_ftp.tsv:md5,146d7f2ec778b32b7da7ad040e554114",
-            "GSE214215.runinfo_ftp.tsv:md5,adf62affe371dc9bad8e271450bdc2fe",
-            "SRR12848126.runinfo_ftp.tsv:md5,cf8827612a76645824e83418d7d76cbf",
-            "SRR13191702.runinfo_ftp.tsv:md5,2031ca9b7ab736dbde37d05b10cdb0ad",
-            "SRR14593545.runinfo_ftp.tsv:md5,3a1ac14d71744224a61ab542f869e180",
-            "SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1",
-            "SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236"
-        ],
-        "timestamp": "2023-08-28T09:29:59+0000"
-    },
-    "samplesheet": {
-        "content": [
-            "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f",
-            "samplesheet.csv:md5,7bca96e409bd9eb6790e0d6737af686c"
-        ],
-        "timestamp": "2023-08-28T09:29:59+0000"
-    },
-    "software_versions": {
-        "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
-        ],
-        "timestamp": "2023-08-28T09:29:59+0000"
-    },
-    "Parameters: '--nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...'": {
+    "Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...": {
         "content": [
             {
-                
+                "0": [
+                    [
+                        {
+                            "id": "DRX024467_DRR026872",
+                            "run_accession": "DRR026872",
+                            "experiment_accession": "DRX024467",
+                            "library_layout": "SINGLE",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_md5": "515e5448c55e054113c4a22df5f62791",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "515e5448c55e054113c4a22df5f62791",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791"
+                    ],
+                    [
+                        {
+                            "id": "DRX026011_DRR028935",
+                            "run_accession": "DRR028935",
+                            "experiment_accession": "DRX026011",
+                            "library_layout": "PAIRED",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
+                            "md5_2": "941c9998d746416dad53c94c480ddf30",
+                            "single_end": false
+                        },
+                        [
+                            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
+                            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "ERX1188904_ERR1109373",
+                            "run_accession": "ERR1109373",
+                            "experiment_accession": "ERX1188904",
+                            "library_layout": "PAIRED",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
+                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
+                            "single_end": false
+                        },
+                        [
+                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
+                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "ERX1234253_ERR1160846",
+                            "run_accession": "ERR1160846",
+                            "experiment_accession": "ERX1234253",
+                            "library_layout": "SINGLE",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6"
+                    ],
+                    [
+                        {
+                            "id": "SRX10940790_SRR14593545",
+                            "run_accession": "SRR14593545",
+                            "experiment_accession": "SRX10940790",
+                            "library_layout": "PAIRED",
+                            "fastq_ftp": "",
+                            "fastq_md5": "",
+                            "fastq_1": "",
+                            "fastq_2": "",
+                            "md5_1": "",
+                            "md5_2": "",
+                            "single_end": false
+                        },
+                        [
+                            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
+                            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX11047067_SRR14709033",
+                            "run_accession": "SRR14709033",
+                            "experiment_accession": "SRX11047067",
+                            "library_layout": "SINGLE",
+                            "fastq_ftp": "",
+                            "fastq_md5": "",
+                            "fastq_1": "",
+                            "fastq_2": "",
+                            "md5_1": "",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda"
+                    ],
+                    [
+                        {
+                            "id": "SRX17709227_SRR21711856",
+                            "run_accession": "SRR21711856",
+                            "experiment_accession": "SRX17709227",
+                            "library_layout": "SINGLE",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                            "fastq_md5": "7cd1402155befc87be338132d1f31f64",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "7cd1402155befc87be338132d1f31f64",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64"
+                    ],
+                    [
+                        {
+                            "id": "SRX17709228_SRR21711855",
+                            "run_accession": "SRR21711855",
+                            "experiment_accession": "SRX17709228",
+                            "library_layout": "SINGLE",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                            "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83"
+                    ],
+                    [
+                        {
+                            "id": "SRX6725035_SRR9984183",
+                            "run_accession": "SRR9984183",
+                            "experiment_accession": "SRX6725035",
+                            "library_layout": "SINGLE",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                            "fastq_md5": "0b512d2dc31685983456bd56fd836544",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "0b512d2dc31685983456bd56fd836544",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544"
+                    ],
+                    [
+                        {
+                            "id": "SRX9315476_SRR12848126",
+                            "run_accession": "SRR12848126",
+                            "experiment_accession": "SRX9315476",
+                            "library_layout": "PAIRED",
+                            "fastq_ftp": "",
+                            "fastq_md5": "",
+                            "fastq_1": "",
+                            "fastq_2": "",
+                            "md5_1": "",
+                            "md5_2": "",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
+                            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX9504942_SRR13055517",
+                            "run_accession": "SRR13055517",
+                            "experiment_accession": "SRX9504942",
+                            "library_layout": "PAIRED",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_2.fastq.gz",
+                            "fastq_md5": "dcf4438c0b682242ee90c5f3a803fb40;18dbe96e7f58b63406d9058938df1962",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_2.fastq.gz",
+                            "md5_1": "dcf4438c0b682242ee90c5f3a803fb40",
+                            "md5_2": "18dbe96e7f58b63406d9058938df1962",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
+                            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX9504942_SRR13055518",
+                            "run_accession": "SRR13055518",
+                            "experiment_accession": "SRX9504942",
+                            "library_layout": "PAIRED",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_2.fastq.gz",
+                            "fastq_md5": "5ec894d863fcefe394470a0925aefde4;aead170df9851773d5202b5760c76d76",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_2.fastq.gz",
+                            "md5_1": "5ec894d863fcefe394470a0925aefde4",
+                            "md5_2": "aead170df9851773d5202b5760c76d76",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
+                            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX9504942_SRR13055519",
+                            "run_accession": "SRR13055519",
+                            "experiment_accession": "SRX9504942",
+                            "library_layout": "PAIRED",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_2.fastq.gz",
+                            "fastq_md5": "5ad51460c6c4a850dd37a206e2c441c1;a977367bf41dacf4c21bc0c8201b8b88",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_2.fastq.gz",
+                            "md5_1": "5ad51460c6c4a850dd37a206e2c441c1",
+                            "md5_2": "a977367bf41dacf4c21bc0c8201b8b88",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
+                            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX9504942_SRR13055520",
+                            "run_accession": "SRR13055520",
+                            "experiment_accession": "SRX9504942",
+                            "library_layout": "PAIRED",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "fastq_md5": "795d460abff6009c7f5ff7c14b773fbe;c3f34379356b28d6dac7212abc1a0a04",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "md5_1": "795d460abff6009c7f5ff7c14b773fbe",
+                            "md5_2": "c3f34379356b28d6dac7212abc1a0a04",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
+                            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "run_accession": "SRR13191702",
+                            "experiment_accession": "SRX9626017",
+                            "library_layout": "PAIRED",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_md5": "89c5be920021a035084d8aeb74f32df7;56271be38a80db78ef3bdfc5d9909b98",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "samplesheet.csv:md5,7bca96e409bd9eb6790e0d6737af686c"
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-                "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86",
-                "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499",
-                "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff",
-                "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75",
-                "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85",
-                "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4",
-                "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc",
-                "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0",
-                "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368",
-                "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8",
-                "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f",
-                "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3",
-                "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8",
-                "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882",
-                "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
-                "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
-            ]
-        ],
-        "timestamp": "2023-08-28T09:29:59+0000"
+        "timestamp": "2023-09-11T16:47:26.813819"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
index 331943c5..2c779c84 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
@@ -1,31 +1,1351 @@
 {
-    "fastq": {
+    "Parameters: --force_sratools_download": {
         "content": [
-            "DRX024467_DRR026872.fastq.gz:md5,bd3f113c3b06cf4499fa0e00c634ec85",
-            "DRX026011_DRR028935_1.fastq.gz:md5,0f96fb60e903c8cbd55a6977e66f7c93",
-            "DRX026011_DRR028935_2.fastq.gz:md5,b97b1e0e806bcae10a7443e2f22d6ca2",
-            "ERX1188904_ERR1109373_1.fastq.gz:md5,e7edae2715dfaf4c318d37959fd9ae22",
-            "ERX1188904_ERR1109373_2.fastq.gz:md5,34ab048c92201a5ec4ab36d8dc1c5732",
-            "ERX1234253_ERR1160846.fastq.gz:md5,22683b24b2467494e430643423f1e275",
-            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
-            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
-            "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
-            "SRX17709227_SRR21711856.fastq.gz:md5,eae43f1368d4568f415581394dc9726e",
-            "SRX17709228_SRR21711855.fastq.gz:md5,5194f8009b74552595c4ec5b7605d231",
-            "SRX6725035_SRR9984183.fastq.gz:md5,7a70e678c400366869601c8be41fe74b",
-            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
-            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
-            "SRX9504942_SRR13055517_1.fastq.gz:md5,b6d912a73466c8f27b1d8021f80ec2bb",
-            "SRX9504942_SRR13055517_2.fastq.gz:md5,7c6e220694fa5d6d9124c739aa70ea92",
-            "SRX9504942_SRR13055518_1.fastq.gz:md5,ed29278c21a1bb2d8907a74be0dd4bc4",
-            "SRX9504942_SRR13055518_2.fastq.gz:md5,83785b728312deb81483fc1fd5b14264",
-            "SRX9504942_SRR13055519_1.fastq.gz:md5,28babc59a625b5161d97392efd4d0018",
-            "SRX9504942_SRR13055519_2.fastq.gz:md5,cf1eb4c61ab3522f4d473c86b2f696e1",
-            "SRX9504942_SRR13055520_1.fastq.gz:md5,cc75af896ec8a7cececb37851b0c6fcd",
-            "SRX9504942_SRR13055520_2.fastq.gz:md5,fe3e2bf9f738e4959243fad59e879eae",
-            "SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7",
-            "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af"
+            {
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+                        {
+                            "id": "DRX024467_DRR026872",
+                            "run_accession": "DRR026872",
+                            "experiment_accession": "DRX024467",
+                            "sample_accession": "SAMD00023098",
+                            "secondary_sample_accession": "DRS033740",
+                            "study_accession": "PRJDB4356",
+                            "secondary_study_accession": "DRP003256",
+                            "submission_accession": "DRA002758",
+                            "run_alias": "DRR026872",
+                            "experiment_alias": "DRX024467",
+                            "sample_alias": "SAMD00023098",
+                            "study_alias": "DRP003256",
+                            "library_layout": "SINGLE",
+                            "library_selection": "Restriction Digest",
+                            "library_source": "GENOMIC",
+                            "library_strategy": "OTHER",
+                            "library_name": "IpeRAD1_3",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "62550",
+                            "read_count": "417",
+                            "tax_id": "35883",
+                            "scientific_name": "Ipomoea nil",
+                            "sample_title": "F2 plant dreived from a cross between Tokyo Kokei-standard and Africa #21",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Illumina HiSeq 2500 sequencing of SAMD00023098",
+                            "study_title": "The Japanese morning glory genome sequence",
+                            "sample_description": "Keywords: GSC:MIxS MIGS:6.0",
+                            "fastq_md5": "515e5448c55e054113c4a22df5f62791",
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+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
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+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
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+                            "fastq_2": "",
+                            "md5_1": "515e5448c55e054113c4a22df5f62791",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "DRX024467_DRR026872.fastq.gz:md5,bd3f113c3b06cf4499fa0e00c634ec85"
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+                    [
+                        {
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+                            "run_accession": "DRR028935",
+                            "experiment_accession": "DRX026011",
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+                            "read_count": "965",
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+                            "single_end": false
+                        },
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+                        ]
+                    ],
+                    [
+                        {
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+                            "sample_alias": "sample_56",
+                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
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+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "29700",
+                            "read_count": "169",
+                            "tax_id": "63433",
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+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
+                            "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
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+                    [
+                        {
+                            "id": "SRX10940790_SRR14593545",
+                            "run_accession": "SRR14593545",
+                            "experiment_accession": "SRX10940790",
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+                            "study_accession": "PRJNA728650",
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+                            "library_layout": "PAIRED",
+                            "library_selection": "PCR",
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+                            "library_strategy": "AMPLICON",
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+                            "instrument_model": "AB 3500xL Genetic Analyzer",
+                            "instrument_platform": "CAPILLARY",
+                            "base_count": "828",
+                            "read_count": "1",
+                            "tax_id": "9925",
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+                            "sample_title": "MIGS Eukaryotic sample from Capra hircus",
+                            "experiment_title": "AB 3500xL Genetic Analyzer sequencing: prp_2765",
+                            "study_title": "Capra hircus Raw sequence reads",
+                            "sample_description": "Keywords: GSC:MIxS MIGS:5.0",
+                            "fastq_md5": "",
+                            "fastq_bytes": "",
+                            "fastq_ftp": "",
+                            "fastq_galaxy": "",
+                            "fastq_aspera": "",
+                            "fastq_1": "",
+                            "fastq_2": "",
+                            "md5_1": "",
+                            "md5_2": "",
+                            "single_end": false
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+                            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2"
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+                    [
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+                            "run_accession": "SRR14709033",
+                            "experiment_accession": "SRX11047067",
+                            "sample_accession": "SAMN19373034",
+                            "secondary_sample_accession": "SRS9115923",
+                            "study_accession": "PRJNA733285",
+                            "secondary_study_accession": "SRP322267",
+                            "submission_accession": "SRA1239521",
+                            "run_alias": "Sebastes_levis-2.fastq",
+                            "experiment_alias": "Sebastes_macdonaldi-1",
+                            "sample_alias": "S._macdonaldi-1",
+                            "study_alias": "PRJNA733285",
+                            "library_layout": "SINGLE",
+                            "library_selection": "PCR",
+                            "library_source": "GENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "Sebastes_macdonaldi-1",
+                            "instrument_model": "AB 5500 Genetic Analyzer",
+                            "instrument_platform": "ABI_SOLID",
+                            "base_count": "153",
+                            "read_count": "1",
+                            "tax_id": "394693",
+                            "scientific_name": "Sebastes macdonaldi",
+                            "sample_title": "Sebastes_macdonaldi-1",
+                            "experiment_title": "AB 5500 Genetic Analyzer sequencing: Sebastes macdonaldi",
+                            "study_title": "MiSebastes: An eDNA metabarcoding primer set for rockfishes (genus Sebastes)",
+                            "sample_description": "Sebastes_macdonaldi-1",
+                            "fastq_md5": "",
+                            "fastq_bytes": "",
+                            "fastq_ftp": "",
+                            "fastq_galaxy": "",
+                            "fastq_aspera": "",
+                            "fastq_1": "",
+                            "fastq_2": "",
+                            "md5_1": "",
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+                            "run_accession": "SRR13191702",
+                            "experiment_accession": "SRX9626017",
+                            "sample_accession": "SAMN16980141",
+                            "secondary_sample_accession": "SRS7827211",
+                            "study_accession": "PRJNA682076",
+                            "secondary_study_accession": "SRP295653",
+                            "submission_accession": "SRA1166126",
+                            "run_alias": "S.170804.00784_662_L001_R1_001.fastq.gz",
+                            "experiment_alias": "S.170804.00784",
+                            "sample_alias": "S.170804.00784_662",
+                            "study_alias": "PRJNA682076",
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+                            "library_selection": "PCR",
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+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "45682",
+                            "read_count": "91",
+                            "tax_id": "408170",
+                            "scientific_name": "human gut metagenome",
+                            "sample_title": "Metagenome or environmental sample from human gut metagenome",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
+                            "study_title": "Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
+                            "sample_description": "Metagenome or environmental sample from human gut metagenome",
+                            "fastq_md5": "89c5be920021a035084d8aeb74f32df7;56271be38a80db78ef3bdfc5d9909b98",
+                            "fastq_bytes": "15420;16324",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
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+                        },
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+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af"
+                        ]
+                    ]
+                ],
+                "mappings": [
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+                ],
+                "samplesheet": [
+                    "samplesheet.csv:md5,9d4b95a31702af34a6f57d963137340d"
+                ],
+                "versions": [
+                    "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                ]
+            }
         ],
-        "timestamp": "2023-08-28T12:35:42+0000"
+        "timestamp": "2023-09-11T17:03:59.154427"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
index 0ccec99b..069e3390 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
@@ -1,88 +1,1353 @@
 {
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-            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
-            "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
-            "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
-            "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
-            "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
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-            "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
-            "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
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-            "samplesheet.csv:md5,252449b9f66687af076bb5a9dfea4551"
-        ],
-        "timestamp": "2023-08-28T10:05:53+0000"
-    },
-    "software_versions": {
-        "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
-        ],
-        "timestamp": "2023-08-28T10:05:53+0000"
-    },
-    "Parameters: '--nf_core_pipeline atacseq'": {
+    "Parameters: --nf_core_pipeline atacseq": {
         "content": [
             {
-                
+                "0": [
+                    [
+                        {
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+                            "run_accession": "DRR026872",
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+                            "scientific_name": "Ipomoea nil",
+                            "sample_title": "F2 plant dreived from a cross between Tokyo Kokei-standard and Africa #21",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Illumina HiSeq 2500 sequencing of SAMD00023098",
+                            "study_title": "The Japanese morning glory genome sequence",
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+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
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+                            "tax_id": "9925",
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+                            "study_accession": "PRJNA733285",
+                            "secondary_study_accession": "SRP322267",
+                            "submission_accession": "SRA1239521",
+                            "run_alias": "Sebastes_levis-2.fastq",
+                            "experiment_alias": "Sebastes_macdonaldi-1",
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+                            "study_alias": "PRJNA733285",
+                            "library_layout": "SINGLE",
+                            "library_selection": "PCR",
+                            "library_source": "GENOMIC",
+                            "library_strategy": "AMPLICON",
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+                            "instrument_model": "AB 5500 Genetic Analyzer",
+                            "instrument_platform": "ABI_SOLID",
+                            "base_count": "153",
+                            "read_count": "1",
+                            "tax_id": "394693",
+                            "scientific_name": "Sebastes macdonaldi",
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+                            "md5_1": "795d460abff6009c7f5ff7c14b773fbe",
+                            "md5_2": "c3f34379356b28d6dac7212abc1a0a04",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
+                            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "run_accession": "SRR13191702",
+                            "experiment_accession": "SRX9626017",
+                            "sample_accession": "SAMN16980141",
+                            "secondary_sample_accession": "SRS7827211",
+                            "study_accession": "PRJNA682076",
+                            "secondary_study_accession": "SRP295653",
+                            "submission_accession": "SRA1166126",
+                            "run_alias": "S.170804.00784_662_L001_R1_001.fastq.gz",
+                            "experiment_alias": "S.170804.00784",
+                            "sample_alias": "S.170804.00784_662",
+                            "study_alias": "PRJNA682076",
+                            "library_layout": "PAIRED",
+                            "library_selection": "PCR",
+                            "library_source": "METAGENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "S.170804.00784",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "45682",
+                            "read_count": "91",
+                            "tax_id": "408170",
+                            "scientific_name": "human gut metagenome",
+                            "sample_title": "Metagenome or environmental sample from human gut metagenome",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
+                            "study_title": "Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
+                            "sample_description": "Metagenome or environmental sample from human gut metagenome",
+                            "fastq_md5": "89c5be920021a035084d8aeb74f32df7;56271be38a80db78ef3bdfc5d9909b98",
+                            "fastq_bytes": "15420;16324",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
+                        ]
+                    ]
+                ],
+                "mappings": [
+                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                ],
+                "samplesheet": [
+                    "samplesheet.csv:md5,252449b9f66687af076bb5a9dfea4551"
+                ],
+                "versions": [
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                ]
             }
         ],
-        "timestamp": "2023-08-28T10:05:53+0000"
-    },
-    "fastq": {
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-            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
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-            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
-            "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6",
-            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
-            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
-            "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
-            "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64",
-            "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83",
-            "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544",
-            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
-            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
-            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
-            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962",
-            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
-            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76",
-            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
-            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88",
-            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
-            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04",
-            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98",
-            [
-                "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d",
-                "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9",
-                "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f",
-                "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86",
-                "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499",
-                "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff",
-                "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75",
-                "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85",
-                "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4",
-                "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc",
-                "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0",
-                "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368",
-                "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8",
-                "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f",
-                "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3",
-                "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8",
-                "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882",
-                "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
-                "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
-            ]
-        ],
-        "timestamp": "2023-08-28T10:05:57+0000"
+        "timestamp": "2023-09-11T16:36:17.537997"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
index af68569e..4c2abc45 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
@@ -1,88 +1,1353 @@
 {
-    "metadata": {
-        "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
-            "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
-            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
-            "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
-            "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
-            "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
-            "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
-            "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54",
-            "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
-            "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
-        ],
-        "timestamp": "2023-08-28T09:32:33+0000"
-    },
-    "samplesheet": {
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-            "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
-            "samplesheet.csv:md5,f0b7e9436c6feb1a31c49c2c8ab761a2"
-        ],
-        "timestamp": "2023-08-28T09:32:33+0000"
-    },
-    "software_versions": {
-        "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
-        ],
-        "timestamp": "2023-08-28T09:32:33+0000"
-    },
-    "Parameters: '--nf_core_pipeline rnaseq'": {
+    "Parameters: --nf_core_pipeline rnaseq": {
         "content": [
             {
-                
+                "0": [
+                    [
+                        {
+                            "id": "DRX024467_DRR026872",
+                            "run_accession": "DRR026872",
+                            "experiment_accession": "DRX024467",
+                            "sample_accession": "SAMD00023098",
+                            "secondary_sample_accession": "DRS033740",
+                            "study_accession": "PRJDB4356",
+                            "secondary_study_accession": "DRP003256",
+                            "submission_accession": "DRA002758",
+                            "run_alias": "DRR026872",
+                            "experiment_alias": "DRX024467",
+                            "sample_alias": "SAMD00023098",
+                            "study_alias": "DRP003256",
+                            "library_layout": "SINGLE",
+                            "library_selection": "Restriction Digest",
+                            "library_source": "GENOMIC",
+                            "library_strategy": "OTHER",
+                            "library_name": "IpeRAD1_3",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "62550",
+                            "read_count": "417",
+                            "tax_id": "35883",
+                            "scientific_name": "Ipomoea nil",
+                            "sample_title": "F2 plant dreived from a cross between Tokyo Kokei-standard and Africa #21",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Illumina HiSeq 2500 sequencing of SAMD00023098",
+                            "study_title": "The Japanese morning glory genome sequence",
+                            "sample_description": "Keywords: GSC:MIxS MIGS:6.0",
+                            "fastq_md5": "515e5448c55e054113c4a22df5f62791",
+                            "fastq_bytes": "38447",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "515e5448c55e054113c4a22df5f62791",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791"
+                    ],
+                    [
+                        {
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+                            "run_accession": "DRR028935",
+                            "experiment_accession": "DRX026011",
+                            "sample_accession": "SAMD00024405",
+                            "secondary_sample_accession": "DRS019431",
+                            "study_accession": "PRJDB3420",
+                            "secondary_study_accession": "DRP002616",
+                            "submission_accession": "DRA002949",
+                            "run_alias": "DRR028935",
+                            "experiment_alias": "DRX026011",
+                            "sample_alias": "SAMD00024405",
+                            "study_alias": "DRP002616",
+                            "library_layout": "PAIRED",
+                            "library_selection": "cDNA",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "RNA-Seq",
+                            "library_name": "day0_BbSQE-I",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "194930",
+                            "read_count": "965",
+                            "tax_id": "1202541",
+                            "scientific_name": "Botryococcus braunii Showa",
+                            "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
+                            "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
+                            "sample_description": "Liquid culture",
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+                            "fastq_bytes": "60275;61610",
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+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
+                            "md5_2": "941c9998d746416dad53c94c480ddf30",
+                            "single_end": false
+                        },
+                        [
+                            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
+                            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "ERX1188904_ERR1109373",
+                            "run_accession": "ERR1109373",
+                            "experiment_accession": "ERX1188904",
+                            "sample_accession": "SAMEA3643867",
+                            "secondary_sample_accession": "ERS951016",
+                            "study_accession": "PRJEB11633",
+                            "secondary_study_accession": "ERP013030",
+                            "submission_accession": "ERA528939",
+                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
+                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
+                            "sample_alias": "sample_56",
+                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
+                            "library_layout": "PAIRED",
+                            "library_selection": "RT-PCR",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "RNA-Seq",
+                            "library_name": "unspecified",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "29700",
+                            "read_count": "169",
+                            "tax_id": "63433",
+                            "scientific_name": "Leptopilina boulardi",
+                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
+                            "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
+                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
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+                            "run_alias": "GSM4907283_r3",
+                            "experiment_alias": "GSM4907283",
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+                            "study_alias": "GSE159787",
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+                            "sample_title": "A20-35 A11A20-35 A11_ROI009PanCK+",
+                            "experiment_title": "NextSeq 550 sequencing: GSM4907283: A20-35 A11A20-35 A11_ROI009PanCK+ Homo sapiens OTHER",
+                            "study_title": "Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]",
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+                        ]
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+                    [
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+                            "run_accession": "SRR13055520",
+                            "experiment_accession": "SRX9504942",
+                            "sample_accession": "SAMN16793052",
+                            "secondary_sample_accession": "SRS7713669",
+                            "study_accession": "PRJNA678298",
+                            "secondary_study_accession": "SRP292504",
+                            "submission_accession": "SRA1158402",
+                            "run_alias": "GSM4907283_r4",
+                            "experiment_alias": "GSM4907283",
+                            "sample_alias": "GSM4907283",
+                            "study_alias": "GSE159787",
+                            "library_layout": "PAIRED",
+                            "library_selection": "other",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "OTHER",
+                            "library_name": "",
+                            "instrument_model": "NextSeq 550",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "2214488",
+                            "read_count": "29138",
+                            "tax_id": "9606",
+                            "scientific_name": "Homo sapiens",
+                            "sample_title": "A20-35 A11A20-35 A11_ROI009PanCK+",
+                            "experiment_title": "NextSeq 550 sequencing: GSM4907283: A20-35 A11A20-35 A11_ROI009PanCK+ Homo sapiens OTHER",
+                            "study_title": "Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]",
+                            "sample_description": "A20-35 A11A20-35 A11_ROI009PanCK+",
+                            "fastq_md5": "795d460abff6009c7f5ff7c14b773fbe;c3f34379356b28d6dac7212abc1a0a04",
+                            "fastq_bytes": "709867;716862",
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+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "md5_1": "795d460abff6009c7f5ff7c14b773fbe",
+                            "md5_2": "c3f34379356b28d6dac7212abc1a0a04",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
+                            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "run_accession": "SRR13191702",
+                            "experiment_accession": "SRX9626017",
+                            "sample_accession": "SAMN16980141",
+                            "secondary_sample_accession": "SRS7827211",
+                            "study_accession": "PRJNA682076",
+                            "secondary_study_accession": "SRP295653",
+                            "submission_accession": "SRA1166126",
+                            "run_alias": "S.170804.00784_662_L001_R1_001.fastq.gz",
+                            "experiment_alias": "S.170804.00784",
+                            "sample_alias": "S.170804.00784_662",
+                            "study_alias": "PRJNA682076",
+                            "library_layout": "PAIRED",
+                            "library_selection": "PCR",
+                            "library_source": "METAGENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "S.170804.00784",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "45682",
+                            "read_count": "91",
+                            "tax_id": "408170",
+                            "scientific_name": "human gut metagenome",
+                            "sample_title": "Metagenome or environmental sample from human gut metagenome",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
+                            "study_title": "Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
+                            "sample_description": "Metagenome or environmental sample from human gut metagenome",
+                            "fastq_md5": "89c5be920021a035084d8aeb74f32df7;56271be38a80db78ef3bdfc5d9909b98",
+                            "fastq_bytes": "15420;16324",
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+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
+                        ]
+                    ]
+                ],
+                "mappings": [
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+                ],
+                "samplesheet": [
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+                ],
+                "versions": [
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+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                ]
             }
         ],
-        "timestamp": "2023-08-28T09:32:33+0000"
-    },
-    "fastq": {
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-            "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6",
-            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
-            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
-            "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
-            "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64",
-            "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83",
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-            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
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-            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04",
-            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98",
-            [
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-                "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9",
-                "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f",
-                "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86",
-                "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499",
-                "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff",
-                "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75",
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-                "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4",
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-                "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0",
-                "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368",
-                "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8",
-                "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f",
-                "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3",
-                "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8",
-                "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882",
-                "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
-                "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
-            ]
-        ],
-        "timestamp": "2023-08-28T09:32:33+0000"
+        "timestamp": "2023-09-11T16:53:44.32524"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
index da686d45..a94fc295 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
@@ -1,88 +1,1353 @@
 {
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-            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
-            "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
-            "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
-            "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
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-            "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54",
-            "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
-            "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
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-        "timestamp": "2023-08-28T09:27:41+0000"
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-        "timestamp": "2023-08-28T09:27:41+0000"
-    },
-    "software_versions": {
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-        ],
-        "timestamp": "2023-08-28T09:27:41+0000"
-    },
     "Parameters: --nf_core_pipeline taxprofiler": {
         "content": [
             {
-                
+                "0": [
+                    [
+                        {
+                            "id": "DRX024467_DRR026872",
+                            "run_accession": "DRR026872",
+                            "experiment_accession": "DRX024467",
+                            "sample_accession": "SAMD00023098",
+                            "secondary_sample_accession": "DRS033740",
+                            "study_accession": "PRJDB4356",
+                            "secondary_study_accession": "DRP003256",
+                            "submission_accession": "DRA002758",
+                            "run_alias": "DRR026872",
+                            "experiment_alias": "DRX024467",
+                            "sample_alias": "SAMD00023098",
+                            "study_alias": "DRP003256",
+                            "library_layout": "SINGLE",
+                            "library_selection": "Restriction Digest",
+                            "library_source": "GENOMIC",
+                            "library_strategy": "OTHER",
+                            "library_name": "IpeRAD1_3",
+                            "instrument_model": "Illumina HiSeq 2500",
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-                "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
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-        ],
-        "timestamp": "2023-08-28T09:27:41+0000"
+        "timestamp": "2023-09-11T16:42:06.867767"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
index a30d8377..8b6be6a1 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
@@ -1,88 +1,1353 @@
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+                            "fastq_md5": "89c5be920021a035084d8aeb74f32df7;56271be38a80db78ef3bdfc5d9909b98",
+                            "fastq_bytes": "15420;16324",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
+                        ]
+                    ]
+                ],
+                "mappings": [
+                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                ],
+                "samplesheet": [
+                    "samplesheet.csv:md5,3e32e2cfa3c8b23c9cd32d91b885c0de"
+                ],
+                "versions": [
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                ]
             }
         ],
-        "timestamp": "2023-08-28T10:03:01+0000"
-    },
-    "software_versions": {
-        "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
-        ],
-        "timestamp": "2023-08-28T10:03:01+0000"
-    },
-    "fastq": {
-        "content": [
-            "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791",
-            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
-            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30",
-            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
-            "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6",
-            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
-            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
-            "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
-            "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64",
-            "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83",
-            "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544",
-            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
-            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
-            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
-            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962",
-            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
-            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76",
-            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
-            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88",
-            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
-            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04",
-            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98",
-            [
-                "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d",
-                "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9",
-                "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f",
-                "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86",
-                "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499",
-                "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff",
-                "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75",
-                "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85",
-                "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4",
-                "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc",
-                "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0",
-                "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368",
-                "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8",
-                "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f",
-                "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3",
-                "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8",
-                "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882",
-                "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
-                "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
-            ]
-        ],
-        "timestamp": "2023-08-28T10:03:06+0000"
+        "timestamp": "2023-09-11T16:33:01.320808"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
new file mode 100644
index 00000000..921bed59
--- /dev/null
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
@@ -0,0 +1,37 @@
+{
+    "Parameters: --skip_fastq_download": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    "samplesheet.csv:md5,7cf3503b651fe016bc1e5fb3c2e996d5"
+                ],
+                "2": [
+                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                ],
+                "3": [
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                ],
+                "fastq": [
+                    
+                ],
+                "mappings": [
+                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                ],
+                "samplesheet": [
+                    "samplesheet.csv:md5,7cf3503b651fe016bc1e5fb3c2e996d5"
+                ],
+                "versions": [
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                ]
+            }
+        ],
+        "timestamp": "2023-09-11T16:58:42.10055"
+    }
+}
\ No newline at end of file

From 07be381748947cf5d6c8d1d85be47c61c6735f52 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 11 Sep 2023 17:30:23 +0200
Subject: [PATCH 424/852] update snapshot

---
 workflows/synapse/tests/main.nf.test.snap | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/workflows/synapse/tests/main.nf.test.snap b/workflows/synapse/tests/main.nf.test.snap
index 8528f776..9b25ee0c 100644
--- a/workflows/synapse/tests/main.nf.test.snap
+++ b/workflows/synapse/tests/main.nf.test.snap
@@ -3,14 +3,14 @@
         "content": [
             "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
             "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548",
-            "samplesheet.csv:md5,9b3c35e8af74e9af194baa2498aaf4d4"
+            "samplesheet.csv:md5,296e139d533c7a67567dd073ec0f945a"
         ],
-        "timestamp": "2023-08-24T14:05:07+0000"
+        "timestamp": "2023-09-11T17:08:51.001588"
     },
     "software_versions": {
         "content": [
-            "software_versions.yml:md5,f37983a6b1ce2334fe62fa188b31ca51"
+            "software_versions.yml:md5,966251d4b7717464ccea77d6e8841e58"
         ],
-        "timestamp": "2023-08-24T14:05:07+0000"
+        "timestamp": "2023-09-11T17:08:50.994607"
     }
 }
\ No newline at end of file

From cedcf471f8c39d7f66c589fa36c1919ffe025ad1 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 11 Sep 2023 18:26:47 +0200
Subject: [PATCH 425/852] relative path

---
 workflows/sra/tests/main.nf.test      | 2 +-
 workflows/sra/tests/main.nf.test.snap | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 2652eb80..ef35c80a 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
+                outdir = "results"
             }
         }
 
diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
index 1c969bc2..1692d4cd 100644
--- a/workflows/sra/tests/main.nf.test.snap
+++ b/workflows/sra/tests/main.nf.test.snap
@@ -662,7 +662,7 @@
                     ]
                 ],
                 "1": [
-                    "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341"
+                    "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556"
                 ],
                 "2": [
                     "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
@@ -1337,7 +1337,7 @@
                     "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341"
+                    "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556"
                 ],
                 "versions": [
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
@@ -1348,6 +1348,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-11T16:58:15.05829"
+        "timestamp": "2023-09-11T18:23:09.598326"
     }
 }
\ No newline at end of file

From b26115d7e453393355ca7d5638fcd0ed40f583eb Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 11 Sep 2023 19:35:04 +0200
Subject: [PATCH 426/852] update tests and snapshot

---
 workflows/sra/tests/main.nf.test.snap                  |  2 +-
 .../sra/tests/sra_custom_ena_metadata_fields.nf.test   |  2 +-
 .../tests/sra_custom_ena_metadata_fields.nf.test.snap  | 10 +++++-----
 .../sra/tests/sra_force_sratools_download.nf.test      |  2 +-
 .../sra/tests/sra_force_sratools_download.nf.test.snap |  6 +++---
 .../sra/tests/sra_nf_core_pipeline_atacseq.nf.test     |  2 +-
 .../tests/sra_nf_core_pipeline_atacseq.nf.test.snap    |  6 +++---
 .../sra/tests/sra_nf_core_pipeline_rnaseq.nf.test      |  2 +-
 .../sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap | 10 +++++-----
 .../sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test |  2 +-
 .../sra_nf_core_pipeline_taxprofiler.nf.test.snap      | 10 +++++-----
 .../sra/tests/sra_nf_core_pipeline_viralrecon.nf.test  |  2 +-
 .../tests/sra_nf_core_pipeline_viralrecon.nf.test.snap |  6 +++---
 workflows/sra/tests/sra_skip_fastq_download.nf.test    |  2 +-
 .../sra/tests/sra_skip_fastq_download.nf.test.snap     |  2 +-
 15 files changed, 33 insertions(+), 33 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
index 1692d4cd..b8dc88ca 100644
--- a/workflows/sra/tests/main.nf.test.snap
+++ b/workflows/sra/tests/main.nf.test.snap
@@ -1348,6 +1348,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-11T18:23:09.598326"
+        "timestamp": "2023-09-11T18:56:05.693225"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index 4dc9ba8b..45280ab0 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -16,7 +16,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
+                outdir = "results"
                 nf_core_pipeline = "rnaseq"
                 ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5"
                 sample_mapping_fields = "run_accession,library_layout"
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
index c2782552..a2537a95 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
@@ -272,14 +272,14 @@
                     ]
                 ],
                 "1": [
-                    "samplesheet.csv:md5,7bca96e409bd9eb6790e0d6737af686c"
+                    "samplesheet.csv:md5,be5465f34924356e136c804d63e1b562"
                 ],
                 "2": [
                     "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f"
                 ],
                 "3": [
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
                     "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
                     "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
@@ -557,17 +557,17 @@
                     "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f"
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,7bca96e409bd9eb6790e0d6737af686c"
+                    "samplesheet.csv:md5,be5465f34924356e136c804d63e1b562"
                 ],
                 "versions": [
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
                     "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
                     "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
                 ]
             }
         ],
-        "timestamp": "2023-09-11T16:47:26.813819"
+        "timestamp": "2023-09-11T18:48:18.757655"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index 2b1b5953..76ce7cd3 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -16,7 +16,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
+                outdir = "results"
                 force_sratools_download = true
             }
         }
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
index 2c779c84..4e1b8aaf 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
@@ -662,7 +662,7 @@
                     ]
                 ],
                 "1": [
-                    "samplesheet.csv:md5,9d4b95a31702af34a6f57d963137340d"
+                    "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556"
                 ],
                 "2": [
                     "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
@@ -1336,7 +1336,7 @@
                     "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,9d4b95a31702af34a6f57d963137340d"
+                    "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556"
                 ],
                 "versions": [
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
@@ -1346,6 +1346,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-11T17:03:59.154427"
+        "timestamp": "2023-09-11T19:02:05.556134"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index 3d946fea..0ce0c230 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -16,7 +16,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
+                outdir = "results"
                 nf_core_pipeline = "atacseq"
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
index 069e3390..f6528e52 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
@@ -662,7 +662,7 @@
                     ]
                 ],
                 "1": [
-                    "samplesheet.csv:md5,252449b9f66687af076bb5a9dfea4551"
+                    "samplesheet.csv:md5,16e5161103702777b2d763c1ed660d3c"
                 ],
                 "2": [
                     "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
@@ -1337,7 +1337,7 @@
                     "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,252449b9f66687af076bb5a9dfea4551"
+                    "samplesheet.csv:md5,16e5161103702777b2d763c1ed660d3c"
                 ],
                 "versions": [
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
@@ -1348,6 +1348,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-11T16:36:17.537997"
+        "timestamp": "2023-09-11T18:37:54.607231"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index f51aa4ca..67c0fbe4 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -16,7 +16,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
+                outdir = "results"
                 nf_core_pipeline = "rnaseq"
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
index 4c2abc45..124877ae 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
@@ -662,14 +662,14 @@
                     ]
                 ],
                 "1": [
-                    "samplesheet.csv:md5,f0b7e9436c6feb1a31c49c2c8ab761a2"
+                    "samplesheet.csv:md5,fcbb1fbe56dc14561ec83e5f6a70ee80"
                 ],
                 "2": [
                     "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
                 ],
                 "3": [
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
                     "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
                     "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
@@ -1337,17 +1337,17 @@
                     "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,f0b7e9436c6feb1a31c49c2c8ab761a2"
+                    "samplesheet.csv:md5,fcbb1fbe56dc14561ec83e5f6a70ee80"
                 ],
                 "versions": [
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
                     "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
                     "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
                 ]
             }
         ],
-        "timestamp": "2023-09-11T16:53:44.32524"
+        "timestamp": "2023-09-11T18:51:38.198125"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index 97cd4a44..e00793cd 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -16,7 +16,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
+                outdir = "results"
                 nf_core_pipeline = "taxprofiler"
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
index a94fc295..b63ad4b7 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
@@ -662,14 +662,14 @@
                     ]
                 ],
                 "1": [
-                    "samplesheet.csv:md5,484efbb550b50f5ac63e4864282edea7"
+                    "samplesheet.csv:md5,0df1f60a9b5bc94f8a85e96edcc90f5c"
                 ],
                 "2": [
                     "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
                 ],
                 "3": [
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
                     "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
                     "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
@@ -1337,17 +1337,17 @@
                     "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,484efbb550b50f5ac63e4864282edea7"
+                    "samplesheet.csv:md5,0df1f60a9b5bc94f8a85e96edcc90f5c"
                 ],
                 "versions": [
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
                     "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
                     "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
                 ]
             }
         ],
-        "timestamp": "2023-09-11T16:42:06.867767"
+        "timestamp": "2023-09-11T18:44:02.293186"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index 434fac63..045e0363 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -16,7 +16,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
+                outdir = "results"
                 nf_core_pipeline = "viralrecon"
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
index 8b6be6a1..1387f422 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
@@ -662,7 +662,7 @@
                     ]
                 ],
                 "1": [
-                    "samplesheet.csv:md5,3e32e2cfa3c8b23c9cd32d91b885c0de"
+                    "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556"
                 ],
                 "2": [
                     "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
@@ -1337,7 +1337,7 @@
                     "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,3e32e2cfa3c8b23c9cd32d91b885c0de"
+                    "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556"
                 ],
                 "versions": [
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
@@ -1348,6 +1348,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-11T16:33:01.320808"
+        "timestamp": "2023-09-11T18:34:25.049818"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index dbe40144..67abee3b 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -16,7 +16,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
+                outdir = "results"
                 skip_fastq_download = true
             }
         }
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
index 921bed59..3b04b917 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
@@ -32,6 +32,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-11T16:58:42.10055"
+        "timestamp": "2023-09-11T18:56:34.175665"
     }
 }
\ No newline at end of file

From 410321c8f88e2d28abd328e5d098d4780b76276d Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 12 Sep 2023 12:51:28 +0200
Subject: [PATCH 427/852] implement changes in GHA CI

---
 .github/workflows/ci.yml | 46 ++++++++++++++++++++++------------------
 1 file changed, 25 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 5c5df959..4fe23a91 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,18 +1,17 @@
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 name: nf-core CI
+# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on:
-  push:
-    branches:
-      - dev
-      - refactor
   pull_request:
+  release:
+    types: [published]
+  merge_group:
+    types:
+      - checks_requested
     branches:
-      - dev
       - master
+      - dev
       - refactor
-  release:
-    types:
-      - "published"
 
 env:
   NXF_ANSI_LOG: false
@@ -23,6 +22,19 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  changes:
+    name: Check for changes
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose matched filters as job 'tags' output variable
+      tags: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: "tests/config/tags.yml"
+
   define_nxf_versions:
     name: Choose nextflow versions to test against depending on target branch
     runs-on: ubuntu-latest
@@ -38,23 +50,15 @@ jobs:
           fi
 
   test:
-    name: Run pipeline with test data
-    needs: define_nxf_versions
+    name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }}
+    needs: [changes, define_nxf_versions]
+    if: needs.changes.outputs.tags != '[]'
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
         NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
-        test_tags:
-          - "modules_local"
-          - "sra_default_parameters"
-          - "sra_custom_ena_metadata_fields"
-          - "sra_force_sratools_download"
-          - "sra_nf_core_pipeline_atacseq"
-          - "sra_nf_core_pipeline_rnaseq"
-          - "sra_nf_core_pipeline_taxprofiler"
-          - "sra_nf_core_pipeline_viralrecon"
-          - "sra_skip_fastq_download"
+        tags: ["${{ fromJson(needs.changes.outputs.tags) }}"]
         profile:
           - "docker"
 
@@ -74,7 +78,7 @@ jobs:
 
       - name: Run nf-test
         run: |
-          nf-test test --tag ${{ matrix.test_tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml
+          nf-test test --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml
 
       - name: Output log on failure
         if: failure()

From 57d6921e74bbfca14d021964bcd03723e42ad33c Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 12 Sep 2023 14:45:11 +0200
Subject: [PATCH 428/852] add tags

---
 .github/tags.yml | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 .github/tags.yml

diff --git a/.github/tags.yml b/.github/tags.yml
new file mode 100644
index 00000000..8fe923f5
--- /dev/null
+++ b/.github/tags.yml
@@ -0,0 +1,40 @@
+# local modules
+
+multiqc_mappings_config:
+  - modules/local/multiqc_mappings_config/*
+sra_fastq_ftp:
+  - modules/local/sra_fastq_ftp/*
+sra_ids_to_runinfo:
+  - modules/local/sra_ids_to_runinfo/*
+sra_merge_samplesheet:
+  - modules/local/sra_merge_samplesheet/*
+sra_runinfo_to_ftp:
+  - modules/local/sra_runinfo_to_ftp/*
+sra_to_samplesheet:
+  - modules/local/sra_to_samplesheet/*
+
+# workflow: sra
+sra_custom_ena_metadata_fields:
+  - conf/modules/sra.config
+  - workflows/sra/main.nf
+sra_default_parameters:
+  - conf/modules/sra.config
+  - workflows/sra/main.nf
+sra_force_sratools_download:
+  - conf/modules/sra.config
+  - workflows/sra/main.nf
+sra_nf_core_pipeline_atacseq:
+  - conf/modules/sra.config
+  - workflows/sra/main.nf
+sra_nf_core_pipeline_rnaseq:
+  - conf/modules/sra.config
+  - workflows/sra/main.nf
+sra_nf_core_pipeline_taxprofiler:
+  - conf/modules/sra.config
+  - workflows/sra/main.nf
+sra_nf_core_pipeline_viralrecon:
+  - conf/modules/sra.config
+  - workflows/sra/main.nf
+sra_skip_fastq_download:
+  - conf/modules/sra.config
+  - workflows/sra/main.nf

From e9d38bb614c8d93d2a8c542ff3d1ec53e3aed38d Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 12 Sep 2023 14:45:19 +0200
Subject: [PATCH 429/852] fix path to tags

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4fe23a91..7b7070e7 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -33,7 +33,7 @@ jobs:
       - uses: dorny/paths-filter@v2
         id: filter
         with:
-          filters: "tests/config/tags.yml"
+          filters: ".github/tags.yml"
 
   define_nxf_versions:
     name: Choose nextflow versions to test against depending on target branch

From 54f954ca4371ea42f3e5cc0610cd747eb111bf3b Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 12 Sep 2023 15:16:10 +0200
Subject: [PATCH 430/852] rename files

---
 .../sra/tests/{main.nf.test => sra_default_parameters.nf.test}    | 0
 .../{main.nf.test.snap => sra_default_parameters.nf.test.snap}    | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 rename workflows/sra/tests/{main.nf.test => sra_default_parameters.nf.test} (100%)
 rename workflows/sra/tests/{main.nf.test.snap => sra_default_parameters.nf.test.snap} (100%)

diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/sra_default_parameters.nf.test
similarity index 100%
rename from workflows/sra/tests/main.nf.test
rename to workflows/sra/tests/sra_default_parameters.nf.test
diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/sra_default_parameters.nf.test.snap
similarity index 100%
rename from workflows/sra/tests/main.nf.test.snap
rename to workflows/sra/tests/sra_default_parameters.nf.test.snap

From 82510e8b9297fb1106cf86c4e191cfedbd6c4101 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 12 Sep 2023 15:16:19 +0200
Subject: [PATCH 431/852] add tests to tags

---
 .github/tags.yml | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/.github/tags.yml b/.github/tags.yml
index 8fe923f5..68607d79 100644
--- a/.github/tags.yml
+++ b/.github/tags.yml
@@ -1,5 +1,4 @@
 # local modules
-
 multiqc_mappings_config:
   - modules/local/multiqc_mappings_config/*
 sra_fastq_ftp:
@@ -16,25 +15,33 @@ sra_to_samplesheet:
 # workflow: sra
 sra_custom_ena_metadata_fields:
   - conf/modules/sra.config
+  - workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
   - workflows/sra/main.nf
 sra_default_parameters:
   - conf/modules/sra.config
+  - workflows/sra/tests/sra_default_parameters.nf.test
   - workflows/sra/main.nf
 sra_force_sratools_download:
   - conf/modules/sra.config
+  - workflows/sra/tests/sra_force_sratools_download.nf.test
   - workflows/sra/main.nf
 sra_nf_core_pipeline_atacseq:
   - conf/modules/sra.config
+  - workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
   - workflows/sra/main.nf
 sra_nf_core_pipeline_rnaseq:
   - conf/modules/sra.config
+  - workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
   - workflows/sra/main.nf
 sra_nf_core_pipeline_taxprofiler:
   - conf/modules/sra.config
+  - workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
   - workflows/sra/main.nf
 sra_nf_core_pipeline_viralrecon:
   - conf/modules/sra.config
+  - workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
   - workflows/sra/main.nf
 sra_skip_fastq_download:
   - conf/modules/sra.config
+  - workflows/sra/tests/sra_skip_fastq_download.nf.test
   - workflows/sra/main.nf

From c707eef5871a8a82bdfc1b6f3f918ced7b0b252f Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 12 Sep 2023 15:24:45 +0200
Subject: [PATCH 432/852] alphabetical order

---
 .github/tags.yml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/tags.yml b/.github/tags.yml
index 68607d79..aa7b69c9 100644
--- a/.github/tags.yml
+++ b/.github/tags.yml
@@ -15,33 +15,33 @@ sra_to_samplesheet:
 # workflow: sra
 sra_custom_ena_metadata_fields:
   - conf/modules/sra.config
-  - workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
   - workflows/sra/main.nf
+  - workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
 sra_default_parameters:
   - conf/modules/sra.config
-  - workflows/sra/tests/sra_default_parameters.nf.test
   - workflows/sra/main.nf
+  - workflows/sra/tests/sra_default_parameters.nf.test
 sra_force_sratools_download:
   - conf/modules/sra.config
-  - workflows/sra/tests/sra_force_sratools_download.nf.test
   - workflows/sra/main.nf
+  - workflows/sra/tests/sra_force_sratools_download.nf.test
 sra_nf_core_pipeline_atacseq:
   - conf/modules/sra.config
-  - workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
   - workflows/sra/main.nf
+  - workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
 sra_nf_core_pipeline_rnaseq:
   - conf/modules/sra.config
-  - workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
   - workflows/sra/main.nf
+  - workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
 sra_nf_core_pipeline_taxprofiler:
   - conf/modules/sra.config
-  - workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
   - workflows/sra/main.nf
+  - workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
 sra_nf_core_pipeline_viralrecon:
   - conf/modules/sra.config
-  - workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
   - workflows/sra/main.nf
+  - workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
 sra_skip_fastq_download:
   - conf/modules/sra.config
-  - workflows/sra/tests/sra_skip_fastq_download.nf.test
   - workflows/sra/main.nf
+  - workflows/sra/tests/sra_skip_fastq_download.nf.test

From b5d80fb8ad782d6366fa77cc41bde11000f257c4 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 12 Sep 2023 15:33:28 +0200
Subject: [PATCH 433/852] add modules to changes

---
 .github/tags.yml | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/.github/tags.yml b/.github/tags.yml
index aa7b69c9..ed5c9dcc 100644
--- a/.github/tags.yml
+++ b/.github/tags.yml
@@ -15,33 +15,73 @@ sra_to_samplesheet:
 # workflow: sra
 sra_custom_ena_metadata_fields:
   - conf/modules/sra.config
+  - modules/local/sra_ids_to_runinfo/main.nf
+  - modules/local/sra_runinfo_to_ftp/main.nf
+  - modules/local/sra_fastq_ftp/main.nf
+  - modules/local/sra_to_samplesheet/main.nf
+  - modules/local/sra_merge_samplesheet/main.nf
   - workflows/sra/main.nf
   - workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
 sra_default_parameters:
   - conf/modules/sra.config
+  - modules/local/sra_ids_to_runinfo/main.nf
+  - modules/local/sra_runinfo_to_ftp/main.nf
+  - modules/local/sra_fastq_ftp/main.nf
+  - modules/local/sra_to_samplesheet/main.nf
+  - modules/local/sra_merge_samplesheet/main.nf
   - workflows/sra/main.nf
   - workflows/sra/tests/sra_default_parameters.nf.test
 sra_force_sratools_download:
   - conf/modules/sra.config
+  - modules/local/sra_ids_to_runinfo/main.nf
+  - modules/local/sra_runinfo_to_ftp/main.nf
+  - modules/local/sra_fastq_ftp/main.nf
+  - modules/local/sra_to_samplesheet/main.nf
+  - modules/local/sra_merge_samplesheet/main.nf
   - workflows/sra/main.nf
   - workflows/sra/tests/sra_force_sratools_download.nf.test
 sra_nf_core_pipeline_atacseq:
   - conf/modules/sra.config
+  - modules/local/sra_ids_to_runinfo/main.nf
+  - modules/local/sra_runinfo_to_ftp/main.nf
+  - modules/local/sra_fastq_ftp/main.nf
+  - modules/local/sra_to_samplesheet/main.nf
+  - modules/local/sra_merge_samplesheet/main.nf
   - workflows/sra/main.nf
   - workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
 sra_nf_core_pipeline_rnaseq:
   - conf/modules/sra.config
+  - modules/local/sra_ids_to_runinfo/main.nf
+  - modules/local/sra_runinfo_to_ftp/main.nf
+  - modules/local/sra_fastq_ftp/main.nf
+  - modules/local/sra_to_samplesheet/main.nf
+  - modules/local/sra_merge_samplesheet/main.nf
   - workflows/sra/main.nf
   - workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
 sra_nf_core_pipeline_taxprofiler:
   - conf/modules/sra.config
+  - modules/local/sra_ids_to_runinfo/main.nf
+  - modules/local/sra_runinfo_to_ftp/main.nf
+  - modules/local/sra_fastq_ftp/main.nf
+  - modules/local/sra_to_samplesheet/main.nf
+  - modules/local/sra_merge_samplesheet/main.nf
   - workflows/sra/main.nf
   - workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
 sra_nf_core_pipeline_viralrecon:
   - conf/modules/sra.config
+  - modules/local/sra_ids_to_runinfo/main.nf
+  - modules/local/sra_runinfo_to_ftp/main.nf
+  - modules/local/sra_fastq_ftp/main.nf
+  - modules/local/sra_to_samplesheet/main.nf
+  - modules/local/sra_merge_samplesheet/main.nf
   - workflows/sra/main.nf
   - workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
 sra_skip_fastq_download:
   - conf/modules/sra.config
+  - modules/local/sra_ids_to_runinfo/main.nf
+  - modules/local/sra_runinfo_to_ftp/main.nf
+  - modules/local/sra_fastq_ftp/main.nf
+  - modules/local/sra_to_samplesheet/main.nf
+  - modules/local/sra_merge_samplesheet/main.nf
   - workflows/sra/main.nf
   - workflows/sra/tests/sra_skip_fastq_download.nf.test

From 9c6bf658cfeba3b1780615faa794f77d85c44000 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 18 Sep 2023 14:57:33 +0100
Subject: [PATCH 434/852] Remove public_aws_ecr profile

---
 .github/workflows/cloud_tests_full.yml  | 2 +-
 .github/workflows/cloud_tests_small.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cloud_tests_full.yml b/.github/workflows/cloud_tests_full.yml
index e25a97aa..d0ed0552 100644
--- a/.github/workflows/cloud_tests_full.yml
+++ b/.github/workflows/cloud_tests_full.yml
@@ -27,7 +27,7 @@ jobs:
           compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
           workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/fetchngs/work-${{ github.sha }}"
           run_name: "aws_fetchngs_full"
-          profiles: test_full,public_aws_ecr
+          profiles: test_full
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
diff --git a/.github/workflows/cloud_tests_small.yml b/.github/workflows/cloud_tests_small.yml
index e7636fdc..12b8daab 100644
--- a/.github/workflows/cloud_tests_small.yml
+++ b/.github/workflows/cloud_tests_small.yml
@@ -25,7 +25,7 @@ jobs:
           compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
           workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/fetchngs/work-${{ github.sha }}"
           run_name: "aws_fetchngs_small"
-          profiles: test,public_aws_ecr
+          profiles: test
           parameters: |
             {
                 "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/fetchngs/results-test-${{ github.sha }}"

From 2c7c13f08909ea069bb0dbb86ed78874f40f38a5 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 18 Sep 2023 15:02:36 +0100
Subject: [PATCH 435/852] Replace large config file with individual configs per
 module

---
 conf/modules/sra.config                       | 88 -------------------
 .../multiqc_mappings_config/nextflow.config   |  9 ++
 modules/local/sra_fastq_ftp/nextflow.config   | 17 ++++
 .../local/sra_ids_to_runinfo/nextflow.config  |  8 ++
 .../sra_merge_samplesheet/nextflow.config     |  9 ++
 .../local/sra_runinfo_to_ftp/nextflow.config  |  9 ++
 .../local/sra_to_samplesheet/nextflow.config  |  8 ++
 .../sratools/fasterqdump/nextflow.config      | 10 +++
 .../nf-core/sratools/prefetch/nextflow.config |  8 ++
 nextflow.config                               |  2 +-
 workflows/sra/nextflow.config                 |  7 ++
 workflows/synapse/nextflow.config             |  0
 12 files changed, 86 insertions(+), 89 deletions(-)
 delete mode 100644 conf/modules/sra.config
 create mode 100644 modules/local/multiqc_mappings_config/nextflow.config
 create mode 100644 modules/local/sra_fastq_ftp/nextflow.config
 create mode 100644 modules/local/sra_ids_to_runinfo/nextflow.config
 create mode 100644 modules/local/sra_merge_samplesheet/nextflow.config
 create mode 100644 modules/local/sra_runinfo_to_ftp/nextflow.config
 create mode 100644 modules/local/sra_to_samplesheet/nextflow.config
 create mode 100644 modules/nf-core/sratools/fasterqdump/nextflow.config
 create mode 100644 modules/nf-core/sratools/prefetch/nextflow.config
 create mode 100644 workflows/sra/nextflow.config
 create mode 100644 workflows/synapse/nextflow.config

diff --git a/conf/modules/sra.config b/conf/modules/sra.config
deleted file mode 100644
index 15802b41..00000000
--- a/conf/modules/sra.config
+++ /dev/null
@@ -1,88 +0,0 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Config file for defining DSL2 per module options and publishing paths
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Available keys to override module options:
-        ext.args   = Additional arguments appended to command in module.
-        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
-        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
-        ext.prefix = File name prefix for output files.
-----------------------------------------------------------------------------------------
-*/
-
-//
-//  Process options for the SRA workflow
-//
-process {
-
-    withName: SRA_IDS_TO_RUNINFO {
-        publishDir = [
-            path: { "${params.outdir}/metadata" },
-            enabled: false
-        ]
-    }
-
-    withName: SRA_RUNINFO_TO_FTP {
-        publishDir = [
-            path: { "${params.outdir}/metadata" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: SRA_FASTQ_FTP {
-        ext.args = '--retry 5 --continue-at - --max-time 1200'
-        publishDir = [
-            [
-                path: { "${params.outdir}/fastq" },
-                mode: params.publish_dir_mode,
-                pattern: "*.fastq.gz"
-            ],
-            [
-                path: { "${params.outdir}/fastq/md5" },
-                mode: params.publish_dir_mode,
-                pattern: "*.md5"
-            ]
-        ]
-    }
-
-    withName: SRATOOLS_PREFETCH {
-        publishDir = [
-            path: { "${params.outdir}/sra" },
-            enabled: false
-        ]
-    }
-
-    withName: SRATOOLS_FASTERQDUMP {
-        ext.args = '--split-files --include-technical'
-        publishDir = [
-            path: { "${params.outdir}/fastq" },
-            mode: params.publish_dir_mode,
-            pattern: "*.fastq.gz"
-        ]
-    }
-
-    withName: SRA_TO_SAMPLESHEET {
-        publishDir = [
-            path: { "${params.outdir}/samplesheet" },
-            enabled: false
-        ]
-    }
-
-    withName: SRA_MERGE_SAMPLESHEET {
-        publishDir = [
-            path: { "${params.outdir}/samplesheet" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: MULTIQC_MAPPINGS_CONFIG {
-        publishDir = [
-            path: { "${params.outdir}/samplesheet" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-}
diff --git a/modules/local/multiqc_mappings_config/nextflow.config b/modules/local/multiqc_mappings_config/nextflow.config
new file mode 100644
index 00000000..e2382930
--- /dev/null
+++ b/modules/local/multiqc_mappings_config/nextflow.config
@@ -0,0 +1,9 @@
+process {
+    withName: 'MULTIQC_MAPPINGS_CONFIG' {
+        publishDir = [
+            path: { "${params.outdir}/samplesheet" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+}
\ No newline at end of file
diff --git a/modules/local/sra_fastq_ftp/nextflow.config b/modules/local/sra_fastq_ftp/nextflow.config
new file mode 100644
index 00000000..7b5ebf70
--- /dev/null
+++ b/modules/local/sra_fastq_ftp/nextflow.config
@@ -0,0 +1,17 @@
+process {
+    withName: 'SRA_FASTQ_FTP' {
+        ext.args = '--retry 5 --continue-at - --max-time 1200'
+        publishDir = [
+            [
+                path: { "${params.outdir}/fastq" },
+                mode: params.publish_dir_mode,
+                pattern: "*.fastq.gz"
+            ],
+            [
+                path: { "${params.outdir}/fastq/md5" },
+                mode: params.publish_dir_mode,
+                pattern: "*.md5"
+            ]
+        ]
+    }
+}
diff --git a/modules/local/sra_ids_to_runinfo/nextflow.config b/modules/local/sra_ids_to_runinfo/nextflow.config
new file mode 100644
index 00000000..73da969a
--- /dev/null
+++ b/modules/local/sra_ids_to_runinfo/nextflow.config
@@ -0,0 +1,8 @@
+process {
+    withName: 'SRA_IDS_TO_RUNINFO' {
+        publishDir = [
+            path: { "${params.outdir}/metadata" },
+            enabled: false
+        ]
+    }
+}
\ No newline at end of file
diff --git a/modules/local/sra_merge_samplesheet/nextflow.config b/modules/local/sra_merge_samplesheet/nextflow.config
new file mode 100644
index 00000000..f2926529
--- /dev/null
+++ b/modules/local/sra_merge_samplesheet/nextflow.config
@@ -0,0 +1,9 @@
+process {
+    withName: 'SRA_MERGE_SAMPLESHEET' {
+        publishDir = [
+            path: { "${params.outdir}/samplesheet" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+}
\ No newline at end of file
diff --git a/modules/local/sra_runinfo_to_ftp/nextflow.config b/modules/local/sra_runinfo_to_ftp/nextflow.config
new file mode 100644
index 00000000..aee1848c
--- /dev/null
+++ b/modules/local/sra_runinfo_to_ftp/nextflow.config
@@ -0,0 +1,9 @@
+process {
+    withName: 'SRA_RUNINFO_TO_FTP' {
+        publishDir = [
+            path: { "${params.outdir}/metadata" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+}
\ No newline at end of file
diff --git a/modules/local/sra_to_samplesheet/nextflow.config b/modules/local/sra_to_samplesheet/nextflow.config
new file mode 100644
index 00000000..da241c1a
--- /dev/null
+++ b/modules/local/sra_to_samplesheet/nextflow.config
@@ -0,0 +1,8 @@
+process {
+    withName: SRA_TO_SAMPLESHEET {
+        publishDir = [
+            path: { "${params.outdir}/samplesheet" },
+            enabled: false
+        ]
+    }
+}
diff --git a/modules/nf-core/sratools/fasterqdump/nextflow.config b/modules/nf-core/sratools/fasterqdump/nextflow.config
new file mode 100644
index 00000000..f98b140d
--- /dev/null
+++ b/modules/nf-core/sratools/fasterqdump/nextflow.config
@@ -0,0 +1,10 @@
+process {
+    withName: SRATOOLS_FASTERQDUMP {
+        ext.args = '--split-files --include-technical'
+        publishDir = [
+            path: { "${params.outdir}/fastq" },
+            mode: params.publish_dir_mode,
+            pattern: "*.fastq.gz"
+        ]
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/sratools/prefetch/nextflow.config b/modules/nf-core/sratools/prefetch/nextflow.config
new file mode 100644
index 00000000..a2ca8848
--- /dev/null
+++ b/modules/nf-core/sratools/prefetch/nextflow.config
@@ -0,0 +1,8 @@
+process {
+    withName: SRATOOLS_PREFETCH {
+        publishDir = [
+            path: { "${params.outdir}/sra" },
+            enabled: false
+        ]
+    }
+}
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index e2584ce6..40149dba 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -219,7 +219,7 @@ manifest {
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules/base.config'
 if ( params.input_type == 'sra' ) {
-    includeConfig 'conf/modules/sra.config'
+    includeConfig 'workflows/sra/nextflow.config'
 }
 if ( params.input_type == 'synapse' ) {
     includeConfig 'conf/modules/synapse.config'
diff --git a/workflows/sra/nextflow.config b/workflows/sra/nextflow.config
new file mode 100644
index 00000000..d4dd6f30
--- /dev/null
+++ b/workflows/sra/nextflow.config
@@ -0,0 +1,7 @@
+includeConfig "../../modules/local/multiqc_mappings_config/nextflow.config"
+includeConfig "../../modules/local/sra_fastq_ftp/nextflow.config"
+includeConfig "../../modules/local/sra_ids_to_runinfo/nextflow.config"
+includeConfig "../../modules/local/sra_merge_samplesheet/nextflow.config"
+includeConfig "../../modules/local/sra_runinfo_to_ftp/nextflow.config"
+includeConfig "../../modules/local/sra_to_samplesheet/nextflow.config"
+includeConfig "../../modules/nf-core/sratools/prefetch/nextflow.config"
diff --git a/workflows/synapse/nextflow.config b/workflows/synapse/nextflow.config
new file mode 100644
index 00000000..e69de29b

From 64aca64197641d7f36df4b3be2ce25c200a42293 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 18 Sep 2023 16:17:33 +0100
Subject: [PATCH 436/852] Inherit Synapse related configuration via separate
 files

---
 conf/modules/synapse.config                   | 66 -------------------
 modules/local/synapse_get/nextflow.config     | 16 +++++
 modules/local/synapse_list/nextflow.config    | 10 +++
 .../synapse_merge_samplesheet/nextflow.config |  9 +++
 modules/local/synapse_show/nextflow.config    |  9 +++
 .../synapse_to_samplesheet/nextflow.config    |  8 +++
 nextflow.config                               | 11 ++--
 workflows/synapse/nextflow.config             |  5 ++
 8 files changed, 63 insertions(+), 71 deletions(-)
 delete mode 100644 conf/modules/synapse.config
 create mode 100644 modules/local/synapse_get/nextflow.config
 create mode 100644 modules/local/synapse_list/nextflow.config
 create mode 100644 modules/local/synapse_merge_samplesheet/nextflow.config
 create mode 100644 modules/local/synapse_show/nextflow.config
 create mode 100644 modules/local/synapse_to_samplesheet/nextflow.config

diff --git a/conf/modules/synapse.config b/conf/modules/synapse.config
deleted file mode 100644
index 2f52aa6f..00000000
--- a/conf/modules/synapse.config
+++ /dev/null
@@ -1,66 +0,0 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Config file for defining DSL2 per module options and publishing paths
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Available keys to override module options:
-        ext.args   = Additional arguments appended to command in module.
-        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
-        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
-        ext.prefix = File name prefix for output files.
-----------------------------------------------------------------------------------------
-*/
-
-//
-//  Process options for the Synapse workflow
-//
-
-process {
-
-    withName: SYNAPSE_LIST {
-        ext.args = '--long'
-        publishDir = [
-            path: { "${params.outdir}/metadata" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: SYNAPSE_GET {
-        publishDir = [
-            [
-                path: { "${params.outdir}/fastq" },
-                mode: params.publish_dir_mode,
-                pattern: "*.fastq.gz"
-            ],
-            [
-                path: { "${params.outdir}/fastq/md5" },
-                mode: params.publish_dir_mode,
-                pattern: "*.md5"
-            ]
-        ]
-    }
-
-    withName: SYNAPSE_SHOW {
-        publishDir = [
-            path: { "${params.outdir}/metadata" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: SYNAPSE_TO_SAMPLESHEET {
-        publishDir = [
-            path: { "${params.outdir}/samplesheet" },
-            enabled: false
-        ]
-    }
-
-    withName: SYNAPSE_MERGE_SAMPLESHEET {
-        publishDir = [
-            path: { "${params.outdir}/samplesheet" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-}
diff --git a/modules/local/synapse_get/nextflow.config b/modules/local/synapse_get/nextflow.config
new file mode 100644
index 00000000..869f80aa
--- /dev/null
+++ b/modules/local/synapse_get/nextflow.config
@@ -0,0 +1,16 @@
+process {
+    withName: 'SYNAPSE_GET' {
+        publishDir = [
+            [
+                path: { "${params.outdir}/fastq" },
+                mode: params.publish_dir_mode,
+                pattern: "*.fastq.gz"
+            ],
+            [
+                path: { "${params.outdir}/fastq/md5" },
+                mode: params.publish_dir_mode,
+                pattern: "*.md5"
+            ]
+        ]
+    }
+}
\ No newline at end of file
diff --git a/modules/local/synapse_list/nextflow.config b/modules/local/synapse_list/nextflow.config
new file mode 100644
index 00000000..15124234
--- /dev/null
+++ b/modules/local/synapse_list/nextflow.config
@@ -0,0 +1,10 @@
+process {
+    withName: SYNAPSE_LIST {
+        ext.args = '--long'
+        publishDir = [
+            path: { "${params.outdir}/metadata" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+}
diff --git a/modules/local/synapse_merge_samplesheet/nextflow.config b/modules/local/synapse_merge_samplesheet/nextflow.config
new file mode 100644
index 00000000..9befef9c
--- /dev/null
+++ b/modules/local/synapse_merge_samplesheet/nextflow.config
@@ -0,0 +1,9 @@
+process {
+    withName: SYNAPSE_MERGE_SAMPLESHEET {
+        publishDir = [
+            path: { "${params.outdir}/samplesheet" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+}
\ No newline at end of file
diff --git a/modules/local/synapse_show/nextflow.config b/modules/local/synapse_show/nextflow.config
new file mode 100644
index 00000000..a1864dfe
--- /dev/null
+++ b/modules/local/synapse_show/nextflow.config
@@ -0,0 +1,9 @@
+process {
+    withName: 'SYNAPSE_SHOW' {
+        publishDir = [
+            path: { "${params.outdir}/metadata" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+}
\ No newline at end of file
diff --git a/modules/local/synapse_to_samplesheet/nextflow.config b/modules/local/synapse_to_samplesheet/nextflow.config
new file mode 100644
index 00000000..b286c12c
--- /dev/null
+++ b/modules/local/synapse_to_samplesheet/nextflow.config
@@ -0,0 +1,8 @@
+process {
+    withName: SYNAPSE_TO_SAMPLESHEET {
+        publishDir = [
+            path: { "${params.outdir}/samplesheet" },
+            enabled: false
+        ]
+    }
+}
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 40149dba..4ee1bb88 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -218,11 +218,12 @@ manifest {
 
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules/base.config'
-if ( params.input_type == 'sra' ) {
-    includeConfig 'workflows/sra/nextflow.config'
-}
-if ( params.input_type == 'synapse' ) {
-    includeConfig 'conf/modules/synapse.config'
+
+switch ( params.input_type ) {
+    case "sra":
+        includeConfig './workflows/sra/nextflow.config'
+    case "synapse":
+        includeConfig './workflows/synapse/nextflow.config'
 }
 
 // Function to ensure that resource requirements don't go beyond
diff --git a/workflows/synapse/nextflow.config b/workflows/synapse/nextflow.config
index e69de29b..01b71558 100644
--- a/workflows/synapse/nextflow.config
+++ b/workflows/synapse/nextflow.config
@@ -0,0 +1,5 @@
+includeConfig "../../modules/local/synapse_get/nextflow.config"
+includeConfig "../../modules/local/synapse_to_samplesheet/nextflow.config"
+includeConfig "../../modules/local/synapse_list/nextflow.config"
+includeConfig "../../modules/local/synapse_merge_samplesheet/nextflow.config"
+includeConfig "../../modules/local/synapse_show/nextflow.config"
\ No newline at end of file

From 63caf19616aacac49992ac058bff13b9fa60bb3e Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 18 Sep 2023 16:23:54 +0100
Subject: [PATCH 437/852] Revert switch for inheritance of correct config

---
 nextflow.config | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 4ee1bb88..84d8b42e 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -219,11 +219,10 @@ manifest {
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules/base.config'
 
-switch ( params.input_type ) {
-    case "sra":
-        includeConfig './workflows/sra/nextflow.config'
-    case "synapse":
-        includeConfig './workflows/synapse/nextflow.config'
+if ( params.input_type == "sra" ) {
+    includeConfig './workflows/sra/nextflow.config'
+} else if ( params.input_type == "synapse" ) {
+    includeConfig './workflows/synapse/nextflow.config'
 }
 
 // Function to ensure that resource requirements don't go beyond

From 1dba48c4a0d95bac089557a552ac5d17fcb08393 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 18 Sep 2023 16:36:14 +0100
Subject: [PATCH 438/852] Handle custom/dumpsoftwareversions via config

---
 conf/base.config                       |  9 ++++++---
 conf/modules/base.config               |  1 +
 modules/nf-core/custom/nextflow.config | 10 ++++++++++
 nextflow.config                        |  4 ++--
 workflows/nextflow.config              | 15 +++++++++++++++
 5 files changed, 34 insertions(+), 5 deletions(-)
 create mode 100644 modules/nf-core/custom/nextflow.config
 create mode 100644 workflows/nextflow.config

diff --git a/conf/base.config b/conf/base.config
index 4767e522..6af79a7b 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -14,6 +14,12 @@ process {
     memory = { check_max( 6.GB * task.attempt, 'memory' ) }
     time   = { check_max( 4.h  * task.attempt, 'time'   ) }
 
+    publishDir = [
+        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+    ]
+
     errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
     maxRetries    = 1
     maxErrors     = '-1'
@@ -57,7 +63,4 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
-    }
 }
diff --git a/conf/modules/base.config b/conf/modules/base.config
index d7eb6c86..035487c5 100644
--- a/conf/modules/base.config
+++ b/conf/modules/base.config
@@ -22,6 +22,7 @@ process {
     ]
 
     withName: CUSTOM_DUMPSOFTWAREVERSIONS {
+        cache = false
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },
             mode: params.publish_dir_mode,
diff --git a/modules/nf-core/custom/nextflow.config b/modules/nf-core/custom/nextflow.config
new file mode 100644
index 00000000..241654e7
--- /dev/null
+++ b/modules/nf-core/custom/nextflow.config
@@ -0,0 +1,10 @@
+process {
+    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
+        cache = false
+        publishDir = [
+            path: { "${params.outdir}/pipeline_info" },
+            mode: params.publish_dir_mode,
+            pattern: '*_versions.yml'
+        ]
+    }
+}
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 84d8b42e..a11a769d 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -216,8 +216,8 @@ manifest {
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
 
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules/base.config'
+// Module specific configs
+includeConfig 'modules/nf-core/custom/nextflow.config'
 
 if ( params.input_type == "sra" ) {
     includeConfig './workflows/sra/nextflow.config'
diff --git a/workflows/nextflow.config b/workflows/nextflow.config
new file mode 100644
index 00000000..db80204c
--- /dev/null
+++ b/workflows/nextflow.config
@@ -0,0 +1,15 @@
+process {
+    publishDir = [
+        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+    ]
+
+    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
+        publishDir = [
+            path: { "${params.outdir}/pipeline_info" },
+            mode: params.publish_dir_mode,
+            pattern: '*_versions.yml'
+        ]
+    }
+}

From f86a80ba422bf993783988ecf46c1485ea262e1f Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 18 Sep 2023 16:37:18 +0100
Subject: [PATCH 439/852] Update multiqc to v1.15

---
 modules.json                                        | 2 +-
 modules/nf-core/custom/dumpsoftwareversions/main.nf | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules.json b/modules.json
index 3137b88b..ab610dfb 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
                         "installed_by": ["modules"]
                     },
                     "custom/sratoolsncbisettings": {
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
index ebc87273..c9d014b1 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     label 'process_single'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda "bioconda::multiqc=1.14"
+    conda "bioconda::multiqc=1.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.14--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.15--pyhdfd78af_0' }"
 
     input:
     path versions

From 31e10bb27f66dd6fe6ec8bd8d92935b31434df3b Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 18 Sep 2023 16:39:20 +0100
Subject: [PATCH 440/852] Use switch statement to avoid nested if-else

---
 nextflow.config | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/nextflow.config b/nextflow.config
index a11a769d..dc2a5d2b 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -219,11 +219,24 @@ manifest {
 // Module specific configs
 includeConfig 'modules/nf-core/custom/nextflow.config'
 
+/*
 if ( params.input_type == "sra" ) {
     includeConfig './workflows/sra/nextflow.config'
 } else if ( params.input_type == "synapse" ) {
     includeConfig './workflows/synapse/nextflow.config'
 }
+*/
+
+switch ( params.input_type ) {
+    case "sra":
+        includeConfig './workflows/sra/nextflow.config'
+        break
+    case "synapse":
+        includeConfig './workflows/synapse/nextflow.config'
+        break
+    default:
+        break
+}
 
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit

From 105a65f8597b18b4397e6e075153090f9244d604 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 18 Sep 2023 16:44:42 +0100
Subject: [PATCH 441/852] Moved workflows configuration to
 workflows/nextflow.config

---
 .../nextflow.config                           |  0
 nextflow.config                               | 23 +++--------------
 workflows/nextflow.config                     | 25 ++++++++-----------
 3 files changed, 15 insertions(+), 33 deletions(-)
 rename modules/nf-core/custom/{ => dumpsoftwareversions}/nextflow.config (100%)

diff --git a/modules/nf-core/custom/nextflow.config b/modules/nf-core/custom/dumpsoftwareversions/nextflow.config
similarity index 100%
rename from modules/nf-core/custom/nextflow.config
rename to modules/nf-core/custom/dumpsoftwareversions/nextflow.config
diff --git a/nextflow.config b/nextflow.config
index dc2a5d2b..4fad92ca 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -217,26 +217,11 @@ manifest {
 }
 
 // Module specific configs
-includeConfig 'modules/nf-core/custom/nextflow.config'
+// Currently just dumpsoftwareversions
+includeConfig 'modules/nf-core/custom/dumpsoftwareversions/nextflow.config'
 
-/*
-if ( params.input_type == "sra" ) {
-    includeConfig './workflows/sra/nextflow.config'
-} else if ( params.input_type == "synapse" ) {
-    includeConfig './workflows/synapse/nextflow.config'
-}
-*/
-
-switch ( params.input_type ) {
-    case "sra":
-        includeConfig './workflows/sra/nextflow.config'
-        break
-    case "synapse":
-        includeConfig './workflows/synapse/nextflow.config'
-        break
-    default:
-        break
-}
+// Workflow specific configs
+includeConfig 'workflows/nextflow.config'
 
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit
diff --git a/workflows/nextflow.config b/workflows/nextflow.config
index db80204c..d27deb3a 100644
--- a/workflows/nextflow.config
+++ b/workflows/nextflow.config
@@ -1,15 +1,12 @@
-process {
-    publishDir = [
-        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-    ]
+// Read in specific config relating to workflow.
 
-    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            pattern: '*_versions.yml'
-        ]
-    }
-}
+switch ( params.input_type ) {
+    case "sra":
+        includeConfig './sra/nextflow.config'
+        break
+    case "synapse":
+        includeConfig './synapse/nextflow.config'
+        break
+    default:
+        break
+}
\ No newline at end of file

From 8b256afb6466d3834488adf9b8e58cf334bff6b7 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 18 Sep 2023 16:55:39 +0100
Subject: [PATCH 442/852] Addition of subworkflow specific configuration file

---
 .../nextflow.config                                             | 2 ++
 workflows/sra/nextflow.config                                   | 1 +
 2 files changed, 3 insertions(+)
 create mode 100644 subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config

diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config
new file mode 100644
index 00000000..b11c499f
--- /dev/null
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config
@@ -0,0 +1,2 @@
+includeConfig '../../../modules/nf-core/sratools/prefetch/nextflow.config'
+includeConfig '../../../modules/nf-core/sratools/fasterqdump/nextflow.config'
\ No newline at end of file
diff --git a/workflows/sra/nextflow.config b/workflows/sra/nextflow.config
index d4dd6f30..6b66fcd5 100644
--- a/workflows/sra/nextflow.config
+++ b/workflows/sra/nextflow.config
@@ -5,3 +5,4 @@ includeConfig "../../modules/local/sra_merge_samplesheet/nextflow.config"
 includeConfig "../../modules/local/sra_runinfo_to_ftp/nextflow.config"
 includeConfig "../../modules/local/sra_to_samplesheet/nextflow.config"
 includeConfig "../../modules/nf-core/sratools/prefetch/nextflow.config"
+includeConfig "../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config"

From 57b46e4d93b7d463f1d6079c8d88f73611690314 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 18 Sep 2023 16:57:25 +0100
Subject: [PATCH 443/852] Add empty config for sratoolsncbisettings to make it
 consistent

---
 modules/nf-core/custom/sratoolsncbisettings/nextflow.config    | 0
 .../nextflow.config                                            | 3 ++-
 2 files changed, 2 insertions(+), 1 deletion(-)
 create mode 100644 modules/nf-core/custom/sratoolsncbisettings/nextflow.config

diff --git a/modules/nf-core/custom/sratoolsncbisettings/nextflow.config b/modules/nf-core/custom/sratoolsncbisettings/nextflow.config
new file mode 100644
index 00000000..e69de29b
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config
index b11c499f..996c1888 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config
@@ -1,2 +1,3 @@
 includeConfig '../../../modules/nf-core/sratools/prefetch/nextflow.config'
-includeConfig '../../../modules/nf-core/sratools/fasterqdump/nextflow.config'
\ No newline at end of file
+includeConfig '../../../modules/nf-core/sratools/fasterqdump/nextflow.config'
+includeConfig '../../../modules/nf-core/custom/sratoolsncbisettings/nextflow.config'
\ No newline at end of file

From 32561205d47040660d539cdd9a37a1bc4d50a3b5 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 18 Sep 2023 17:07:55 +0100
Subject: [PATCH 444/852] CHANGELOG

---
 CHANGELOG.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 20dd21f8..92e31da4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -18,7 +18,8 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 ### Enhancements & fixes
 
 - [#166](https://github.com/nf-core/fetchngs/issues/175) - Add NF-TEST pipeline end-to-end tests for existing CI tests
-- [#184](https://github.com/nf-core/fetchngs/pull/184/files) Emits all files in workflow for testing and enabling workflow to be imported (not supported by Nextflow)
+- [#184](https://github.com/nf-core/fetchngs/pull/184) Emits all files in workflow for testing and enabling workflow to be imported (not supported by Nextflow)
+- [#195](https://github.com/nf-core/fetchngs/pull/195) Separate configuration files for all modules
 
 ## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-16
 

From 8284cc4003a71307d7e5eacf4e028eb72c23da7b Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 18 Sep 2023 17:09:51 +0100
Subject: [PATCH 445/852] Update change tags

---
 .github/tags.yml | 104 ++++++++++++++++++++++-------------------------
 1 file changed, 48 insertions(+), 56 deletions(-)

diff --git a/.github/tags.yml b/.github/tags.yml
index ed5c9dcc..9fc74a2c 100644
--- a/.github/tags.yml
+++ b/.github/tags.yml
@@ -14,74 +14,66 @@ sra_to_samplesheet:
 
 # workflow: sra
 sra_custom_ena_metadata_fields:
-  - conf/modules/sra.config
-  - modules/local/sra_ids_to_runinfo/main.nf
-  - modules/local/sra_runinfo_to_ftp/main.nf
-  - modules/local/sra_fastq_ftp/main.nf
-  - modules/local/sra_to_samplesheet/main.nf
-  - modules/local/sra_merge_samplesheet/main.nf
-  - workflows/sra/main.nf
+  - modules/local/sra_ids_to_runinfo/*
+  - modules/local/sra_runinfo_to_ftp/*
+  - modules/local/sra_fastq_ftp/*
+  - modules/local/sra_to_samplesheet/*
+  - modules/local/sra_merge_samplesheet/*
+  - workflows/sra/*
   - workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
 sra_default_parameters:
-  - conf/modules/sra.config
-  - modules/local/sra_ids_to_runinfo/main.nf
-  - modules/local/sra_runinfo_to_ftp/main.nf
-  - modules/local/sra_fastq_ftp/main.nf
-  - modules/local/sra_to_samplesheet/main.nf
-  - modules/local/sra_merge_samplesheet/main.nf
-  - workflows/sra/main.nf
+  - modules/local/sra_ids_to_runinfo/*
+  - modules/local/sra_runinfo_to_ftp/*
+  - modules/local/sra_fastq_ftp/*
+  - modules/local/sra_to_samplesheet/*
+  - modules/local/sra_merge_samplesheet/*
+  - workflows/sra/*
   - workflows/sra/tests/sra_default_parameters.nf.test
 sra_force_sratools_download:
-  - conf/modules/sra.config
-  - modules/local/sra_ids_to_runinfo/main.nf
-  - modules/local/sra_runinfo_to_ftp/main.nf
-  - modules/local/sra_fastq_ftp/main.nf
-  - modules/local/sra_to_samplesheet/main.nf
-  - modules/local/sra_merge_samplesheet/main.nf
-  - workflows/sra/main.nf
+  - modules/local/sra_ids_to_runinfo/*
+  - modules/local/sra_runinfo_to_ftp/*
+  - modules/local/sra_fastq_ftp/*
+  - modules/local/sra_to_samplesheet/*
+  - modules/local/sra_merge_samplesheet/*
+  - workflows/sra/*
   - workflows/sra/tests/sra_force_sratools_download.nf.test
 sra_nf_core_pipeline_atacseq:
-  - conf/modules/sra.config
-  - modules/local/sra_ids_to_runinfo/main.nf
-  - modules/local/sra_runinfo_to_ftp/main.nf
-  - modules/local/sra_fastq_ftp/main.nf
-  - modules/local/sra_to_samplesheet/main.nf
-  - modules/local/sra_merge_samplesheet/main.nf
-  - workflows/sra/main.nf
+  - modules/local/sra_ids_to_runinfo/*
+  - modules/local/sra_runinfo_to_ftp/*
+  - modules/local/sra_fastq_ftp/*
+  - modules/local/sra_to_samplesheet/*
+  - modules/local/sra_merge_samplesheet/*
+  - workflows/sra/*
   - workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
 sra_nf_core_pipeline_rnaseq:
-  - conf/modules/sra.config
-  - modules/local/sra_ids_to_runinfo/main.nf
-  - modules/local/sra_runinfo_to_ftp/main.nf
-  - modules/local/sra_fastq_ftp/main.nf
-  - modules/local/sra_to_samplesheet/main.nf
-  - modules/local/sra_merge_samplesheet/main.nf
-  - workflows/sra/main.nf
+  - modules/local/sra_ids_to_runinfo/*
+  - modules/local/sra_runinfo_to_ftp/*
+  - modules/local/sra_fastq_ftp/*
+  - modules/local/sra_to_samplesheet/*
+  - modules/local/sra_merge_samplesheet/*
+  - workflows/sra/*
   - workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
 sra_nf_core_pipeline_taxprofiler:
-  - conf/modules/sra.config
-  - modules/local/sra_ids_to_runinfo/main.nf
-  - modules/local/sra_runinfo_to_ftp/main.nf
-  - modules/local/sra_fastq_ftp/main.nf
-  - modules/local/sra_to_samplesheet/main.nf
-  - modules/local/sra_merge_samplesheet/main.nf
-  - workflows/sra/main.nf
+  - modules/local/sra_ids_to_runinfo/*
+  - modules/local/sra_runinfo_to_ftp/*
+  - modules/local/sra_fastq_ftp/*
+  - modules/local/sra_to_samplesheet/*
+  - modules/local/sra_merge_samplesheet/*
+  - workflows/sra/*
   - workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
 sra_nf_core_pipeline_viralrecon:
-  - conf/modules/sra.config
-  - modules/local/sra_ids_to_runinfo/main.nf
-  - modules/local/sra_runinfo_to_ftp/main.nf
-  - modules/local/sra_fastq_ftp/main.nf
-  - modules/local/sra_to_samplesheet/main.nf
-  - modules/local/sra_merge_samplesheet/main.nf
-  - workflows/sra/main.nf
+  - modules/local/sra_ids_to_runinfo/*
+  - modules/local/sra_runinfo_to_ftp/*
+  - modules/local/sra_fastq_ftp/*
+  - modules/local/sra_to_samplesheet/*
+  - modules/local/sra_merge_samplesheet/*
+  - workflows/sra/*
   - workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
 sra_skip_fastq_download:
-  - conf/modules/sra.config
-  - modules/local/sra_ids_to_runinfo/main.nf
-  - modules/local/sra_runinfo_to_ftp/main.nf
-  - modules/local/sra_fastq_ftp/main.nf
-  - modules/local/sra_to_samplesheet/main.nf
-  - modules/local/sra_merge_samplesheet/main.nf
-  - workflows/sra/main.nf
+  - modules/local/sra_ids_to_runinfo/*
+  - modules/local/sra_runinfo_to_ftp/*
+  - modules/local/sra_fastq_ftp/*
+  - modules/local/sra_to_samplesheet/*
+  - modules/local/sra_merge_samplesheet/*
+  - workflows/sra/*
   - workflows/sra/tests/sra_skip_fastq_download.nf.test

From 4bec2990de02ed84c3df5d37acea8a70e46a3934 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 21 Sep 2023 10:29:23 +0100
Subject: [PATCH 446/852] Revert dev to release 1.10

This reverts commit 624d420ecbb1f039695132fa02db78fcd65002f6, reversing
changes made to 1b9d1876b3973e436618652ffa485395f8f57213.
---
 .gitattributes                                |   1 -
 .github/workflows/ci.yml                      |  82 ++++------
 .gitignore                                    |   2 -
 .nf-core.yml                                  |  10 --
 CHANGELOG.md                                  |  16 --
 bin/sra_runinfo_to_ftp.py                     |   3 +-
 conf/test.config                              |   3 -
 conf/test_data.config                         |  36 -----
 docs/usage.md                                 |   6 -
 lib/NftestUtils.groovy                        |  38 -----
 modules.json                                  |   3 +-
 .../main.nf => multiqc_mappings_config.nf}    |   0
 .../tests/main.nf.test                        |  31 ----
 .../tests/main.nf.test.snap                   |  52 -------
 .../main.nf => sra_fastq_ftp.nf}              |   0
 .../local/sra_fastq_ftp/tests/main.nf.test    |  34 -----
 .../sra_fastq_ftp/tests/main.nf.test.snap     | 140 ------------------
 .../main.nf => sra_ids_to_runinfo.nf}         |   0
 .../sra_ids_to_runinfo/tests/main.nf.test     |  32 ----
 .../tests/main.nf.test.snap                   |  21 ---
 .../main.nf => sra_merge_samplesheet.nf}      |   0
 .../sra_merge_samplesheet/tests/main.nf.test  |  32 ----
 .../tests/main.nf.test.snap                   |  27 ----
 .../main.nf => sra_runinfo_to_ftp.nf}         |   0
 .../sra_runinfo_to_ftp/tests/main.nf.test     |  31 ----
 .../tests/main.nf.test.snap                   |  21 ---
 .../main.nf => sra_to_samplesheet.nf}         |   0
 .../sra_to_samplesheet/tests/main.nf.test     |  34 -----
 .../tests/main.nf.test.snap                   | 113 --------------
 .../{synapse_get/main.nf => synapse_get.nf}   |   0
 .../{synapse_list/main.nf => synapse_list.nf} |   0
 .../main.nf => synapse_merge_samplesheet.nf}  |   0
 .../{synapse_show/main.nf => synapse_show.nf} |   0
 .../main.nf => synapse_to_samplesheet.nf}     |   0
 .../custom-dumpsoftwareversions.diff          |  13 --
 .../templates/dumpsoftwareversions.py         |   1 +
 nextflow.config                               |   2 +-
 nf-test.config                                |  16 --
 workflows/{sra/main.nf => sra.nf}             |  16 +-
 workflows/sra/tests/main.nf.test              |  24 ---
 workflows/sra/tests/main.nf.test.snap         |  88 -----------
 .../sra_custom_ena_metadata_fields.nf.test    |  27 ----
 ...ra_custom_ena_metadata_fields.nf.test.snap |  88 -----------
 .../tests/sra_force_sratools_download.nf.test |  25 ----
 .../sra_force_sratools_download.nf.test.snap  |  67 ---------
 .../sra_nf_core_pipeline_atacseq.nf.test      |  25 ----
 .../sra_nf_core_pipeline_atacseq.nf.test.snap |  88 -----------
 .../tests/sra_nf_core_pipeline_rnaseq.nf.test |  25 ----
 .../sra_nf_core_pipeline_rnaseq.nf.test.snap  |  88 -----------
 .../sra_nf_core_pipeline_taxprofiler.nf.test  |  25 ----
 ..._nf_core_pipeline_taxprofiler.nf.test.snap |  88 -----------
 .../sra_nf_core_pipeline_viralrecon.nf.test   |  25 ----
 ...a_nf_core_pipeline_viralrecon.nf.test.snap |  88 -----------
 .../sra/tests/sra_skip_fastq_download.nf.test |  25 ----
 .../sra_skip_fastq_download.nf.test.snap      |  46 ------
 workflows/{synapse/main.nf => synapse.nf}     |  12 +-
 workflows/synapse/tests/main.nf.test          |  28 ----
 57 files changed, 47 insertions(+), 1651 deletions(-)
 delete mode 100644 conf/test_data.config
 delete mode 100644 lib/NftestUtils.groovy
 rename modules/local/{multiqc_mappings_config/main.nf => multiqc_mappings_config.nf} (100%)
 delete mode 100644 modules/local/multiqc_mappings_config/tests/main.nf.test
 delete mode 100644 modules/local/multiqc_mappings_config/tests/main.nf.test.snap
 rename modules/local/{sra_fastq_ftp/main.nf => sra_fastq_ftp.nf} (100%)
 delete mode 100644 modules/local/sra_fastq_ftp/tests/main.nf.test
 delete mode 100644 modules/local/sra_fastq_ftp/tests/main.nf.test.snap
 rename modules/local/{sra_ids_to_runinfo/main.nf => sra_ids_to_runinfo.nf} (100%)
 delete mode 100644 modules/local/sra_ids_to_runinfo/tests/main.nf.test
 delete mode 100644 modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap
 rename modules/local/{sra_merge_samplesheet/main.nf => sra_merge_samplesheet.nf} (100%)
 delete mode 100644 modules/local/sra_merge_samplesheet/tests/main.nf.test
 delete mode 100644 modules/local/sra_merge_samplesheet/tests/main.nf.test.snap
 rename modules/local/{sra_runinfo_to_ftp/main.nf => sra_runinfo_to_ftp.nf} (100%)
 delete mode 100644 modules/local/sra_runinfo_to_ftp/tests/main.nf.test
 delete mode 100644 modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap
 rename modules/local/{sra_to_samplesheet/main.nf => sra_to_samplesheet.nf} (100%)
 delete mode 100644 modules/local/sra_to_samplesheet/tests/main.nf.test
 delete mode 100644 modules/local/sra_to_samplesheet/tests/main.nf.test.snap
 rename modules/local/{synapse_get/main.nf => synapse_get.nf} (100%)
 rename modules/local/{synapse_list/main.nf => synapse_list.nf} (100%)
 rename modules/local/{synapse_merge_samplesheet/main.nf => synapse_merge_samplesheet.nf} (100%)
 rename modules/local/{synapse_show/main.nf => synapse_show.nf} (100%)
 rename modules/local/{synapse_to_samplesheet/main.nf => synapse_to_samplesheet.nf} (100%)
 delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff
 delete mode 100644 nf-test.config
 rename workflows/{sra/main.nf => sra.nf} (89%)
 delete mode 100644 workflows/sra/tests/main.nf.test
 delete mode 100644 workflows/sra/tests/main.nf.test.snap
 delete mode 100644 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
 delete mode 100644 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
 delete mode 100644 workflows/sra/tests/sra_force_sratools_download.nf.test
 delete mode 100644 workflows/sra/tests/sra_force_sratools_download.nf.test.snap
 delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
 delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
 delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
 delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
 delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
 delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
 delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
 delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
 delete mode 100644 workflows/sra/tests/sra_skip_fastq_download.nf.test
 delete mode 100644 workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
 rename workflows/{synapse/main.nf => synapse.nf} (89%)
 delete mode 100644 workflows/synapse/tests/main.nf.test

diff --git a/.gitattributes b/.gitattributes
index c1c17000..7a2dabc2 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1,5 +1,4 @@
 *.config linguist-language=nextflow
 *.nf.test linguist-language=nextflow
-tests/**/*nf.test.snap linguist-generated
 modules/nf-core/** linguist-generated
 subworkflows/nf-core/** linguist-generated
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 451613fb..5bef3edd 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,61 +1,31 @@
-# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 name: nf-core CI
+# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on:
   push:
     branches:
       - dev
   pull_request:
-    branches:
-      - dev
-      - master
   release:
-    types:
-      - "published"
+    types: [published]
 
 env:
   NXF_ANSI_LOG: false
-  NFTEST_VER: "0.7.3"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
 
 jobs:
-  define_nxf_versions:
-    name: Choose nextflow versions to test against depending on target branch
-    runs-on: ubuntu-latest
-    outputs:
-      matrix: ${{ steps.nxf_versions.outputs.matrix }}
-    steps:
-      - id: nxf_versions
-        run: |
-          if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
-            echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT
-          else
-            echo matrix='["latest-everything", "22.10.1"]' | tee -a $GITHUB_OUTPUT
-          fi
-
   test:
     name: Run pipeline with test data
-    needs: define_nxf_versions
+    # Only run on push if this is the nf-core dev branch (merged PRs)
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}"
     runs-on: ubuntu-latest
     strategy:
-      fail-fast: false
       matrix:
-        NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
-        test_tags:
-          - "modules_local"
-          - "sra_default_parameters"
-          - "sra_custom_ena_metadata_fields"
-          - "sra_force_sratools_download"
-          - "sra_nf_core_pipeline_atacseq"
-          - "sra_nf_core_pipeline_rnaseq"
-          - "sra_nf_core_pipeline_taxprofiler"
-          - "sra_nf_core_pipeline_viralrecon"
-          - "sra_skip_fastq_download"
-        profile:
-          - "docker"
-
+        NXF_VER:
+          - "22.10.1"
+          - "latest-everything"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v3
@@ -65,23 +35,29 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Install nf-test
+      - name: Run pipeline with test data
         run: |
-          wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
-          sudo mv nf-test /usr/local/bin/
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
 
-      - name: Run nf-test
-        run: |
-          nf-test test --tag ${{ matrix.test_tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml
+  parameters:
+    name: Test workflow parameters
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        parameters:
+          - "--nf_core_pipeline rnaseq"
+          - "--ena_metadata_fields run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5 --sample_mapping_fields run_accession,library_layout"
+          - "--skip_fastq_download"
+          - "--force_sratools_download"
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
 
-      - name: Output log on failure
-        if: failure()
+      - name: Install Nextflow
         run: |
-          sudo apt install bat > /dev/null
-          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml
-
-      - name: Publish Test Report
-        uses: mikepenz/action-junit-report@v3
-        if: always() # always run even if the previous step fails
-        with:
-          report_paths: test.xml
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+      - name: Run pipeline with various parameters
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
diff --git a/.gitignore b/.gitignore
index 935326a7..5124c9ac 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,5 +6,3 @@ results/
 testing/
 testing*
 *.pyc
-.nf-test/
-nf-test
diff --git a/.nf-core.yml b/.nf-core.yml
index 253f86e2..cafd671c 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,15 +1,5 @@
 repository_type: pipeline
 lint:
   files_unchanged:
-    - .github/CONTRIBUTING.md
-    - .github/ISSUE_TEMPLATE/bug_report.yml
-    - assets/nf-core-fetchngs_logo_light.png
     - assets/sendmail_template.txt
     - lib/NfcoreTemplate.groovy
-    - .gitattributes
-  actions_ci: false
-  multiqc_config: false
-  nextflow_config:
-    - "params.validationShowHiddenParams"
-    - "params.validationSchemaIgnoreParams"
-  schema_params: false
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 146b93b6..12ef2d50 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,22 +3,6 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[1.10.1](https://github.com/nf-core/fetchngs/releases/tag/1.10.1)] - 2023-06-29
-
-### Credits
-
-Special thanks to the following for their contributions to the release:
-
-- [Sateesh Peri](https://github.com/sateeshperi)
-- [Edmund Miller](https://github.com/Emiller88)
-- [Maxime Garcia](https://github.com/maxulysse)
-
-Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
-
-### Enhancements & fixes
-
-- [#166](https://github.com/nf-core/fetchngs/issues/175) - Add NF-TEST pipeline end-to-end tests for existing CI tests
-
 ## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-16
 
 ### Credits
diff --git a/bin/sra_runinfo_to_ftp.py b/bin/sra_runinfo_to_ftp.py
index c220f74e..ef80ec80 100755
--- a/bin/sra_runinfo_to_ftp.py
+++ b/bin/sra_runinfo_to_ftp.py
@@ -61,8 +61,7 @@ def parse_sra_runinfo(file_in):
     with open(file_in, "r", newline="") as fin:
         reader = csv.DictReader(fin, delimiter="\t", skipinitialspace=True)
         header = list(reader.fieldnames)
-        missing = frozenset(columns).difference(frozenset(header))
-        if missing:
+        if missing := frozenset(columns).difference(frozenset(header)):
             logger.critical(f"The following expected columns are missing from {file_in}: " f"{', '.join(missing)}.")
             sys.exit(1)
         for row in reader:
diff --git a/conf/test.config b/conf/test.config
index 0bc98595..3c58e9cf 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -22,6 +22,3 @@ params {
     // Input data
     input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv'
 }
-
-// Load test_data.config for nf-tests
-includeConfig 'test_data.config'
diff --git a/conf/test_data.config b/conf/test_data.config
deleted file mode 100644
index 42d3d818..00000000
--- a/conf/test_data.config
+++ /dev/null
@@ -1,36 +0,0 @@
-params {
-    // Base directory for test data
-    test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs"
-
-    merge_samplesheet_ids = [ "DRX024467_DRR026872", "SRX11047067_SRR14709033", "SRX9504942_SRR13055517", "DRX026011_DRR028935", "SRX17709227_SRR21711856", "SRX9504942_SRR13055518", "ERX1188904_ERR1109373", "SRX17709228_SRR21711855", "SRX9504942_SRR13055519", "ERX1234253_ERR1160846", "SRX6725035_SRR9984183", "SRX9504942_SRR13055520", "SRX10940790_SRR14593545", "SRX9315476_SRR12848126", "SRX9626017_SRR13191702" ]
-
-    def merge_samplesheet_url  = "${params.test_data_base}/modules/local/sra_merge_samplesheet/samplesheets/"
-    def merge_mappings_url     = "${params.test_data_base}/modules/local/sra_merge_samplesheet/mappings/"
-    def merge_samplesheet_urls = []
-    def merge_mappings_urls    = []
-
-    merge_samplesheet_ids.each { id ->
-        merge_samplesheet_urls += "${merge_samplesheet_url}${id}.samplesheet.csv"
-        merge_mappings_urls    += "${merge_mappings_url}/${id}.mappings.csv"
-    }
-
-    fastq_ftp_ids      = ["SRR13191702"]
-    def fastq_ftp_url  = "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/"
-    def fastq_ftp_urls = []
-
-    fastq_ftp_ids.each { id ->
-        fastq_ftp_urls += "${fastq_ftp_url}${id}_1.fastq.gz"
-        fastq_ftp_urls += "${fastq_ftp_url}${id}_2.fastq.gz"
-    }
-
-    test_data {
-        'modules_local' {
-                multiqc_mappings_config             = "${params.test_data_base}/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv"
-                sra_merge_samplesheet_samplesheets  = merge_samplesheet_urls
-                sra_merge_samplesheet_mappings      = merge_mappings_urls
-                sra_to_samplesheet                  = "${params.test_data_base}/modules/local/sra_to_samplesheet/SRX9626017_SRR13191702.mappings.csv"
-                sra_fastq_ftp                       = fastq_ftp_urls
-                sra_runinfo_to_ftp                  = "${params.test_data_base}/modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv"
-        }
-    }
-}
diff --git a/docs/usage.md b/docs/usage.md
index b2cd7b50..0720a680 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -70,12 +70,6 @@ From v1.9 of this pipeline the default `strandedness` in the output samplesheet
 
 If FTP connections are blocked on your network use the [`--force_sratools_download`](https://nf-co.re/fetchngs/parameters#force_sratools_download) parameter to force the pipeline to download data using sra-tools instead of the ENA FTP.
 
-### Downloading 10X Genomics Data
-
-As of v1.10.0, this pipeline now supports downloading of 10X Genomics data. For 10X data sets, the output needs to be split into three fastq files, consisting of the feature barcode+UMI, cDNA sequence reads, and sample index. Adding the `--force_sratools_download` parameter will cause the pipeline to use the sra-tools fasterq-dump program with appropriate setting to ensure that all three files are generated.
-
-Please note that in our experience the downloaded R1, R2, and R3 fastq files do not always correspond to the same data types across different submissions. In many cases, R1 will be the cell barcode + UMI, R2 is the cDNA sequence, and R3 is the sample index. However, this is not alway the case. Users are strongly encouraged to verify their data before proceeding with downstream analysis.
-
 ### Downloading dbGAP data with JWT
 
 As of v1.10.0, the SRA Toolkit used in this pipeline can be configured to access protected data from dbGAP using a [JWT cart file](https://www.ncbi.nlm.nih.gov/sra/docs/sra-dbGAP-cloud-download/) on a supported cloud computing environment (Amazon Web Services or Google Cloud Platform). The JWT cart file can be specified with `--dbgap_key /path/to/cart.jwt`.
diff --git a/lib/NftestUtils.groovy b/lib/NftestUtils.groovy
deleted file mode 100644
index ce6fc8b4..00000000
--- a/lib/NftestUtils.groovy
+++ /dev/null
@@ -1,38 +0,0 @@
-// Helper functions for pipeline tests
-
-class NftestUtils {
-
-    // Function to remove Nextflow version from software_versions.yml
-    public static String removeNextflowVersion(outputDir) {
-        def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
-        if (softwareVersions.containsKey("Workflow")) {
-            softwareVersions.Workflow.remove("Nextflow")
-        }
-        return softwareVersions
-    }
-
-    // Function to filter lines from a file and return a new file
-    public static File filterLines(String inFilePath, int linesToSkip) {
-        if (linesToSkip >= 0) {
-            File inputFile = new File(inFilePath)
-            File outputFile = new File(inFilePath + ".filtered")
-            def lineCount = 0
-            inputFile.eachLine { line ->
-                lineCount++
-                if (lineCount > linesToSkip) {
-                    outputFile.append(line + '\n')
-                }
-            }
-            return outputFile
-        } else {
-            File inputFile = new File(inFilePath)
-            File outputFile = new File(inFilePath + ".filtered")
-            def lines = inputFile.readLines()
-            def totalLines = lines.size()
-            lines.take(totalLines + linesToSkip).each { line ->
-                outputFile.append(line + '\n')
-            }
-            return outputFile
-        }
-    }
-}
diff --git a/modules.json b/modules.json
index 2244addd..3137b88b 100644
--- a/modules.json
+++ b/modules.json
@@ -8,8 +8,7 @@
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff"
+                        "installed_by": ["modules"]
                     },
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
diff --git a/modules/local/multiqc_mappings_config/main.nf b/modules/local/multiqc_mappings_config.nf
similarity index 100%
rename from modules/local/multiqc_mappings_config/main.nf
rename to modules/local/multiqc_mappings_config.nf
diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test
deleted file mode 100644
index 3bf79537..00000000
--- a/modules/local/multiqc_mappings_config/tests/main.nf.test
+++ /dev/null
@@ -1,31 +0,0 @@
-nextflow_process {
-
-    name "Test process: MULTIQC_MAPPINGS_CONFIG"
-    script "modules/local/multiqc_mappings_config/main.nf"
-    process "MULTIQC_MAPPINGS_CONFIG"
-    tag "modules"
-    tag "modules_local"
-    tag "multiqc_mappings_config"
-
-    test("Should run without failures") {
-
-        when {
-            params {
-                outdir = "$outputDir"
-            }
-
-            process {
-                """
-                input[0] = file(params.test_data['modules_local']['multiqc_mappings_config'], checkIfExists: true)
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-}
diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap
deleted file mode 100644
index 9cf7fb38..00000000
--- a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap
+++ /dev/null
@@ -1,52 +0,0 @@
-{
-    "SRX9626017_SRR13191702": {
-        "content": [
-            {
-                "0": [
-                    [
-                        "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
-                        "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
-                ],
-                "versions": [
-                    "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
-                ],
-                "yml": [
-                    [
-                        "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
-                        "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
-                    ]
-                ]
-            }
-        ],
-        "timestamp": "2023-08-17T12:02:35+0000"
-    },
-    "Should run without failures": {
-        "content": [
-            {
-                "0": [
-                    [
-                        "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
-                        "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
-                ],
-                "versions": [
-                    "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
-                ],
-                "yml": [
-                    [
-                        "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
-                        "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
-                    ]
-                ]
-            }
-        ],
-        "timestamp": "2023-08-17T12:02:35+0000"
-    }
-}
\ No newline at end of file
diff --git a/modules/local/sra_fastq_ftp/main.nf b/modules/local/sra_fastq_ftp.nf
similarity index 100%
rename from modules/local/sra_fastq_ftp/main.nf
rename to modules/local/sra_fastq_ftp.nf
diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test
deleted file mode 100644
index 7892d156..00000000
--- a/modules/local/sra_fastq_ftp/tests/main.nf.test
+++ /dev/null
@@ -1,34 +0,0 @@
-nextflow_process {
-
-    name "Test process: SRA_FASTQ_FTP"
-    script "modules/local/sra_fastq_ftp/main.nf"
-    process "SRA_FASTQ_FTP"
-    tag "modules"
-    tag "modules_local"
-    tag "sra_fastq_ftp"
-
-    test("Should run without failures") {
-
-        when {
-            params {
-                outdir = "$outputDir"
-            }
-
-            process {
-                """
-                input[0] = [
-                    [ id:'SRX9626017_SRR13191702', single_end:false, md5_1: '89c5be920021a035084d8aeb74f32df7', md5_2: '56271be38a80db78ef3bdfc5d9909b98' ], // meta map
-                    params.test_data['modules_local']['sra_fastq_ftp']
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-}
diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap
deleted file mode 100644
index c0d5ffdc..00000000
--- a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap
+++ /dev/null
@@ -1,140 +0,0 @@
-{
-    "SRX9626017_SRR13191702": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "SRX9626017_SRR13191702",
-                            "single_end": false,
-                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
-                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
-                        },
-                        [
-                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
-                        ]
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "SRX9626017_SRR13191702",
-                            "single_end": false,
-                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
-                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
-                        },
-                        [
-                            "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
-                            "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
-                        ]
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b"
-                ],
-                "fastq": [
-                    [
-                        {
-                            "id": "SRX9626017_SRR13191702",
-                            "single_end": false,
-                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
-                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
-                        },
-                        [
-                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
-                        ]
-                    ]
-                ],
-                "md5": [
-                    [
-                        {
-                            "id": "SRX9626017_SRR13191702",
-                            "single_end": false,
-                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
-                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
-                        },
-                        [
-                            "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
-                            "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
-                        ]
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b"
-                ]
-            }
-        ],
-        "timestamp": "2023-08-06T23:31:57+0000"
-    },
-    "Should run without failures": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "SRX9626017_SRR13191702",
-                            "single_end": false,
-                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
-                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
-                        },
-                        [
-                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
-                        ]
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "SRX9626017_SRR13191702",
-                            "single_end": false,
-                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
-                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
-                        },
-                        [
-                            "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
-                            "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
-                        ]
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b"
-                ],
-                "fastq": [
-                    [
-                        {
-                            "id": "SRX9626017_SRR13191702",
-                            "single_end": false,
-                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
-                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
-                        },
-                        [
-                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
-                        ]
-                    ]
-                ],
-                "md5": [
-                    [
-                        {
-                            "id": "SRX9626017_SRR13191702",
-                            "single_end": false,
-                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
-                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
-                        },
-                        [
-                            "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
-                            "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
-                        ]
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b"
-                ]
-            }
-        ],
-        "timestamp": "2023-08-06T23:31:57+0000"
-    }
-}
\ No newline at end of file
diff --git a/modules/local/sra_ids_to_runinfo/main.nf b/modules/local/sra_ids_to_runinfo.nf
similarity index 100%
rename from modules/local/sra_ids_to_runinfo/main.nf
rename to modules/local/sra_ids_to_runinfo.nf
diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test
deleted file mode 100644
index f8a44086..00000000
--- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test
+++ /dev/null
@@ -1,32 +0,0 @@
-nextflow_process {
-
-    name "Test process: SRA_IDS_TO_RUNINFO"
-    script "modules/local/sra_ids_to_runinfo/main.nf"
-    process "SRA_IDS_TO_RUNINFO"
-    tag "modules"
-    tag "modules_local"
-    tag "sra_ids_to_runinfo"
-
-    test("Should run without failures") {
-
-        when {
-            params {
-                outdir = "$outputDir"
-            }
-
-            process {
-                """
-                input[0] = 'SRR13191702'
-                input[1] = ''
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-}
diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap
deleted file mode 100644
index dbca931f..00000000
--- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap
+++ /dev/null
@@ -1,21 +0,0 @@
-{
-    "Should run without failures": {
-        "content": [
-            {
-                "0": [
-                    "SRR13191702.runinfo.tsv:md5,3a1be35781ca6e8a28d8fd4d2f3bbe85"
-                ],
-                "1": [
-                    "versions.yml:md5,1c14442e9b494b586eafe41e77300fae"
-                ],
-                "tsv": [
-                    "SRR13191702.runinfo.tsv:md5,3a1be35781ca6e8a28d8fd4d2f3bbe85"
-                ],
-                "versions": [
-                    "versions.yml:md5,1c14442e9b494b586eafe41e77300fae"
-                ]
-            }
-        ],
-        "timestamp": "2023-08-06T23:30:51+0000"
-    }
-}
\ No newline at end of file
diff --git a/modules/local/sra_merge_samplesheet/main.nf b/modules/local/sra_merge_samplesheet.nf
similarity index 100%
rename from modules/local/sra_merge_samplesheet/main.nf
rename to modules/local/sra_merge_samplesheet.nf
diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test b/modules/local/sra_merge_samplesheet/tests/main.nf.test
deleted file mode 100644
index e37039bd..00000000
--- a/modules/local/sra_merge_samplesheet/tests/main.nf.test
+++ /dev/null
@@ -1,32 +0,0 @@
-nextflow_process {
-
-    name "Test process: SRA_MERGE_SAMPLESHEET"
-    script "modules/local/sra_merge_samplesheet/main.nf"
-    process "SRA_MERGE_SAMPLESHEET"
-    tag "modules"
-    tag "modules_local"
-    tag "sra_merge_samplesheet"
-
-    test("Should run without failures") {
-
-        when {
-            params {
-                outdir = "$outputDir"
-            }
-
-            process {
-                """
-                input[0] = params.test_data['modules_local']['sra_merge_samplesheet_samplesheets'].collect { file(it, checkIfExists: true) }
-                input[1] = params.test_data['modules_local']['sra_merge_samplesheet_mappings'].collect { file(it, checkIfExists: true) }
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-}
diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap b/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap
deleted file mode 100644
index c5f06aac..00000000
--- a/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap
+++ /dev/null
@@ -1,27 +0,0 @@
-{
-    "Should run without failures": {
-        "content": [
-            {
-                "0": [
-                    "samplesheet.csv:md5,ef756557b0735becd2574c2a3f5840b2"
-                ],
-                "1": [
-                    "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253"
-                ],
-                "2": [
-                    "versions.yml:md5,410006679d5e496d8c55e58e78ca6b34"
-                ],
-                "mappings": [
-                    "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253"
-                ],
-                "samplesheet": [
-                    "samplesheet.csv:md5,ef756557b0735becd2574c2a3f5840b2"
-                ],
-                "versions": [
-                    "versions.yml:md5,410006679d5e496d8c55e58e78ca6b34"
-                ]
-            }
-        ],
-        "timestamp": "2023-07-06T13:16:36+0000"
-    }
-}
\ No newline at end of file
diff --git a/modules/local/sra_runinfo_to_ftp/main.nf b/modules/local/sra_runinfo_to_ftp.nf
similarity index 100%
rename from modules/local/sra_runinfo_to_ftp/main.nf
rename to modules/local/sra_runinfo_to_ftp.nf
diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
deleted file mode 100644
index 1558ff39..00000000
--- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
+++ /dev/null
@@ -1,31 +0,0 @@
-nextflow_process {
-
-    name "Test process: SRA_RUNINFO_TO_FTP"
-    script "modules/local/sra_runinfo_to_ftp/main.nf"
-    process "SRA_RUNINFO_TO_FTP"
-    tag "modules"
-    tag "modules_local"
-    tag "sra_runinfo_to_ftp"
-
-    test("Should run without failures") {
-
-        when {
-            params {
-                outdir = "$outputDir"
-            }
-
-            process {
-                """
-                input[0] = file(params.test_data['modules_local']['sra_runinfo_to_ftp'], checkIfExists: true)
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-}
diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap
deleted file mode 100644
index 71a25f99..00000000
--- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap
+++ /dev/null
@@ -1,21 +0,0 @@
-{
-    "Should run without failures": {
-        "content": [
-            {
-                "0": [
-                    "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e"
-                ],
-                "1": [
-                    "versions.yml:md5,e95f8185f665127a73622a19d321bcca"
-                ],
-                "tsv": [
-                    "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e"
-                ],
-                "versions": [
-                    "versions.yml:md5,e95f8185f665127a73622a19d321bcca"
-                ]
-            }
-        ],
-        "timestamp": "2023-08-06T23:13:20+0000"
-    }
-}
\ No newline at end of file
diff --git a/modules/local/sra_to_samplesheet/main.nf b/modules/local/sra_to_samplesheet.nf
similarity index 100%
rename from modules/local/sra_to_samplesheet/main.nf
rename to modules/local/sra_to_samplesheet.nf
diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test
deleted file mode 100644
index b2ec5b11..00000000
--- a/modules/local/sra_to_samplesheet/tests/main.nf.test
+++ /dev/null
@@ -1,34 +0,0 @@
-nextflow_process {
-
-    name "Test process: SRA_TO_SAMPLESHEET"
-    script "modules/local/sra_to_samplesheet/main.nf"
-    process "SRA_TO_SAMPLESHEET"
-    tag "modules"
-    tag "modules_local"
-    tag "sra_to_samplesheet"
-
-    test("Should run without failures") {
-
-        when {
-            params {
-                outdir = "$outputDir"
-            }
-
-            process {
-                """
-                input[0] = [id:'ERX1188904_ERR1109373', run_accession:'ERR1109373', experiment_accession:'ERX1188904', sample_accession:'SAMEA3643867',  experiment_alias:'ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7', run_alias:'ena-RUN-CAM-03-11-2015-17:01:52:847-7',  sample_alias:'sample_56', study_alias:'ena-STUDY-CAM-02-11-2015-17:42:24:189-13', library_layout:'PAIRED', experiment_title:'Illumina HiSeq 2500 paired end sequencing', sample_title:'RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome', sample_description:'RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome', fastq_md5:'8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9', fastq_ftp:'ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz', fastq_1:'./results/fastq/ERX1188904_ERR1109373_1.fastq.gz', fastq_2:'./results/fastq/ERX1188904_ERR1109373_2.fastq.gz', md5_1:'9fd57225d6c07a31843276d6df9b15c0', md5_2:'5a62e8f785687dce890cfb4fe3e607f9', single_end:false]
-                input[1] = 'rnaseq'
-                input[2] = 'auto'
-                input[3] = 'experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description'
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-}
diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap
deleted file mode 100644
index 8b5f4947..00000000
--- a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap
+++ /dev/null
@@ -1,113 +0,0 @@
-{
-    "Should run without failures": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "ERX1188904_ERR1109373",
-                            "run_accession": "ERR1109373",
-                            "experiment_accession": "ERX1188904",
-                            "sample_accession": "SAMEA3643867",
-                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
-                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
-                            "sample_alias": "sample_56",
-                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
-                            "library_layout": "PAIRED",
-                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
-                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
-                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
-                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
-                            "single_end": false
-                        },
-                        "ERX1188904_ERR1109373.samplesheet.csv:md5,e7898191d57258e049ee7129d36f5c08"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "ERX1188904_ERR1109373",
-                            "run_accession": "ERR1109373",
-                            "experiment_accession": "ERX1188904",
-                            "sample_accession": "SAMEA3643867",
-                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
-                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
-                            "sample_alias": "sample_56",
-                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
-                            "library_layout": "PAIRED",
-                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
-                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
-                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
-                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
-                            "single_end": false
-                        },
-                        "ERX1188904_ERR1109373.mappings.csv:md5,d09ddb4f0709675e5dfe1eadf12c608f"
-                    ]
-                ],
-                "mappings": [
-                    [
-                        {
-                            "id": "ERX1188904_ERR1109373",
-                            "run_accession": "ERR1109373",
-                            "experiment_accession": "ERX1188904",
-                            "sample_accession": "SAMEA3643867",
-                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
-                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
-                            "sample_alias": "sample_56",
-                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
-                            "library_layout": "PAIRED",
-                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
-                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
-                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
-                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
-                            "single_end": false
-                        },
-                        "ERX1188904_ERR1109373.mappings.csv:md5,d09ddb4f0709675e5dfe1eadf12c608f"
-                    ]
-                ],
-                "samplesheet": [
-                    [
-                        {
-                            "id": "ERX1188904_ERR1109373",
-                            "run_accession": "ERR1109373",
-                            "experiment_accession": "ERX1188904",
-                            "sample_accession": "SAMEA3643867",
-                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
-                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
-                            "sample_alias": "sample_56",
-                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
-                            "library_layout": "PAIRED",
-                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
-                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
-                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
-                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
-                            "single_end": false
-                        },
-                        "ERX1188904_ERR1109373.samplesheet.csv:md5,e7898191d57258e049ee7129d36f5c08"
-                    ]
-                ]
-            }
-        ],
-        "timestamp": "2023-08-17T10:55:52+0000"
-    }
-}
\ No newline at end of file
diff --git a/modules/local/synapse_get/main.nf b/modules/local/synapse_get.nf
similarity index 100%
rename from modules/local/synapse_get/main.nf
rename to modules/local/synapse_get.nf
diff --git a/modules/local/synapse_list/main.nf b/modules/local/synapse_list.nf
similarity index 100%
rename from modules/local/synapse_list/main.nf
rename to modules/local/synapse_list.nf
diff --git a/modules/local/synapse_merge_samplesheet/main.nf b/modules/local/synapse_merge_samplesheet.nf
similarity index 100%
rename from modules/local/synapse_merge_samplesheet/main.nf
rename to modules/local/synapse_merge_samplesheet.nf
diff --git a/modules/local/synapse_show/main.nf b/modules/local/synapse_show.nf
similarity index 100%
rename from modules/local/synapse_show/main.nf
rename to modules/local/synapse_show.nf
diff --git a/modules/local/synapse_to_samplesheet/main.nf b/modules/local/synapse_to_samplesheet.nf
similarity index 100%
rename from modules/local/synapse_to_samplesheet/main.nf
rename to modules/local/synapse_to_samplesheet.nf
diff --git a/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff b/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff
deleted file mode 100644
index a7893b24..00000000
--- a/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff
+++ /dev/null
@@ -1,13 +0,0 @@
-Changes in module 'nf-core/custom/dumpsoftwareversions'
---- modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
-+++ modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
-@@ -75,7 +75,6 @@
-             versions_by_module[module] = process_versions
- 
-     versions_by_module["Workflow"] = {
--        "Nextflow": "$workflow.nextflow.version",
-         "$workflow.manifest.name": "$workflow.manifest.version",
-     }
- 
-
-************************************************************
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
index 33d127f8..da033408 100755
--- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
@@ -75,6 +75,7 @@ def main():
             versions_by_module[module] = process_versions
 
     versions_by_module["Workflow"] = {
+        "Nextflow": "$workflow.nextflow.version",
         "$workflow.manifest.name": "$workflow.manifest.version",
     }
 
diff --git a/nextflow.config b/nextflow.config
index 6eb5c18d..1e9aaed0 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -212,7 +212,7 @@ manifest {
     description     = """Pipeline to fetch metadata and raw FastQ files from public databases"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '1.10.1'
+    version         = '1.10.0'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
 
diff --git a/nf-test.config b/nf-test.config
deleted file mode 100644
index 0799cb40..00000000
--- a/nf-test.config
+++ /dev/null
@@ -1,16 +0,0 @@
-config {
-    // location for all nf-tests
-    testsDir "."
-
-    // nf-test directory including temporary files for each test
-    workDir ".nf-test"
-
-    // location of library folder that is added automatically to the classpath
-    libDir "lib/"
-
-    // location of an optional nextflow.config file specific for executing tests
-    configFile "nextflow.config"
-
-    // run all test with the defined docker profile from the main nextflow.config
-    profile ""
-}
diff --git a/workflows/sra/main.nf b/workflows/sra.nf
similarity index 89%
rename from workflows/sra/main.nf
rename to workflows/sra.nf
index 512a73d4..44ff8346 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra.nf
@@ -19,12 +19,12 @@ WorkflowSra.initialise(params, valid_params)
 ========================================================================================
 */
 
-include { SRA_IDS_TO_RUNINFO      } from '../../modules/local/sra_ids_to_runinfo'
-include { SRA_RUNINFO_TO_FTP      } from '../../modules/local/sra_runinfo_to_ftp'
-include { SRA_FASTQ_FTP           } from '../../modules/local/sra_fastq_ftp'
-include { SRA_TO_SAMPLESHEET      } from '../../modules/local/sra_to_samplesheet'
-include { SRA_MERGE_SAMPLESHEET   } from '../../modules/local/sra_merge_samplesheet'
-include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_config'
+include { SRA_IDS_TO_RUNINFO      } from '../modules/local/sra_ids_to_runinfo'
+include { SRA_RUNINFO_TO_FTP      } from '../modules/local/sra_runinfo_to_ftp'
+include { SRA_FASTQ_FTP           } from '../modules/local/sra_fastq_ftp'
+include { SRA_TO_SAMPLESHEET      } from '../modules/local/sra_to_samplesheet'
+include { SRA_MERGE_SAMPLESHEET   } from '../modules/local/sra_merge_samplesheet'
+include { MULTIQC_MAPPINGS_CONFIG } from '../modules/local/multiqc_mappings_config'
 
 /*
 ========================================================================================
@@ -32,9 +32,9 @@ include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_c
 ========================================================================================
 */
 
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions'
+include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
 
-include { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS } from '../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools'
+include { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS } from '../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main'
 
 /*
 ========================================================================================
diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
deleted file mode 100644
index 39a5cc3f..00000000
--- a/workflows/sra/tests/main.nf.test
+++ /dev/null
@@ -1,24 +0,0 @@
-nextflow_pipeline {
-
-    name "Test workflow: sra.nf"
-    script "main.nf"
-    tag "workflows"
-    tag "workflows_sra"
-    tag "sra_default_parameters"
-
-    test("Parameters: default") {
-
-        when {
-            params {
-                outdir = "$outputDir"
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-}
diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
deleted file mode 100644
index 88ea9654..00000000
--- a/workflows/sra/tests/main.nf.test.snap
+++ /dev/null
@@ -1,88 +0,0 @@
-{
-    "Parameters: default": {
-        "content": [
-            {
-                
-            }
-        ],
-        "timestamp": "2023-08-17T12:09:45+0000"
-    },
-    "metadata": {
-        "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
-            "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
-            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
-            "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
-            "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
-            "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
-            "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
-            "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54",
-            "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
-            "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
-        ],
-        "timestamp": "2023-08-17T12:09:45+0000"
-    },
-    "samplesheet": {
-        "content": [
-            "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
-            "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
-        ],
-        "timestamp": "2023-08-17T12:09:45+0000"
-    },
-    "software_versions": {
-        "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
-        ],
-        "timestamp": "2023-08-17T12:09:45+0000"
-    },
-    "fastq": {
-        "content": [
-            "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791",
-            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
-            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30",
-            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
-            "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6",
-            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
-            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
-            "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
-            "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64",
-            "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83",
-            "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544",
-            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
-            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
-            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
-            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962",
-            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
-            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76",
-            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
-            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88",
-            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
-            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04",
-            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98",
-            [
-                "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d",
-                "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9",
-                "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f",
-                "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86",
-                "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499",
-                "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff",
-                "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75",
-                "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85",
-                "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4",
-                "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc",
-                "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0",
-                "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368",
-                "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8",
-                "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f",
-                "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3",
-                "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8",
-                "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882",
-                "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
-                "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
-            ]
-        ],
-        "timestamp": "2023-08-17T12:09:45+0000"
-    }
-}
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
deleted file mode 100644
index 6e27c4a9..00000000
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ /dev/null
@@ -1,27 +0,0 @@
-nextflow_pipeline {
-
-    name "Test workflow: sra.nf"
-    script "main.nf"
-    tag "workflows"
-    tag "workflows_sra"
-    tag "sra_custom_ena_metadata_fields"
-
-    test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") {
-
-        when {
-            params {
-                outdir = "$outputDir"
-                nf_core_pipeline = "rnaseq"
-                ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5"
-                sample_mapping_fields = "run_accession,library_layout"
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-}
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
deleted file mode 100644
index 55c39d4f..00000000
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
+++ /dev/null
@@ -1,88 +0,0 @@
-{
-    "metadata": {
-        "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,74a5f7058f27a565ce59db481355ca54",
-            "DRR028935.runinfo_ftp.tsv:md5,07a98fdcec207686a4ea2c9a3997edf3",
-            "ERR1109373.runinfo_ftp.tsv:md5,868897310855c50b1d5fc77d1195a1f9",
-            "ERR1160846.runinfo_ftp.tsv:md5,146d7f2ec778b32b7da7ad040e554114",
-            "GSE214215.runinfo_ftp.tsv:md5,adf62affe371dc9bad8e271450bdc2fe",
-            "SRR12848126.runinfo_ftp.tsv:md5,cf8827612a76645824e83418d7d76cbf",
-            "SRR13191702.runinfo_ftp.tsv:md5,2031ca9b7ab736dbde37d05b10cdb0ad",
-            "SRR14593545.runinfo_ftp.tsv:md5,3a1ac14d71744224a61ab542f869e180",
-            "SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1",
-            "SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236"
-        ],
-        "timestamp": "2023-08-17T12:11:42+0000"
-    },
-    "samplesheet": {
-        "content": [
-            "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f",
-            "multiqc_config.yml:md5,6f6189ee58855de81eaf82ad86e21040"
-        ],
-        "timestamp": "2023-08-17T12:11:42+0000"
-    },
-    "software_versions": {
-        "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
-        ],
-        "timestamp": "2023-08-17T12:11:42+0000"
-    },
-    "Parameters: '--nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...'": {
-        "content": [
-            {
-                
-            }
-        ],
-        "timestamp": "2023-08-17T12:11:42+0000"
-    },
-    "fastq": {
-        "content": [
-            "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791",
-            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
-            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30",
-            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
-            "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6",
-            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
-            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
-            "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
-            "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64",
-            "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83",
-            "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544",
-            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
-            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
-            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
-            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962",
-            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
-            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76",
-            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
-            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88",
-            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
-            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04",
-            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98",
-            [
-                "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d",
-                "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9",
-                "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f",
-                "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86",
-                "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499",
-                "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff",
-                "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75",
-                "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85",
-                "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4",
-                "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc",
-                "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0",
-                "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368",
-                "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8",
-                "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f",
-                "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3",
-                "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8",
-                "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882",
-                "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
-                "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
-            ]
-        ],
-        "timestamp": "2023-08-17T12:11:42+0000"
-    }
-}
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
deleted file mode 100644
index 1b501975..00000000
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ /dev/null
@@ -1,25 +0,0 @@
-nextflow_pipeline {
-
-    name "Test workflow: sra.nf"
-    script "main.nf"
-    tag "workflows"
-    tag "workflows_sra"
-    tag "sra_force_sratools_download"
-
-    test("Parameters: --force_sratools_download") {
-
-        when {
-            params {
-                outdir = "$outputDir"
-                force_sratools_download = true
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-}
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
deleted file mode 100644
index d5d694da..00000000
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
+++ /dev/null
@@ -1,67 +0,0 @@
-{
-    "Parameters: '--force_sratools_download'": {
-        "content": [
-            {
-                
-            }
-        ],
-        "timestamp": "2023-08-17T12:15:55+0000"
-    },
-    "metadata": {
-        "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
-            "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
-            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
-            "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
-            "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
-            "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
-            "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
-            "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54",
-            "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
-            "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
-        ],
-        "timestamp": "2023-08-17T12:15:55+0000"
-    },
-    "samplesheet": {
-        "content": [
-            "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
-            "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
-        ],
-        "timestamp": "2023-08-17T12:15:55+0000"
-    },
-    "software_versions": {
-        "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
-        ],
-        "timestamp": "2023-08-17T12:15:55+0000"
-    },
-    "fastq": {
-        "content": [
-            "DRX024467_DRR026872.fastq.gz:md5,bd3f113c3b06cf4499fa0e00c634ec85",
-            "DRX026011_DRR028935_1.fastq.gz:md5,0f96fb60e903c8cbd55a6977e66f7c93",
-            "DRX026011_DRR028935_2.fastq.gz:md5,b97b1e0e806bcae10a7443e2f22d6ca2",
-            "ERX1188904_ERR1109373_1.fastq.gz:md5,e7edae2715dfaf4c318d37959fd9ae22",
-            "ERX1188904_ERR1109373_2.fastq.gz:md5,34ab048c92201a5ec4ab36d8dc1c5732",
-            "ERX1234253_ERR1160846.fastq.gz:md5,22683b24b2467494e430643423f1e275",
-            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
-            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
-            "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
-            "SRX17709227_SRR21711856.fastq.gz:md5,eae43f1368d4568f415581394dc9726e",
-            "SRX17709228_SRR21711855.fastq.gz:md5,5194f8009b74552595c4ec5b7605d231",
-            "SRX6725035_SRR9984183.fastq.gz:md5,7a70e678c400366869601c8be41fe74b",
-            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
-            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
-            "SRX9504942_SRR13055517_1.fastq.gz:md5,b6d912a73466c8f27b1d8021f80ec2bb",
-            "SRX9504942_SRR13055517_2.fastq.gz:md5,7c6e220694fa5d6d9124c739aa70ea92",
-            "SRX9504942_SRR13055518_1.fastq.gz:md5,ed29278c21a1bb2d8907a74be0dd4bc4",
-            "SRX9504942_SRR13055518_2.fastq.gz:md5,83785b728312deb81483fc1fd5b14264",
-            "SRX9504942_SRR13055519_1.fastq.gz:md5,28babc59a625b5161d97392efd4d0018",
-            "SRX9504942_SRR13055519_2.fastq.gz:md5,cf1eb4c61ab3522f4d473c86b2f696e1",
-            "SRX9504942_SRR13055520_1.fastq.gz:md5,cc75af896ec8a7cececb37851b0c6fcd",
-            "SRX9504942_SRR13055520_2.fastq.gz:md5,fe3e2bf9f738e4959243fad59e879eae",
-            "SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7",
-            "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af"
-        ],
-        "timestamp": "2023-08-17T12:15:55+0000"
-    }
-}
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
deleted file mode 100644
index bda1d724..00000000
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ /dev/null
@@ -1,25 +0,0 @@
-nextflow_pipeline {
-
-    name "Test workflow: sra.nf"
-    script "main.nf"
-    tag "workflows"
-    tag "workflows_sra"
-    tag "sra_nf_core_pipeline_atacseq"
-
-    test("Parameters: --nf_core_pipeline atacseq") {
-
-        when {
-            params {
-                outdir = "$outputDir"
-                nf_core_pipeline = "atacseq"
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-}
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
deleted file mode 100644
index c99f258e..00000000
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
+++ /dev/null
@@ -1,88 +0,0 @@
-{
-    "metadata": {
-        "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
-            "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
-            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
-            "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
-            "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
-            "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
-            "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
-            "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54",
-            "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
-            "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
-        ],
-        "timestamp": "2023-08-17T12:21:36+0000"
-    },
-    "samplesheet": {
-        "content": [
-            "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
-            "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
-        ],
-        "timestamp": "2023-08-17T12:21:36+0000"
-    },
-    "software_versions": {
-        "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
-        ],
-        "timestamp": "2023-08-17T12:21:36+0000"
-    },
-    "Parameters: '--nf_core_pipeline atacseq'": {
-        "content": [
-            {
-                
-            }
-        ],
-        "timestamp": "2023-08-17T12:21:36+0000"
-    },
-    "fastq": {
-        "content": [
-            "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791",
-            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
-            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30",
-            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
-            "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6",
-            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
-            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
-            "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
-            "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64",
-            "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83",
-            "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544",
-            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
-            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
-            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
-            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962",
-            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
-            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76",
-            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
-            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88",
-            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
-            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04",
-            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98",
-            [
-                "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d",
-                "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9",
-                "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f",
-                "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86",
-                "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499",
-                "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff",
-                "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75",
-                "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85",
-                "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4",
-                "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc",
-                "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0",
-                "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368",
-                "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8",
-                "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f",
-                "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3",
-                "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8",
-                "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882",
-                "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
-                "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
-            ]
-        ],
-        "timestamp": "2023-08-17T12:21:36+0000"
-    }
-}
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
deleted file mode 100644
index 438b7f55..00000000
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ /dev/null
@@ -1,25 +0,0 @@
-nextflow_pipeline {
-
-    name "Test workflow: sra.nf"
-    script "main.nf"
-    tag "workflows"
-    tag "workflows_sra"
-    tag "sra_nf_core_pipeline_rnaseq"
-
-    test("Parameters: --nf_core_pipeline rnaseq") {
-
-        when {
-            params {
-                outdir = "$outputDir"
-                nf_core_pipeline = "rnaseq"
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-}
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
deleted file mode 100644
index 1da0381a..00000000
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
+++ /dev/null
@@ -1,88 +0,0 @@
-{
-    "metadata": {
-        "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
-            "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
-            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
-            "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
-            "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
-            "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
-            "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
-            "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54",
-            "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
-            "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
-        ],
-        "timestamp": "2023-08-17T12:19:51+0000"
-    },
-    "samplesheet": {
-        "content": [
-            "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
-            "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
-        ],
-        "timestamp": "2023-08-17T12:19:51+0000"
-    },
-    "software_versions": {
-        "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
-        ],
-        "timestamp": "2023-08-17T12:19:51+0000"
-    },
-    "Parameters: '--nf_core_pipeline rnaseq'": {
-        "content": [
-            {
-                
-            }
-        ],
-        "timestamp": "2023-08-17T12:19:51+0000"
-    },
-    "fastq": {
-        "content": [
-            "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791",
-            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
-            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30",
-            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
-            "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6",
-            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
-            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
-            "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
-            "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64",
-            "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83",
-            "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544",
-            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
-            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
-            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
-            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962",
-            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
-            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76",
-            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
-            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88",
-            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
-            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04",
-            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98",
-            [
-                "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d",
-                "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9",
-                "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f",
-                "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86",
-                "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499",
-                "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff",
-                "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75",
-                "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85",
-                "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4",
-                "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc",
-                "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0",
-                "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368",
-                "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8",
-                "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f",
-                "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3",
-                "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8",
-                "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882",
-                "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
-                "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
-            ]
-        ],
-        "timestamp": "2023-08-17T12:19:51+0000"
-    }
-}
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
deleted file mode 100644
index 301938c4..00000000
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ /dev/null
@@ -1,25 +0,0 @@
-nextflow_pipeline {
-
-    name "Test workflow: sra.nf"
-    script "main.nf"
-    tag "workflows"
-    tag "workflows_sra"
-    tag "sra_nf_core_pipeline_taxprofiler"
-
-    test("Parameters: --nf_core_pipeline taxprofiler") {
-
-        when {
-            params {
-                outdir = "$outputDir"
-                nf_core_pipeline = "taxprofiler"
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-}
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
deleted file mode 100644
index 85f3957b..00000000
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
+++ /dev/null
@@ -1,88 +0,0 @@
-{
-    "metadata": {
-        "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
-            "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
-            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
-            "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
-            "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
-            "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
-            "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
-            "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54",
-            "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
-            "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
-        ],
-        "timestamp": "2023-08-17T12:24:34+0000"
-    },
-    "samplesheet": {
-        "content": [
-            "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
-            "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
-        ],
-        "timestamp": "2023-08-17T12:24:34+0000"
-    },
-    "software_versions": {
-        "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
-        ],
-        "timestamp": "2023-08-17T12:24:34+0000"
-    },
-    "Parameters: --nf_core_pipeline taxprofiler": {
-        "content": [
-            {
-                
-            }
-        ],
-        "timestamp": "2023-08-17T12:24:34+0000"
-    },
-    "fastq": {
-        "content": [
-            "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791",
-            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
-            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30",
-            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
-            "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6",
-            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
-            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
-            "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
-            "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64",
-            "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83",
-            "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544",
-            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
-            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
-            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
-            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962",
-            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
-            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76",
-            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
-            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88",
-            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
-            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04",
-            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98",
-            [
-                "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d",
-                "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9",
-                "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f",
-                "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86",
-                "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499",
-                "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff",
-                "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75",
-                "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85",
-                "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4",
-                "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc",
-                "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0",
-                "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368",
-                "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8",
-                "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f",
-                "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3",
-                "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8",
-                "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882",
-                "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
-                "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
-            ]
-        ],
-        "timestamp": "2023-08-17T12:24:34+0000"
-    }
-}
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
deleted file mode 100644
index 892a7c3a..00000000
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ /dev/null
@@ -1,25 +0,0 @@
-nextflow_pipeline {
-
-    name "Test workflow: sra.nf"
-    script "main.nf"
-    tag "workflows"
-    tag "workflows_sra"
-    tag "sra_nf_core_pipeline_viralrecon"
-
-    test("Parameters: --nf_core_pipeline viralrecon") {
-
-        when {
-            params {
-                outdir = "$outputDir"
-                nf_core_pipeline = "viralrecon"
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-}
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
deleted file mode 100644
index 13c59b5d..00000000
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
+++ /dev/null
@@ -1,88 +0,0 @@
-{
-    "metadata": {
-        "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
-            "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
-            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
-            "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
-            "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
-            "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
-            "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
-            "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54",
-            "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
-            "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
-        ],
-        "timestamp": "2023-08-17T12:26:57+0000"
-    },
-    "samplesheet": {
-        "content": [
-            "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
-            "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
-        ],
-        "timestamp": "2023-08-17T12:26:57+0000"
-    },
-    "Parameters: --nf_core_pipeline viralrecon": {
-        "content": [
-            {
-                
-            }
-        ],
-        "timestamp": "2023-08-17T12:26:57+0000"
-    },
-    "software_versions": {
-        "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
-        ],
-        "timestamp": "2023-08-17T12:26:57+0000"
-    },
-    "fastq": {
-        "content": [
-            "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791",
-            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
-            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30",
-            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9",
-            "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6",
-            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
-            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2",
-            "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda",
-            "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64",
-            "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83",
-            "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544",
-            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
-            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79",
-            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
-            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962",
-            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
-            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76",
-            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
-            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88",
-            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
-            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04",
-            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98",
-            [
-                "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d",
-                "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9",
-                "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f",
-                "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86",
-                "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499",
-                "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff",
-                "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75",
-                "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85",
-                "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4",
-                "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc",
-                "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0",
-                "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368",
-                "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8",
-                "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f",
-                "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3",
-                "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8",
-                "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882",
-                "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
-                "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
-            ]
-        ],
-        "timestamp": "2023-08-17T12:26:57+0000"
-    }
-}
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
deleted file mode 100644
index 7d218cf7..00000000
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ /dev/null
@@ -1,25 +0,0 @@
-nextflow_pipeline {
-
-    name "Test workflow: sra.nf"
-    script "main.nf"
-    tag "workflows"
-    tag "workflows_sra"
-    tag "sra_skip_fastq_download"
-
-    test("Parameters: --skip_fastq_download") {
-
-        when {
-            params {
-                outdir = "$outputDir"
-                skip_fastq_download = true
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-}
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
deleted file mode 100644
index d004d5d2..00000000
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
+++ /dev/null
@@ -1,46 +0,0 @@
-{
-    "Parameters: '--skip_fastq_download'": {
-        "content": [
-            {
-                
-            }
-        ],
-        "timestamp": "2023-08-17T12:25:19+0000"
-    },
-    "metadata": {
-        "content": [
-            "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
-            "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2",
-            "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4",
-            "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345",
-            "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f",
-            "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d",
-            "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d",
-            "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54",
-            "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
-            "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
-        ],
-        "timestamp": "2023-08-17T12:25:19+0000"
-    },
-    "samplesheet": {
-        "content": [
-            "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
-            "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
-        ],
-        "timestamp": "2023-08-17T12:25:19+0000"
-    },
-    "software_versions": {
-        "content": [
-            "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
-        ],
-        "timestamp": "2023-08-17T12:25:19+0000"
-    },
-    "Parameters: --skip_fastq_download": {
-        "content": [
-            {
-                
-            }
-        ],
-        "timestamp": "2023-08-17T12:25:19+0000"
-    }
-}
\ No newline at end of file
diff --git a/workflows/synapse/main.nf b/workflows/synapse.nf
similarity index 89%
rename from workflows/synapse/main.nf
rename to workflows/synapse.nf
index f8cbeba1..f2138a60 100644
--- a/workflows/synapse/main.nf
+++ b/workflows/synapse.nf
@@ -19,11 +19,11 @@ if (params.synapse_config) {
 ========================================================================================
 */
 
-include { SYNAPSE_LIST              } from '../../modules/local/synapse_list'
-include { SYNAPSE_SHOW              } from '../../modules/local/synapse_show'
-include { SYNAPSE_GET               } from '../../modules/local/synapse_get'
-include { SYNAPSE_TO_SAMPLESHEET    } from '../../modules/local/synapse_to_samplesheet'
-include { SYNAPSE_MERGE_SAMPLESHEET } from '../../modules/local/synapse_merge_samplesheet'
+include { SYNAPSE_LIST              } from '../modules/local/synapse_list'
+include { SYNAPSE_SHOW              } from '../modules/local/synapse_show'
+include { SYNAPSE_GET               } from '../modules/local/synapse_get'
+include { SYNAPSE_TO_SAMPLESHEET    } from '../modules/local/synapse_to_samplesheet'
+include { SYNAPSE_MERGE_SAMPLESHEET } from '../modules/local/synapse_merge_samplesheet'
 
 /*
 ========================================================================================
@@ -31,7 +31,7 @@ include { SYNAPSE_MERGE_SAMPLESHEET } from '../../modules/local/synapse_merge_sa
 ========================================================================================
 */
 
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions'
+include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
 
 /*
 ========================================================================================
diff --git a/workflows/synapse/tests/main.nf.test b/workflows/synapse/tests/main.nf.test
deleted file mode 100644
index 7cbfed11..00000000
--- a/workflows/synapse/tests/main.nf.test
+++ /dev/null
@@ -1,28 +0,0 @@
-nextflow_pipeline {
-
-    name "Test workflow: synapse.nf"
-    script "main.nf"
-    tag "workflows"
-    tag "synapse"
-    tag "synapse_default"
-    profile "test_synapse"
-
-    test("Synapse Input Type") {
-
-        when {
-            params {
-                outdir = "$outputDir"
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") },
-                { assert snapshot(path("$outputDir/samplesheet/").list()).match("samplesheet") }
-            )
-        }
-
-    }
-
-}

From e93c45a9f5fa1c16183e924e99ba4e41539bc328 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 21 Sep 2023 12:31:25 +0200
Subject: [PATCH 447/852] fix nf-core linting

---
 assets/multiqc_config.yml |  4 ++--
 modules.json              | 22 ++++++++++++++++------
 nextflow.config           |  7 -------
 nextflow_schema.json      | 18 ------------------
 4 files changed, 18 insertions(+), 33 deletions(-)

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 70cc1fc7..5e3d9889 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/fetchngs/1.10.1" target="_blank">nf-core/fetchngs</a>
+  This report has been generated by the <a href="https://github.com/nf-core/fetchngs/1.10.1dev" target="_blank">nf-core/fetchngs</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/fetchngs/1.10.1/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/fetchngs/1.10.1dev/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-fetchngs-methods-description":
     order: -1000
diff --git a/modules.json b/modules.json
index 3137b88b..2daacf3a 100644
--- a/modules.json
+++ b/modules.json
@@ -8,22 +8,30 @@
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
+                        "installed_by": [
+                            "fastq_download_prefetch_fasterqdump_sratools"
+                        ]
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
                         "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca",
-                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
+                        "installed_by": [
+                            "fastq_download_prefetch_fasterqdump_sratools"
+                        ]
                     },
                     "sratools/prefetch": {
                         "branch": "master",
                         "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca",
-                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
+                        "installed_by": [
+                            "fastq_download_prefetch_fasterqdump_sratools"
+                        ]
                     }
                 }
             },
@@ -32,10 +40,12 @@
                     "fastq_download_prefetch_fasterqdump_sratools": {
                         "branch": "master",
                         "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     }
                 }
             }
         }
     }
-}
+}
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 9caf9ff2..2a8e9bcc 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -21,13 +21,6 @@ params {
     skip_fastq_download         = false
     dbgap_key                   = null
 
-    // MultiQC options
-    multiqc_config             = null
-    multiqc_title              = null
-    multiqc_logo               = null
-    max_multiqc_email_size     = '25.MB'
-    multiqc_methods_description = null
-
     // Boilerplate options
     outdir                     = null
     publish_dir_mode           = 'copy'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 3816846f..def56011 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -234,24 +234,6 @@
                     "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
                     "hidden": true
                 },
-                "multiqc_config": {
-                    "type": "string",
-                    "format": "file-path",
-                    "description": "Custom config file to supply to MultiQC.",
-                    "fa_icon": "fas fa-cog",
-                    "hidden": true
-                },
-                "multiqc_logo": {
-                    "type": "string",
-                    "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
-                    "fa_icon": "fas fa-image",
-                    "hidden": true
-                },
-                "multiqc_methods_description": {
-                    "type": "string",
-                    "description": "Custom MultiQC yaml file containing HTML including a methods description.",
-                    "fa_icon": "fas fa-cog"
-                },
                 "validate_params": {
                     "type": "boolean",
                     "description": "Boolean whether to validate parameters against the schema at runtime",

From 797a15bfc0afad3eb0a9a628b5fb8d588baa6873 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 21 Sep 2023 14:14:42 +0200
Subject: [PATCH 448/852] syntax fix

---
 lib/NfcoreTemplate.groovy |  3 +--
 main.nf                   |  2 +-
 modules.json              | 22 ++++++----------------
 nextflow_schema.json      |  3 ++-
 workflows/sra.nf          | 20 ++++++++++----------
 5 files changed, 20 insertions(+), 30 deletions(-)

diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
index 9276512a..3d513a92 100755
--- a/lib/NfcoreTemplate.groovy
+++ b/lib/NfcoreTemplate.groovy
@@ -110,8 +110,7 @@ class NfcoreTemplate {
         def email_html    = html_template.toString()
 
         // Render the sendmail template
-        def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
-        def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
+        def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir" ]
         def sf                     = new File("$projectDir/assets/sendmail_template.txt")
         def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
         def sendmail_html          = sendmail_template.toString()
diff --git a/main.nf b/main.nf
index 1d849bd3..b600e82f 100644
--- a/main.nf
+++ b/main.nf
@@ -23,7 +23,7 @@ include { validateParameters; paramsHelp } from 'plugin/nf-validation'
 if (params.help) {
     def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
     def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
-    def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
+    def String command = "nextflow run ${workflow.manifest.name} --input id.csv -profile docker"
     log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
     System.exit(0)
 }
diff --git a/modules.json b/modules.json
index 2daacf3a..3137b88b 100644
--- a/modules.json
+++ b/modules.json
@@ -8,30 +8,22 @@
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "fastq_download_prefetch_fasterqdump_sratools"
-                        ]
+                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
                         "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca",
-                        "installed_by": [
-                            "fastq_download_prefetch_fasterqdump_sratools"
-                        ]
+                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/prefetch": {
                         "branch": "master",
                         "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca",
-                        "installed_by": [
-                            "fastq_download_prefetch_fasterqdump_sratools"
-                        ]
+                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     }
                 }
             },
@@ -40,12 +32,10 @@
                     "fastq_download_prefetch_fasterqdump_sratools": {
                         "branch": "master",
                         "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }
         }
     }
-}
\ No newline at end of file
+}
diff --git a/nextflow_schema.json b/nextflow_schema.json
index def56011..cda974a5 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -69,7 +69,8 @@
                     "type": "string",
                     "fa_icon": "fas fa-address-card",
                     "help_text": "Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit. Users with granted access to controlled data can download the JWT cart file for the study from the SRA Run Selector upon logging in. The JWT file can only be used on cloud platforms and is valid for 1 hour upon creation.",
-                    "format": "file-path"
+                    "format": "file-path",
+                    "description": "dbGaP repository key."
                 },
                 "outdir": {
                     "type": "string",
diff --git a/workflows/sra.nf b/workflows/sra.nf
index 44ff8346..3a4809b6 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -4,14 +4,14 @@
 ========================================================================================
 */
 
-def valid_params = [
-    ena_metadata_fields : ['run_accession', 'experiment_accession', 'library_layout', 'fastq_ftp', 'fastq_md5']
-]
+include { paramsSummaryLog; paramsSummaryMap; fromSamplesheet } from 'plugin/nf-validation'
 
-def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
+def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
+def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
+def summary_params = paramsSummaryMap(workflow)
 
-// Validate input parameters
-WorkflowSra.initialise(params, valid_params)
+// Print parameter summary log to screen
+log.info logo + paramsSummaryLog(workflow) + citation
 
 /*
 ========================================================================================
@@ -84,9 +84,9 @@ workflow SRA {
     if (!params.skip_fastq_download) {
 
         ch_sra_metadata
-            .map { 
-                meta -> 
-                    [ meta, [ meta.fastq_1, meta.fastq_2 ] ] 
+            .map {
+                meta ->
+                    [ meta, [ meta.fastq_1, meta.fastq_2 ] ]
             }
             .branch {
                 ftp: it[0].fastq_1  && !params.force_sratools_download
@@ -115,7 +115,7 @@ workflow SRA {
             .out
             .fastq
             .mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads)
-            .map { 
+            .map {
                 meta, fastq ->
                     def reads = fastq instanceof List ? fastq.flatten() : [ fastq ]
                     def meta_clone = meta.clone()

From 71f6c3ceddbe6f612d62ed01f9f90b53254103b2 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 21 Sep 2023 14:33:05 +0200
Subject: [PATCH 449/852] update module

---
 modules.json                                        | 2 +-
 modules/nf-core/custom/dumpsoftwareversions/main.nf | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules.json b/modules.json
index 3137b88b..ab610dfb 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
                         "installed_by": ["modules"]
                     },
                     "custom/sratoolsncbisettings": {
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
index ebc87273..c9d014b1 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     label 'process_single'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda "bioconda::multiqc=1.14"
+    conda "bioconda::multiqc=1.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.14--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.15--pyhdfd78af_0' }"
 
     input:
     path versions

From 52517c6cfa8e4cca0d87650e7abeb6884438b43f Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 21 Sep 2023 14:33:24 +0200
Subject: [PATCH 450/852] fix issue

---
 nextflow_schema.json | 1 -
 workflows/sra.nf     | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index cda974a5..345601b7 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -18,7 +18,6 @@
                     "exists": true,
                     "mimetype": "text/csv",
                     "pattern": "^\\S+\\.(csv|tsv|txt)$",
-                    "schema": "assets/schema_input.json",
                     "fa_icon": "fas fa-file-excel",
                     "description": "File containing SRA/ENA/GEO/DDBJ identifiers one per line to download their associated metadata and FastQ files."
                 },
diff --git a/workflows/sra.nf b/workflows/sra.nf
index 3a4809b6..8d396ca1 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -4,7 +4,7 @@
 ========================================================================================
 */
 
-include { paramsSummaryLog; paramsSummaryMap; fromSamplesheet } from 'plugin/nf-validation'
+include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'
 
 def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
 def citation = '\n' + WorkflowMain.citation(workflow) + '\n'

From f51446845daaee19d9489f8a6f24191fc6b3ce2d Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 21 Sep 2023 15:03:45 +0200
Subject: [PATCH 451/852] fix nf-validation issue

---
 assets/schema_input.json | 12 +++++++-----
 nextflow_schema.json     |  1 +
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index 9a800216..13044b1b 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -5,11 +5,13 @@
     "description": "Schema for the file provided with params.input",
     "type": "array",
     "items": {
-        "type": "array",
-        "items": {
-            "type": "string",
-            "pattern": "^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM])|(syn))(\\d+)$",
-            "errorMessage": "Please provide a valid SRA, ENA, DDBJ or GEO identifier"
+        "type": "object",
+        "properties": {
+            "": {
+                "type": "string",
+                "pattern": "^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM])|(syn))(\\d+)$",
+                "errorMessage": "Please provide a valid SRA, ENA, DDBJ or GEO identifier"
+            }
         }
     }
 }
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 345601b7..cda974a5 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -18,6 +18,7 @@
                     "exists": true,
                     "mimetype": "text/csv",
                     "pattern": "^\\S+\\.(csv|tsv|txt)$",
+                    "schema": "assets/schema_input.json",
                     "fa_icon": "fas fa-file-excel",
                     "description": "File containing SRA/ENA/GEO/DDBJ identifiers one per line to download their associated metadata and FastQ files."
                 },

From c3ed8e4439b8c65794aa397d820ce9becf507fd8 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 21 Sep 2023 15:08:34 +0200
Subject: [PATCH 452/852] it's actually an id

---
 assets/schema_input.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index 13044b1b..d451f9e9 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -7,7 +7,7 @@
     "items": {
         "type": "object",
         "properties": {
-            "": {
+            "id": {
                 "type": "string",
                 "pattern": "^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM])|(syn))(\\d+)$",
                 "errorMessage": "Please provide a valid SRA, ENA, DDBJ or GEO identifier"

From 131788e37a7519a7fc35efa9b6fbd9d1ff919def Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 21 Sep 2023 17:36:54 +0200
Subject: [PATCH 453/852] restore nf-test tests for sra workflow

---
 .../sra_custom_ena_metadata_fields.nf.test    |   33 +
 ...ra_custom_ena_metadata_fields.nf.test.snap |  573 +++++++
 .../sra/tests/sra_default_parameters.nf.test  |   30 +
 .../tests/sra_default_parameters.nf.test.snap | 1353 +++++++++++++++++
 .../tests/sra_force_sratools_download.nf.test |   31 +
 .../sra_force_sratools_download.nf.test.snap  | 1351 ++++++++++++++++
 .../sra_nf_core_pipeline_atacseq.nf.test      |   31 +
 .../sra_nf_core_pipeline_atacseq.nf.test.snap | 1353 +++++++++++++++++
 .../tests/sra_nf_core_pipeline_rnaseq.nf.test |   31 +
 .../sra_nf_core_pipeline_rnaseq.nf.test.snap  | 1353 +++++++++++++++++
 .../sra_nf_core_pipeline_taxprofiler.nf.test  |   31 +
 ..._nf_core_pipeline_taxprofiler.nf.test.snap | 1353 +++++++++++++++++
 .../sra_nf_core_pipeline_viralrecon.nf.test   |   31 +
 ...a_nf_core_pipeline_viralrecon.nf.test.snap | 1353 +++++++++++++++++
 .../sra/tests/sra_skip_fastq_download.nf.test |   31 +
 .../sra_skip_fastq_download.nf.test.snap      |   37 +
 16 files changed, 8975 insertions(+)
 create mode 100644 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
 create mode 100644 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
 create mode 100644 workflows/sra/tests/sra_default_parameters.nf.test
 create mode 100644 workflows/sra/tests/sra_default_parameters.nf.test.snap
 create mode 100644 workflows/sra/tests/sra_force_sratools_download.nf.test
 create mode 100644 workflows/sra/tests/sra_force_sratools_download.nf.test.snap
 create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
 create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
 create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
 create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
 create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
 create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
 create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
 create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
 create mode 100644 workflows/sra/tests/sra_skip_fastq_download.nf.test
 create mode 100644 workflows/sra/tests/sra_skip_fastq_download.nf.test.snap

diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
new file mode 100644
index 00000000..45280ab0
--- /dev/null
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -0,0 +1,33 @@
+nextflow_workflow {
+
+    name "Test workflow: sra/main.nf"
+    script "workflows/sra/main.nf"
+    workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
+    tag "sra_custom_ena_metadata_fields"
+
+    test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                """
+            }
+            params {
+                outdir = "results"
+                nf_core_pipeline = "rnaseq"
+                ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5"
+                sample_mapping_fields = "run_accession,library_layout"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
new file mode 100644
index 00000000..a2537a95
--- /dev/null
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
@@ -0,0 +1,573 @@
+{
+    "Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "DRX024467_DRR026872",
+                            "run_accession": "DRR026872",
+                            "experiment_accession": "DRX024467",
+                            "library_layout": "SINGLE",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_md5": "515e5448c55e054113c4a22df5f62791",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "515e5448c55e054113c4a22df5f62791",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791"
+                    ],
+                    [
+                        {
+                            "id": "DRX026011_DRR028935",
+                            "run_accession": "DRR028935",
+                            "experiment_accession": "DRX026011",
+                            "library_layout": "PAIRED",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
+                            "md5_2": "941c9998d746416dad53c94c480ddf30",
+                            "single_end": false
+                        },
+                        [
+                            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
+                            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "ERX1188904_ERR1109373",
+                            "run_accession": "ERR1109373",
+                            "experiment_accession": "ERX1188904",
+                            "library_layout": "PAIRED",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
+                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
+                            "single_end": false
+                        },
+                        [
+                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
+                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "ERX1234253_ERR1160846",
+                            "run_accession": "ERR1160846",
+                            "experiment_accession": "ERX1234253",
+                            "library_layout": "SINGLE",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6"
+                    ],
+                    [
+                        {
+                            "id": "SRX10940790_SRR14593545",
+                            "run_accession": "SRR14593545",
+                            "experiment_accession": "SRX10940790",
+                            "library_layout": "PAIRED",
+                            "fastq_ftp": "",
+                            "fastq_md5": "",
+                            "fastq_1": "",
+                            "fastq_2": "",
+                            "md5_1": "",
+                            "md5_2": "",
+                            "single_end": false
+                        },
+                        [
+                            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
+                            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX11047067_SRR14709033",
+                            "run_accession": "SRR14709033",
+                            "experiment_accession": "SRX11047067",
+                            "library_layout": "SINGLE",
+                            "fastq_ftp": "",
+                            "fastq_md5": "",
+                            "fastq_1": "",
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+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_2.fastq.gz",
+                            "fastq_md5": "dcf4438c0b682242ee90c5f3a803fb40;18dbe96e7f58b63406d9058938df1962",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_2.fastq.gz",
+                            "md5_1": "dcf4438c0b682242ee90c5f3a803fb40",
+                            "md5_2": "18dbe96e7f58b63406d9058938df1962",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
+                            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX9504942_SRR13055518",
+                            "run_accession": "SRR13055518",
+                            "experiment_accession": "SRX9504942",
+                            "library_layout": "PAIRED",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_2.fastq.gz",
+                            "fastq_md5": "5ec894d863fcefe394470a0925aefde4;aead170df9851773d5202b5760c76d76",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_2.fastq.gz",
+                            "md5_1": "5ec894d863fcefe394470a0925aefde4",
+                            "md5_2": "aead170df9851773d5202b5760c76d76",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
+                            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX9504942_SRR13055519",
+                            "run_accession": "SRR13055519",
+                            "experiment_accession": "SRX9504942",
+                            "library_layout": "PAIRED",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_2.fastq.gz",
+                            "fastq_md5": "5ad51460c6c4a850dd37a206e2c441c1;a977367bf41dacf4c21bc0c8201b8b88",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_2.fastq.gz",
+                            "md5_1": "5ad51460c6c4a850dd37a206e2c441c1",
+                            "md5_2": "a977367bf41dacf4c21bc0c8201b8b88",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1",
+                            "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX9504942_SRR13055520",
+                            "run_accession": "SRR13055520",
+                            "experiment_accession": "SRX9504942",
+                            "library_layout": "PAIRED",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "fastq_md5": "795d460abff6009c7f5ff7c14b773fbe;c3f34379356b28d6dac7212abc1a0a04",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "md5_1": "795d460abff6009c7f5ff7c14b773fbe",
+                            "md5_2": "c3f34379356b28d6dac7212abc1a0a04",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
+                            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "run_accession": "SRR13191702",
+                            "experiment_accession": "SRX9626017",
+                            "library_layout": "PAIRED",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_md5": "89c5be920021a035084d8aeb74f32df7;56271be38a80db78ef3bdfc5d9909b98",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
+                        ]
+                    ]
+                ],
+                "mappings": [
+                    "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f"
+                ],
+                "samplesheet": [
+                    "samplesheet.csv:md5,be5465f34924356e136c804d63e1b562"
+                ],
+                "versions": [
+                    "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                ]
+            }
+        ],
+        "timestamp": "2023-09-11T18:48:18.757655"
+    }
+}
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_default_parameters.nf.test b/workflows/sra/tests/sra_default_parameters.nf.test
new file mode 100644
index 00000000..ef35c80a
--- /dev/null
+++ b/workflows/sra/tests/sra_default_parameters.nf.test
@@ -0,0 +1,30 @@
+nextflow_workflow {
+
+    name "Test workflow: sra/main.nf"
+    script "workflows/sra/main.nf"
+    workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
+    tag "sra_default_parameters"
+
+    test("Parameters: default") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                """
+            }
+            params {
+                outdir = "results"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/workflows/sra/tests/sra_default_parameters.nf.test.snap b/workflows/sra/tests/sra_default_parameters.nf.test.snap
new file mode 100644
index 00000000..b8dc88ca
--- /dev/null
+++ b/workflows/sra/tests/sra_default_parameters.nf.test.snap
@@ -0,0 +1,1353 @@
+{
+    "Parameters: default": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "DRX024467_DRR026872",
+                            "run_accession": "DRR026872",
+                            "experiment_accession": "DRX024467",
+                            "sample_accession": "SAMD00023098",
+                            "secondary_sample_accession": "DRS033740",
+                            "study_accession": "PRJDB4356",
+                            "secondary_study_accession": "DRP003256",
+                            "submission_accession": "DRA002758",
+                            "run_alias": "DRR026872",
+                            "experiment_alias": "DRX024467",
+                            "sample_alias": "SAMD00023098",
+                            "study_alias": "DRP003256",
+                            "library_layout": "SINGLE",
+                            "library_selection": "Restriction Digest",
+                            "library_source": "GENOMIC",
+                            "library_strategy": "OTHER",
+                            "library_name": "IpeRAD1_3",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "62550",
+                            "read_count": "417",
+                            "tax_id": "35883",
+                            "scientific_name": "Ipomoea nil",
+                            "sample_title": "F2 plant dreived from a cross between Tokyo Kokei-standard and Africa #21",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Illumina HiSeq 2500 sequencing of SAMD00023098",
+                            "study_title": "The Japanese morning glory genome sequence",
+                            "sample_description": "Keywords: GSC:MIxS MIGS:6.0",
+                            "fastq_md5": "515e5448c55e054113c4a22df5f62791",
+                            "fastq_bytes": "38447",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "515e5448c55e054113c4a22df5f62791",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791"
+                    ],
+                    [
+                        {
+                            "id": "DRX026011_DRR028935",
+                            "run_accession": "DRR028935",
+                            "experiment_accession": "DRX026011",
+                            "sample_accession": "SAMD00024405",
+                            "secondary_sample_accession": "DRS019431",
+                            "study_accession": "PRJDB3420",
+                            "secondary_study_accession": "DRP002616",
+                            "submission_accession": "DRA002949",
+                            "run_alias": "DRR028935",
+                            "experiment_alias": "DRX026011",
+                            "sample_alias": "SAMD00024405",
+                            "study_alias": "DRP002616",
+                            "library_layout": "PAIRED",
+                            "library_selection": "cDNA",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "RNA-Seq",
+                            "library_name": "day0_BbSQE-I",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "194930",
+                            "read_count": "965",
+                            "tax_id": "1202541",
+                            "scientific_name": "Botryococcus braunii Showa",
+                            "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
+                            "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
+                            "sample_description": "Liquid culture",
+                            "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
+                            "fastq_bytes": "60275;61610",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
+                            "md5_2": "941c9998d746416dad53c94c480ddf30",
+                            "single_end": false
+                        },
+                        [
+                            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
+                            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "ERX1188904_ERR1109373",
+                            "run_accession": "ERR1109373",
+                            "experiment_accession": "ERX1188904",
+                            "sample_accession": "SAMEA3643867",
+                            "secondary_sample_accession": "ERS951016",
+                            "study_accession": "PRJEB11633",
+                            "secondary_study_accession": "ERP013030",
+                            "submission_accession": "ERA528939",
+                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
+                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
+                            "sample_alias": "sample_56",
+                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
+                            "library_layout": "PAIRED",
+                            "library_selection": "RT-PCR",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "RNA-Seq",
+                            "library_name": "unspecified",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "29700",
+                            "read_count": "169",
+                            "tax_id": "63433",
+                            "scientific_name": "Leptopilina boulardi",
+                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
+                            "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
+                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
+                            "fastq_bytes": "3221;8151;8118",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
+                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
+                            "single_end": false
+                        },
+                        [
+                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
+                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "ERX1234253_ERR1160846",
+                            "run_accession": "ERR1160846",
+                            "experiment_accession": "ERX1234253",
+                            "sample_accession": "SAMEA3687214",
+                            "secondary_sample_accession": "ERS994363",
+                            "study_accession": "PRJEB11419",
+                            "secondary_study_accession": "ERP012803",
+                            "submission_accession": "ERA541392",
+                            "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                            "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                            "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                            "study_alias": "qiita_sid_10317",
+                            "library_layout": "SINGLE",
+                            "library_selection": "PCR",
+                            "library_source": "METAGENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "10317.BLANK.93.3E.r22",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "35658",
+                            "read_count": "283",
+                            "tax_id": "256318",
+                            "scientific_name": "metagenome",
+                            "sample_title": "10317.BLANK.93.3E.r22",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                            "study_title": "American Gut Project",
+                            "sample_description": "American Gut control",
+                            "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                            "fastq_bytes": "18077",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6"
+                    ],
+                    [
+                        {
+                            "id": "SRX10940790_SRR14593545",
+                            "run_accession": "SRR14593545",
+                            "experiment_accession": "SRX10940790",
+                            "sample_accession": "SAMN19097423",
+                            "secondary_sample_accession": "SRS9020442",
+                            "study_accession": "PRJNA728650",
+                            "secondary_study_accession": "SRP319413",
+                            "submission_accession": "SRA1234280",
+                            "run_alias": "577-6_530058_19-037147 Goat_F.ab1",
+                            "experiment_alias": "PRNP_2765",
+                            "sample_alias": "prp_2765",
+                            "study_alias": "PRJNA728650",
+                            "library_layout": "PAIRED",
+                            "library_selection": "PCR",
+                            "library_source": "GENOMIC",
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+                    ],
+                    [
+                        {
+                            "id": "SRX9504942_SRR13055520",
+                            "run_accession": "SRR13055520",
+                            "experiment_accession": "SRX9504942",
+                            "sample_accession": "SAMN16793052",
+                            "secondary_sample_accession": "SRS7713669",
+                            "study_accession": "PRJNA678298",
+                            "secondary_study_accession": "SRP292504",
+                            "submission_accession": "SRA1158402",
+                            "run_alias": "GSM4907283_r4",
+                            "experiment_alias": "GSM4907283",
+                            "sample_alias": "GSM4907283",
+                            "study_alias": "GSE159787",
+                            "library_layout": "PAIRED",
+                            "library_selection": "other",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "OTHER",
+                            "library_name": "",
+                            "instrument_model": "NextSeq 550",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "2214488",
+                            "read_count": "29138",
+                            "tax_id": "9606",
+                            "scientific_name": "Homo sapiens",
+                            "sample_title": "A20-35 A11A20-35 A11_ROI009PanCK+",
+                            "experiment_title": "NextSeq 550 sequencing: GSM4907283: A20-35 A11A20-35 A11_ROI009PanCK+ Homo sapiens OTHER",
+                            "study_title": "Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]",
+                            "sample_description": "A20-35 A11A20-35 A11_ROI009PanCK+",
+                            "fastq_md5": "795d460abff6009c7f5ff7c14b773fbe;c3f34379356b28d6dac7212abc1a0a04",
+                            "fastq_bytes": "709867;716862",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "md5_1": "795d460abff6009c7f5ff7c14b773fbe",
+                            "md5_2": "c3f34379356b28d6dac7212abc1a0a04",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
+                            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "run_accession": "SRR13191702",
+                            "experiment_accession": "SRX9626017",
+                            "sample_accession": "SAMN16980141",
+                            "secondary_sample_accession": "SRS7827211",
+                            "study_accession": "PRJNA682076",
+                            "secondary_study_accession": "SRP295653",
+                            "submission_accession": "SRA1166126",
+                            "run_alias": "S.170804.00784_662_L001_R1_001.fastq.gz",
+                            "experiment_alias": "S.170804.00784",
+                            "sample_alias": "S.170804.00784_662",
+                            "study_alias": "PRJNA682076",
+                            "library_layout": "PAIRED",
+                            "library_selection": "PCR",
+                            "library_source": "METAGENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "S.170804.00784",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "45682",
+                            "read_count": "91",
+                            "tax_id": "408170",
+                            "scientific_name": "human gut metagenome",
+                            "sample_title": "Metagenome or environmental sample from human gut metagenome",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
+                            "study_title": "Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
+                            "sample_description": "Metagenome or environmental sample from human gut metagenome",
+                            "fastq_md5": "89c5be920021a035084d8aeb74f32df7;56271be38a80db78ef3bdfc5d9909b98",
+                            "fastq_bytes": "15420;16324",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
+                        ]
+                    ]
+                ],
+                "mappings": [
+                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                ],
+                "samplesheet": [
+                    "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556"
+                ],
+                "versions": [
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                ]
+            }
+        ],
+        "timestamp": "2023-09-11T18:56:05.693225"
+    }
+}
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
new file mode 100644
index 00000000..76ce7cd3
--- /dev/null
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -0,0 +1,31 @@
+nextflow_workflow {
+
+    name "Test workflow: sra/main.nf"
+    script "workflows/sra/main.nf"
+    workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
+    tag "sra_force_sratools_download"
+
+    test("Parameters: --force_sratools_download") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                """
+            }
+            params {
+                outdir = "results"
+                force_sratools_download = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
new file mode 100644
index 00000000..4e1b8aaf
--- /dev/null
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
@@ -0,0 +1,1351 @@
+{
+    "Parameters: --force_sratools_download": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "DRX024467_DRR026872",
+                            "run_accession": "DRR026872",
+                            "experiment_accession": "DRX024467",
+                            "sample_accession": "SAMD00023098",
+                            "secondary_sample_accession": "DRS033740",
+                            "study_accession": "PRJDB4356",
+                            "secondary_study_accession": "DRP003256",
+                            "submission_accession": "DRA002758",
+                            "run_alias": "DRR026872",
+                            "experiment_alias": "DRX024467",
+                            "sample_alias": "SAMD00023098",
+                            "study_alias": "DRP003256",
+                            "library_layout": "SINGLE",
+                            "library_selection": "Restriction Digest",
+                            "library_source": "GENOMIC",
+                            "library_strategy": "OTHER",
+                            "library_name": "IpeRAD1_3",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "62550",
+                            "read_count": "417",
+                            "tax_id": "35883",
+                            "scientific_name": "Ipomoea nil",
+                            "sample_title": "F2 plant dreived from a cross between Tokyo Kokei-standard and Africa #21",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Illumina HiSeq 2500 sequencing of SAMD00023098",
+                            "study_title": "The Japanese morning glory genome sequence",
+                            "sample_description": "Keywords: GSC:MIxS MIGS:6.0",
+                            "fastq_md5": "515e5448c55e054113c4a22df5f62791",
+                            "fastq_bytes": "38447",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "515e5448c55e054113c4a22df5f62791",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "DRX024467_DRR026872.fastq.gz:md5,bd3f113c3b06cf4499fa0e00c634ec85"
+                    ],
+                    [
+                        {
+                            "id": "DRX026011_DRR028935",
+                            "run_accession": "DRR028935",
+                            "experiment_accession": "DRX026011",
+                            "sample_accession": "SAMD00024405",
+                            "secondary_sample_accession": "DRS019431",
+                            "study_accession": "PRJDB3420",
+                            "secondary_study_accession": "DRP002616",
+                            "submission_accession": "DRA002949",
+                            "run_alias": "DRR028935",
+                            "experiment_alias": "DRX026011",
+                            "sample_alias": "SAMD00024405",
+                            "study_alias": "DRP002616",
+                            "library_layout": "PAIRED",
+                            "library_selection": "cDNA",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "RNA-Seq",
+                            "library_name": "day0_BbSQE-I",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "194930",
+                            "read_count": "965",
+                            "tax_id": "1202541",
+                            "scientific_name": "Botryococcus braunii Showa",
+                            "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
+                            "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
+                            "sample_description": "Liquid culture",
+                            "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
+                            "fastq_bytes": "60275;61610",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
+                            "md5_2": "941c9998d746416dad53c94c480ddf30",
+                            "single_end": false
+                        },
+                        [
+                            "DRX026011_DRR028935_1.fastq.gz:md5,0f96fb60e903c8cbd55a6977e66f7c93",
+                            "DRX026011_DRR028935_2.fastq.gz:md5,b97b1e0e806bcae10a7443e2f22d6ca2"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "ERX1188904_ERR1109373",
+                            "run_accession": "ERR1109373",
+                            "experiment_accession": "ERX1188904",
+                            "sample_accession": "SAMEA3643867",
+                            "secondary_sample_accession": "ERS951016",
+                            "study_accession": "PRJEB11633",
+                            "secondary_study_accession": "ERP013030",
+                            "submission_accession": "ERA528939",
+                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
+                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
+                            "sample_alias": "sample_56",
+                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
+                            "library_layout": "PAIRED",
+                            "library_selection": "RT-PCR",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "RNA-Seq",
+                            "library_name": "unspecified",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "29700",
+                            "read_count": "169",
+                            "tax_id": "63433",
+                            "scientific_name": "Leptopilina boulardi",
+                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
+                            "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
+                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
+                            "fastq_bytes": "3221;8151;8118",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
+                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
+                            "single_end": false
+                        },
+                        [
+                            "ERX1188904_ERR1109373_1.fastq.gz:md5,e7edae2715dfaf4c318d37959fd9ae22",
+                            "ERX1188904_ERR1109373_2.fastq.gz:md5,34ab048c92201a5ec4ab36d8dc1c5732"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "ERX1234253_ERR1160846",
+                            "run_accession": "ERR1160846",
+                            "experiment_accession": "ERX1234253",
+                            "sample_accession": "SAMEA3687214",
+                            "secondary_sample_accession": "ERS994363",
+                            "study_accession": "PRJEB11419",
+                            "secondary_study_accession": "ERP012803",
+                            "submission_accession": "ERA541392",
+                            "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                            "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                            "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                            "study_alias": "qiita_sid_10317",
+                            "library_layout": "SINGLE",
+                            "library_selection": "PCR",
+                            "library_source": "METAGENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "10317.BLANK.93.3E.r22",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "35658",
+                            "read_count": "283",
+                            "tax_id": "256318",
+                            "scientific_name": "metagenome",
+                            "sample_title": "10317.BLANK.93.3E.r22",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                            "study_title": "American Gut Project",
+                            "sample_description": "American Gut control",
+                            "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                            "fastq_bytes": "18077",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "ERX1234253_ERR1160846.fastq.gz:md5,22683b24b2467494e430643423f1e275"
+                    ],
+                    [
+                        {
+                            "id": "SRX10940790_SRR14593545",
+                            "run_accession": "SRR14593545",
+                            "experiment_accession": "SRX10940790",
+                            "sample_accession": "SAMN19097423",
+                            "secondary_sample_accession": "SRS9020442",
+                            "study_accession": "PRJNA728650",
+                            "secondary_study_accession": "SRP319413",
+                            "submission_accession": "SRA1234280",
+                            "run_alias": "577-6_530058_19-037147 Goat_F.ab1",
+                            "experiment_alias": "PRNP_2765",
+                            "sample_alias": "prp_2765",
+                            "study_alias": "PRJNA728650",
+                            "library_layout": "PAIRED",
+                            "library_selection": "PCR",
+                            "library_source": "GENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "PRNP_2765",
+                            "instrument_model": "AB 3500xL Genetic Analyzer",
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+                            "base_count": "828",
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+                            "secondary_sample_accession": "SRS7713669",
+                            "study_accession": "PRJNA678298",
+                            "secondary_study_accession": "SRP292504",
+                            "submission_accession": "SRA1158402",
+                            "run_alias": "GSM4907283_r4",
+                            "experiment_alias": "GSM4907283",
+                            "sample_alias": "GSM4907283",
+                            "study_alias": "GSE159787",
+                            "library_layout": "PAIRED",
+                            "library_selection": "other",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "OTHER",
+                            "library_name": "",
+                            "instrument_model": "NextSeq 550",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "2214488",
+                            "read_count": "29138",
+                            "tax_id": "9606",
+                            "scientific_name": "Homo sapiens",
+                            "sample_title": "A20-35 A11A20-35 A11_ROI009PanCK+",
+                            "experiment_title": "NextSeq 550 sequencing: GSM4907283: A20-35 A11A20-35 A11_ROI009PanCK+ Homo sapiens OTHER",
+                            "study_title": "Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]",
+                            "sample_description": "A20-35 A11A20-35 A11_ROI009PanCK+",
+                            "fastq_md5": "795d460abff6009c7f5ff7c14b773fbe;c3f34379356b28d6dac7212abc1a0a04",
+                            "fastq_bytes": "709867;716862",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "md5_1": "795d460abff6009c7f5ff7c14b773fbe",
+                            "md5_2": "c3f34379356b28d6dac7212abc1a0a04",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9504942_SRR13055520_1.fastq.gz:md5,cc75af896ec8a7cececb37851b0c6fcd",
+                            "SRX9504942_SRR13055520_2.fastq.gz:md5,fe3e2bf9f738e4959243fad59e879eae"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "run_accession": "SRR13191702",
+                            "experiment_accession": "SRX9626017",
+                            "sample_accession": "SAMN16980141",
+                            "secondary_sample_accession": "SRS7827211",
+                            "study_accession": "PRJNA682076",
+                            "secondary_study_accession": "SRP295653",
+                            "submission_accession": "SRA1166126",
+                            "run_alias": "S.170804.00784_662_L001_R1_001.fastq.gz",
+                            "experiment_alias": "S.170804.00784",
+                            "sample_alias": "S.170804.00784_662",
+                            "study_alias": "PRJNA682076",
+                            "library_layout": "PAIRED",
+                            "library_selection": "PCR",
+                            "library_source": "METAGENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "S.170804.00784",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "45682",
+                            "read_count": "91",
+                            "tax_id": "408170",
+                            "scientific_name": "human gut metagenome",
+                            "sample_title": "Metagenome or environmental sample from human gut metagenome",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
+                            "study_title": "Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
+                            "sample_description": "Metagenome or environmental sample from human gut metagenome",
+                            "fastq_md5": "89c5be920021a035084d8aeb74f32df7;56271be38a80db78ef3bdfc5d9909b98",
+                            "fastq_bytes": "15420;16324",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af"
+                        ]
+                    ]
+                ],
+                "mappings": [
+                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                ],
+                "samplesheet": [
+                    "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556"
+                ],
+                "versions": [
+                    "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                ]
+            }
+        ],
+        "timestamp": "2023-09-11T19:02:05.556134"
+    }
+}
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
new file mode 100644
index 00000000..0ce0c230
--- /dev/null
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -0,0 +1,31 @@
+nextflow_workflow {
+
+    name "Test workflow: sra/main.nf"
+    script "workflows/sra/main.nf"
+    workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
+    tag "sra_nf_core_pipeline_atacseq"
+
+    test("Parameters: --nf_core_pipeline atacseq") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                """
+            }
+            params {
+                outdir = "results"
+                nf_core_pipeline = "atacseq"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
new file mode 100644
index 00000000..f6528e52
--- /dev/null
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
@@ -0,0 +1,1353 @@
+{
+    "Parameters: --nf_core_pipeline atacseq": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "DRX024467_DRR026872",
+                            "run_accession": "DRR026872",
+                            "experiment_accession": "DRX024467",
+                            "sample_accession": "SAMD00023098",
+                            "secondary_sample_accession": "DRS033740",
+                            "study_accession": "PRJDB4356",
+                            "secondary_study_accession": "DRP003256",
+                            "submission_accession": "DRA002758",
+                            "run_alias": "DRR026872",
+                            "experiment_alias": "DRX024467",
+                            "sample_alias": "SAMD00023098",
+                            "study_alias": "DRP003256",
+                            "library_layout": "SINGLE",
+                            "library_selection": "Restriction Digest",
+                            "library_source": "GENOMIC",
+                            "library_strategy": "OTHER",
+                            "library_name": "IpeRAD1_3",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "62550",
+                            "read_count": "417",
+                            "tax_id": "35883",
+                            "scientific_name": "Ipomoea nil",
+                            "sample_title": "F2 plant dreived from a cross between Tokyo Kokei-standard and Africa #21",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Illumina HiSeq 2500 sequencing of SAMD00023098",
+                            "study_title": "The Japanese morning glory genome sequence",
+                            "sample_description": "Keywords: GSC:MIxS MIGS:6.0",
+                            "fastq_md5": "515e5448c55e054113c4a22df5f62791",
+                            "fastq_bytes": "38447",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "515e5448c55e054113c4a22df5f62791",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791"
+                    ],
+                    [
+                        {
+                            "id": "DRX026011_DRR028935",
+                            "run_accession": "DRR028935",
+                            "experiment_accession": "DRX026011",
+                            "sample_accession": "SAMD00024405",
+                            "secondary_sample_accession": "DRS019431",
+                            "study_accession": "PRJDB3420",
+                            "secondary_study_accession": "DRP002616",
+                            "submission_accession": "DRA002949",
+                            "run_alias": "DRR028935",
+                            "experiment_alias": "DRX026011",
+                            "sample_alias": "SAMD00024405",
+                            "study_alias": "DRP002616",
+                            "library_layout": "PAIRED",
+                            "library_selection": "cDNA",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "RNA-Seq",
+                            "library_name": "day0_BbSQE-I",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "194930",
+                            "read_count": "965",
+                            "tax_id": "1202541",
+                            "scientific_name": "Botryococcus braunii Showa",
+                            "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
+                            "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
+                            "sample_description": "Liquid culture",
+                            "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
+                            "fastq_bytes": "60275;61610",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
+                            "md5_2": "941c9998d746416dad53c94c480ddf30",
+                            "single_end": false
+                        },
+                        [
+                            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
+                            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "ERX1188904_ERR1109373",
+                            "run_accession": "ERR1109373",
+                            "experiment_accession": "ERX1188904",
+                            "sample_accession": "SAMEA3643867",
+                            "secondary_sample_accession": "ERS951016",
+                            "study_accession": "PRJEB11633",
+                            "secondary_study_accession": "ERP013030",
+                            "submission_accession": "ERA528939",
+                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
+                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
+                            "sample_alias": "sample_56",
+                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
+                            "library_layout": "PAIRED",
+                            "library_selection": "RT-PCR",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "RNA-Seq",
+                            "library_name": "unspecified",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "29700",
+                            "read_count": "169",
+                            "tax_id": "63433",
+                            "scientific_name": "Leptopilina boulardi",
+                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
+                            "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
+                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
+                            "fastq_bytes": "3221;8151;8118",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
+                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
+                            "single_end": false
+                        },
+                        [
+                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
+                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "ERX1234253_ERR1160846",
+                            "run_accession": "ERR1160846",
+                            "experiment_accession": "ERX1234253",
+                            "sample_accession": "SAMEA3687214",
+                            "secondary_sample_accession": "ERS994363",
+                            "study_accession": "PRJEB11419",
+                            "secondary_study_accession": "ERP012803",
+                            "submission_accession": "ERA541392",
+                            "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                            "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                            "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                            "study_alias": "qiita_sid_10317",
+                            "library_layout": "SINGLE",
+                            "library_selection": "PCR",
+                            "library_source": "METAGENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "10317.BLANK.93.3E.r22",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "35658",
+                            "read_count": "283",
+                            "tax_id": "256318",
+                            "scientific_name": "metagenome",
+                            "sample_title": "10317.BLANK.93.3E.r22",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                            "study_title": "American Gut Project",
+                            "sample_description": "American Gut control",
+                            "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                            "fastq_bytes": "18077",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6"
+                    ],
+                    [
+                        {
+                            "id": "SRX10940790_SRR14593545",
+                            "run_accession": "SRR14593545",
+                            "experiment_accession": "SRX10940790",
+                            "sample_accession": "SAMN19097423",
+                            "secondary_sample_accession": "SRS9020442",
+                            "study_accession": "PRJNA728650",
+                            "secondary_study_accession": "SRP319413",
+                            "submission_accession": "SRA1234280",
+                            "run_alias": "577-6_530058_19-037147 Goat_F.ab1",
+                            "experiment_alias": "PRNP_2765",
+                            "sample_alias": "prp_2765",
+                            "study_alias": "PRJNA728650",
+                            "library_layout": "PAIRED",
+                            "library_selection": "PCR",
+                            "library_source": "GENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "PRNP_2765",
+                            "instrument_model": "AB 3500xL Genetic Analyzer",
+                            "instrument_platform": "CAPILLARY",
+                            "base_count": "828",
+                            "read_count": "1",
+                            "tax_id": "9925",
+                            "scientific_name": "Capra hircus",
+                            "sample_title": "MIGS Eukaryotic sample from Capra hircus",
+                            "experiment_title": "AB 3500xL Genetic Analyzer sequencing: prp_2765",
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+                            "library_name": "",
+                            "instrument_model": "NextSeq 550",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "2214488",
+                            "read_count": "29138",
+                            "tax_id": "9606",
+                            "scientific_name": "Homo sapiens",
+                            "sample_title": "A20-35 A11A20-35 A11_ROI009PanCK+",
+                            "experiment_title": "NextSeq 550 sequencing: GSM4907283: A20-35 A11A20-35 A11_ROI009PanCK+ Homo sapiens OTHER",
+                            "study_title": "Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]",
+                            "sample_description": "A20-35 A11A20-35 A11_ROI009PanCK+",
+                            "fastq_md5": "795d460abff6009c7f5ff7c14b773fbe;c3f34379356b28d6dac7212abc1a0a04",
+                            "fastq_bytes": "709867;716862",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "md5_1": "795d460abff6009c7f5ff7c14b773fbe",
+                            "md5_2": "c3f34379356b28d6dac7212abc1a0a04",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
+                            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "run_accession": "SRR13191702",
+                            "experiment_accession": "SRX9626017",
+                            "sample_accession": "SAMN16980141",
+                            "secondary_sample_accession": "SRS7827211",
+                            "study_accession": "PRJNA682076",
+                            "secondary_study_accession": "SRP295653",
+                            "submission_accession": "SRA1166126",
+                            "run_alias": "S.170804.00784_662_L001_R1_001.fastq.gz",
+                            "experiment_alias": "S.170804.00784",
+                            "sample_alias": "S.170804.00784_662",
+                            "study_alias": "PRJNA682076",
+                            "library_layout": "PAIRED",
+                            "library_selection": "PCR",
+                            "library_source": "METAGENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "S.170804.00784",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "45682",
+                            "read_count": "91",
+                            "tax_id": "408170",
+                            "scientific_name": "human gut metagenome",
+                            "sample_title": "Metagenome or environmental sample from human gut metagenome",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
+                            "study_title": "Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
+                            "sample_description": "Metagenome or environmental sample from human gut metagenome",
+                            "fastq_md5": "89c5be920021a035084d8aeb74f32df7;56271be38a80db78ef3bdfc5d9909b98",
+                            "fastq_bytes": "15420;16324",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
+                        ]
+                    ]
+                ],
+                "mappings": [
+                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                ],
+                "samplesheet": [
+                    "samplesheet.csv:md5,16e5161103702777b2d763c1ed660d3c"
+                ],
+                "versions": [
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                ]
+            }
+        ],
+        "timestamp": "2023-09-11T18:37:54.607231"
+    }
+}
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
new file mode 100644
index 00000000..67c0fbe4
--- /dev/null
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -0,0 +1,31 @@
+nextflow_workflow {
+
+    name "Test workflow: sra/main.nf"
+    script "workflows/sra/main.nf"
+    workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
+    tag "sra_nf_core_pipeline_rnaseq"
+
+    test("Parameters: --nf_core_pipeline rnaseq") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                """
+            }
+            params {
+                outdir = "results"
+                nf_core_pipeline = "rnaseq"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
new file mode 100644
index 00000000..124877ae
--- /dev/null
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
@@ -0,0 +1,1353 @@
+{
+    "Parameters: --nf_core_pipeline rnaseq": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "DRX024467_DRR026872",
+                            "run_accession": "DRR026872",
+                            "experiment_accession": "DRX024467",
+                            "sample_accession": "SAMD00023098",
+                            "secondary_sample_accession": "DRS033740",
+                            "study_accession": "PRJDB4356",
+                            "secondary_study_accession": "DRP003256",
+                            "submission_accession": "DRA002758",
+                            "run_alias": "DRR026872",
+                            "experiment_alias": "DRX024467",
+                            "sample_alias": "SAMD00023098",
+                            "study_alias": "DRP003256",
+                            "library_layout": "SINGLE",
+                            "library_selection": "Restriction Digest",
+                            "library_source": "GENOMIC",
+                            "library_strategy": "OTHER",
+                            "library_name": "IpeRAD1_3",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "62550",
+                            "read_count": "417",
+                            "tax_id": "35883",
+                            "scientific_name": "Ipomoea nil",
+                            "sample_title": "F2 plant dreived from a cross between Tokyo Kokei-standard and Africa #21",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Illumina HiSeq 2500 sequencing of SAMD00023098",
+                            "study_title": "The Japanese morning glory genome sequence",
+                            "sample_description": "Keywords: GSC:MIxS MIGS:6.0",
+                            "fastq_md5": "515e5448c55e054113c4a22df5f62791",
+                            "fastq_bytes": "38447",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "515e5448c55e054113c4a22df5f62791",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791"
+                    ],
+                    [
+                        {
+                            "id": "DRX026011_DRR028935",
+                            "run_accession": "DRR028935",
+                            "experiment_accession": "DRX026011",
+                            "sample_accession": "SAMD00024405",
+                            "secondary_sample_accession": "DRS019431",
+                            "study_accession": "PRJDB3420",
+                            "secondary_study_accession": "DRP002616",
+                            "submission_accession": "DRA002949",
+                            "run_alias": "DRR028935",
+                            "experiment_alias": "DRX026011",
+                            "sample_alias": "SAMD00024405",
+                            "study_alias": "DRP002616",
+                            "library_layout": "PAIRED",
+                            "library_selection": "cDNA",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "RNA-Seq",
+                            "library_name": "day0_BbSQE-I",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "194930",
+                            "read_count": "965",
+                            "tax_id": "1202541",
+                            "scientific_name": "Botryococcus braunii Showa",
+                            "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
+                            "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
+                            "sample_description": "Liquid culture",
+                            "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
+                            "fastq_bytes": "60275;61610",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
+                            "md5_2": "941c9998d746416dad53c94c480ddf30",
+                            "single_end": false
+                        },
+                        [
+                            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
+                            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "ERX1188904_ERR1109373",
+                            "run_accession": "ERR1109373",
+                            "experiment_accession": "ERX1188904",
+                            "sample_accession": "SAMEA3643867",
+                            "secondary_sample_accession": "ERS951016",
+                            "study_accession": "PRJEB11633",
+                            "secondary_study_accession": "ERP013030",
+                            "submission_accession": "ERA528939",
+                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
+                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
+                            "sample_alias": "sample_56",
+                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
+                            "library_layout": "PAIRED",
+                            "library_selection": "RT-PCR",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "RNA-Seq",
+                            "library_name": "unspecified",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "29700",
+                            "read_count": "169",
+                            "tax_id": "63433",
+                            "scientific_name": "Leptopilina boulardi",
+                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
+                            "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
+                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
+                            "fastq_bytes": "3221;8151;8118",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
+                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
+                            "single_end": false
+                        },
+                        [
+                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
+                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "ERX1234253_ERR1160846",
+                            "run_accession": "ERR1160846",
+                            "experiment_accession": "ERX1234253",
+                            "sample_accession": "SAMEA3687214",
+                            "secondary_sample_accession": "ERS994363",
+                            "study_accession": "PRJEB11419",
+                            "secondary_study_accession": "ERP012803",
+                            "submission_accession": "ERA541392",
+                            "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                            "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                            "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                            "study_alias": "qiita_sid_10317",
+                            "library_layout": "SINGLE",
+                            "library_selection": "PCR",
+                            "library_source": "METAGENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "10317.BLANK.93.3E.r22",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "35658",
+                            "read_count": "283",
+                            "tax_id": "256318",
+                            "scientific_name": "metagenome",
+                            "sample_title": "10317.BLANK.93.3E.r22",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                            "study_title": "American Gut Project",
+                            "sample_description": "American Gut control",
+                            "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                            "fastq_bytes": "18077",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6"
+                    ],
+                    [
+                        {
+                            "id": "SRX10940790_SRR14593545",
+                            "run_accession": "SRR14593545",
+                            "experiment_accession": "SRX10940790",
+                            "sample_accession": "SAMN19097423",
+                            "secondary_sample_accession": "SRS9020442",
+                            "study_accession": "PRJNA728650",
+                            "secondary_study_accession": "SRP319413",
+                            "submission_accession": "SRA1234280",
+                            "run_alias": "577-6_530058_19-037147 Goat_F.ab1",
+                            "experiment_alias": "PRNP_2765",
+                            "sample_alias": "prp_2765",
+                            "study_alias": "PRJNA728650",
+                            "library_layout": "PAIRED",
+                            "library_selection": "PCR",
+                            "library_source": "GENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "PRNP_2765",
+                            "instrument_model": "AB 3500xL Genetic Analyzer",
+                            "instrument_platform": "CAPILLARY",
+                            "base_count": "828",
+                            "read_count": "1",
+                            "tax_id": "9925",
+                            "scientific_name": "Capra hircus",
+                            "sample_title": "MIGS Eukaryotic sample from Capra hircus",
+                            "experiment_title": "AB 3500xL Genetic Analyzer sequencing: prp_2765",
+                            "study_title": "Capra hircus Raw sequence reads",
+                            "sample_description": "Keywords: GSC:MIxS MIGS:5.0",
+                            "fastq_md5": "",
+                            "fastq_bytes": "",
+                            "fastq_ftp": "",
+                            "fastq_galaxy": "",
+                            "fastq_aspera": "",
+                            "fastq_1": "",
+                            "fastq_2": "",
+                            "md5_1": "",
+                            "md5_2": "",
+                            "single_end": false
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+                            "study_title": "Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]",
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+                            "fastq_md5": "795d460abff6009c7f5ff7c14b773fbe;c3f34379356b28d6dac7212abc1a0a04",
+                            "fastq_bytes": "709867;716862",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "md5_1": "795d460abff6009c7f5ff7c14b773fbe",
+                            "md5_2": "c3f34379356b28d6dac7212abc1a0a04",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
+                            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "run_accession": "SRR13191702",
+                            "experiment_accession": "SRX9626017",
+                            "sample_accession": "SAMN16980141",
+                            "secondary_sample_accession": "SRS7827211",
+                            "study_accession": "PRJNA682076",
+                            "secondary_study_accession": "SRP295653",
+                            "submission_accession": "SRA1166126",
+                            "run_alias": "S.170804.00784_662_L001_R1_001.fastq.gz",
+                            "experiment_alias": "S.170804.00784",
+                            "sample_alias": "S.170804.00784_662",
+                            "study_alias": "PRJNA682076",
+                            "library_layout": "PAIRED",
+                            "library_selection": "PCR",
+                            "library_source": "METAGENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "S.170804.00784",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "45682",
+                            "read_count": "91",
+                            "tax_id": "408170",
+                            "scientific_name": "human gut metagenome",
+                            "sample_title": "Metagenome or environmental sample from human gut metagenome",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
+                            "study_title": "Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
+                            "sample_description": "Metagenome or environmental sample from human gut metagenome",
+                            "fastq_md5": "89c5be920021a035084d8aeb74f32df7;56271be38a80db78ef3bdfc5d9909b98",
+                            "fastq_bytes": "15420;16324",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
+                        ]
+                    ]
+                ],
+                "mappings": [
+                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                ],
+                "samplesheet": [
+                    "samplesheet.csv:md5,fcbb1fbe56dc14561ec83e5f6a70ee80"
+                ],
+                "versions": [
+                    "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                ]
+            }
+        ],
+        "timestamp": "2023-09-11T18:51:38.198125"
+    }
+}
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
new file mode 100644
index 00000000..e00793cd
--- /dev/null
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -0,0 +1,31 @@
+nextflow_workflow {
+
+    name "Test workflow: sra/main.nf"
+    script "workflows/sra/main.nf"
+    workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
+    tag "sra_nf_core_pipeline_taxprofiler"
+
+    test("Parameters: --nf_core_pipeline taxprofiler") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                """
+            }
+            params {
+                outdir = "results"
+                nf_core_pipeline = "taxprofiler"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
new file mode 100644
index 00000000..b63ad4b7
--- /dev/null
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
@@ -0,0 +1,1353 @@
+{
+    "Parameters: --nf_core_pipeline taxprofiler": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "DRX024467_DRR026872",
+                            "run_accession": "DRR026872",
+                            "experiment_accession": "DRX024467",
+                            "sample_accession": "SAMD00023098",
+                            "secondary_sample_accession": "DRS033740",
+                            "study_accession": "PRJDB4356",
+                            "secondary_study_accession": "DRP003256",
+                            "submission_accession": "DRA002758",
+                            "run_alias": "DRR026872",
+                            "experiment_alias": "DRX024467",
+                            "sample_alias": "SAMD00023098",
+                            "study_alias": "DRP003256",
+                            "library_layout": "SINGLE",
+                            "library_selection": "Restriction Digest",
+                            "library_source": "GENOMIC",
+                            "library_strategy": "OTHER",
+                            "library_name": "IpeRAD1_3",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "62550",
+                            "read_count": "417",
+                            "tax_id": "35883",
+                            "scientific_name": "Ipomoea nil",
+                            "sample_title": "F2 plant dreived from a cross between Tokyo Kokei-standard and Africa #21",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Illumina HiSeq 2500 sequencing of SAMD00023098",
+                            "study_title": "The Japanese morning glory genome sequence",
+                            "sample_description": "Keywords: GSC:MIxS MIGS:6.0",
+                            "fastq_md5": "515e5448c55e054113c4a22df5f62791",
+                            "fastq_bytes": "38447",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "515e5448c55e054113c4a22df5f62791",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791"
+                    ],
+                    [
+                        {
+                            "id": "DRX026011_DRR028935",
+                            "run_accession": "DRR028935",
+                            "experiment_accession": "DRX026011",
+                            "sample_accession": "SAMD00024405",
+                            "secondary_sample_accession": "DRS019431",
+                            "study_accession": "PRJDB3420",
+                            "secondary_study_accession": "DRP002616",
+                            "submission_accession": "DRA002949",
+                            "run_alias": "DRR028935",
+                            "experiment_alias": "DRX026011",
+                            "sample_alias": "SAMD00024405",
+                            "study_alias": "DRP002616",
+                            "library_layout": "PAIRED",
+                            "library_selection": "cDNA",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "RNA-Seq",
+                            "library_name": "day0_BbSQE-I",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "194930",
+                            "read_count": "965",
+                            "tax_id": "1202541",
+                            "scientific_name": "Botryococcus braunii Showa",
+                            "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
+                            "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
+                            "sample_description": "Liquid culture",
+                            "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
+                            "fastq_bytes": "60275;61610",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
+                            "md5_2": "941c9998d746416dad53c94c480ddf30",
+                            "single_end": false
+                        },
+                        [
+                            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
+                            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "ERX1188904_ERR1109373",
+                            "run_accession": "ERR1109373",
+                            "experiment_accession": "ERX1188904",
+                            "sample_accession": "SAMEA3643867",
+                            "secondary_sample_accession": "ERS951016",
+                            "study_accession": "PRJEB11633",
+                            "secondary_study_accession": "ERP013030",
+                            "submission_accession": "ERA528939",
+                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
+                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
+                            "sample_alias": "sample_56",
+                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
+                            "library_layout": "PAIRED",
+                            "library_selection": "RT-PCR",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "RNA-Seq",
+                            "library_name": "unspecified",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "29700",
+                            "read_count": "169",
+                            "tax_id": "63433",
+                            "scientific_name": "Leptopilina boulardi",
+                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
+                            "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
+                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
+                            "fastq_bytes": "3221;8151;8118",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
+                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
+                            "single_end": false
+                        },
+                        [
+                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
+                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "ERX1234253_ERR1160846",
+                            "run_accession": "ERR1160846",
+                            "experiment_accession": "ERX1234253",
+                            "sample_accession": "SAMEA3687214",
+                            "secondary_sample_accession": "ERS994363",
+                            "study_accession": "PRJEB11419",
+                            "secondary_study_accession": "ERP012803",
+                            "submission_accession": "ERA541392",
+                            "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                            "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                            "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                            "study_alias": "qiita_sid_10317",
+                            "library_layout": "SINGLE",
+                            "library_selection": "PCR",
+                            "library_source": "METAGENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "10317.BLANK.93.3E.r22",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "35658",
+                            "read_count": "283",
+                            "tax_id": "256318",
+                            "scientific_name": "metagenome",
+                            "sample_title": "10317.BLANK.93.3E.r22",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                            "study_title": "American Gut Project",
+                            "sample_description": "American Gut control",
+                            "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                            "fastq_bytes": "18077",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6"
+                    ],
+                    [
+                        {
+                            "id": "SRX10940790_SRR14593545",
+                            "run_accession": "SRR14593545",
+                            "experiment_accession": "SRX10940790",
+                            "sample_accession": "SAMN19097423",
+                            "secondary_sample_accession": "SRS9020442",
+                            "study_accession": "PRJNA728650",
+                            "secondary_study_accession": "SRP319413",
+                            "submission_accession": "SRA1234280",
+                            "run_alias": "577-6_530058_19-037147 Goat_F.ab1",
+                            "experiment_alias": "PRNP_2765",
+                            "sample_alias": "prp_2765",
+                            "study_alias": "PRJNA728650",
+                            "library_layout": "PAIRED",
+                            "library_selection": "PCR",
+                            "library_source": "GENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "PRNP_2765",
+                            "instrument_model": "AB 3500xL Genetic Analyzer",
+                            "instrument_platform": "CAPILLARY",
+                            "base_count": "828",
+                            "read_count": "1",
+                            "tax_id": "9925",
+                            "scientific_name": "Capra hircus",
+                            "sample_title": "MIGS Eukaryotic sample from Capra hircus",
+                            "experiment_title": "AB 3500xL Genetic Analyzer sequencing: prp_2765",
+                            "study_title": "Capra hircus Raw sequence reads",
+                            "sample_description": "Keywords: GSC:MIxS MIGS:5.0",
+                            "fastq_md5": "",
+                            "fastq_bytes": "",
+                            "fastq_ftp": "",
+                            "fastq_galaxy": "",
+                            "fastq_aspera": "",
+                            "fastq_1": "",
+                            "fastq_2": "",
+                            "md5_1": "",
+                            "md5_2": "",
+                            "single_end": false
+                        },
+                        [
+                            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
+                            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX11047067_SRR14709033",
+                            "run_accession": "SRR14709033",
+                            "experiment_accession": "SRX11047067",
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+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "md5_1": "795d460abff6009c7f5ff7c14b773fbe",
+                            "md5_2": "c3f34379356b28d6dac7212abc1a0a04",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
+                            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "run_accession": "SRR13191702",
+                            "experiment_accession": "SRX9626017",
+                            "sample_accession": "SAMN16980141",
+                            "secondary_sample_accession": "SRS7827211",
+                            "study_accession": "PRJNA682076",
+                            "secondary_study_accession": "SRP295653",
+                            "submission_accession": "SRA1166126",
+                            "run_alias": "S.170804.00784_662_L001_R1_001.fastq.gz",
+                            "experiment_alias": "S.170804.00784",
+                            "sample_alias": "S.170804.00784_662",
+                            "study_alias": "PRJNA682076",
+                            "library_layout": "PAIRED",
+                            "library_selection": "PCR",
+                            "library_source": "METAGENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "S.170804.00784",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "45682",
+                            "read_count": "91",
+                            "tax_id": "408170",
+                            "scientific_name": "human gut metagenome",
+                            "sample_title": "Metagenome or environmental sample from human gut metagenome",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
+                            "study_title": "Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
+                            "sample_description": "Metagenome or environmental sample from human gut metagenome",
+                            "fastq_md5": "89c5be920021a035084d8aeb74f32df7;56271be38a80db78ef3bdfc5d9909b98",
+                            "fastq_bytes": "15420;16324",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
+                        ]
+                    ]
+                ],
+                "mappings": [
+                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                ],
+                "samplesheet": [
+                    "samplesheet.csv:md5,0df1f60a9b5bc94f8a85e96edcc90f5c"
+                ],
+                "versions": [
+                    "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                ]
+            }
+        ],
+        "timestamp": "2023-09-11T18:44:02.293186"
+    }
+}
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
new file mode 100644
index 00000000..045e0363
--- /dev/null
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -0,0 +1,31 @@
+nextflow_workflow {
+
+    name "Test workflow: sra/main.nf"
+    script "workflows/sra/main.nf"
+    workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
+    tag "sra_nf_core_pipeline_viralrecon"
+
+    test("Parameters: --nf_core_pipeline viralrecon") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                """
+            }
+            params {
+                outdir = "results"
+                nf_core_pipeline = "viralrecon"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
new file mode 100644
index 00000000..1387f422
--- /dev/null
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
@@ -0,0 +1,1353 @@
+{
+    "Parameters: --nf_core_pipeline viralrecon": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "DRX024467_DRR026872",
+                            "run_accession": "DRR026872",
+                            "experiment_accession": "DRX024467",
+                            "sample_accession": "SAMD00023098",
+                            "secondary_sample_accession": "DRS033740",
+                            "study_accession": "PRJDB4356",
+                            "secondary_study_accession": "DRP003256",
+                            "submission_accession": "DRA002758",
+                            "run_alias": "DRR026872",
+                            "experiment_alias": "DRX024467",
+                            "sample_alias": "SAMD00023098",
+                            "study_alias": "DRP003256",
+                            "library_layout": "SINGLE",
+                            "library_selection": "Restriction Digest",
+                            "library_source": "GENOMIC",
+                            "library_strategy": "OTHER",
+                            "library_name": "IpeRAD1_3",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "62550",
+                            "read_count": "417",
+                            "tax_id": "35883",
+                            "scientific_name": "Ipomoea nil",
+                            "sample_title": "F2 plant dreived from a cross between Tokyo Kokei-standard and Africa #21",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Illumina HiSeq 2500 sequencing of SAMD00023098",
+                            "study_title": "The Japanese morning glory genome sequence",
+                            "sample_description": "Keywords: GSC:MIxS MIGS:6.0",
+                            "fastq_md5": "515e5448c55e054113c4a22df5f62791",
+                            "fastq_bytes": "38447",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "515e5448c55e054113c4a22df5f62791",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791"
+                    ],
+                    [
+                        {
+                            "id": "DRX026011_DRR028935",
+                            "run_accession": "DRR028935",
+                            "experiment_accession": "DRX026011",
+                            "sample_accession": "SAMD00024405",
+                            "secondary_sample_accession": "DRS019431",
+                            "study_accession": "PRJDB3420",
+                            "secondary_study_accession": "DRP002616",
+                            "submission_accession": "DRA002949",
+                            "run_alias": "DRR028935",
+                            "experiment_alias": "DRX026011",
+                            "sample_alias": "SAMD00024405",
+                            "study_alias": "DRP002616",
+                            "library_layout": "PAIRED",
+                            "library_selection": "cDNA",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "RNA-Seq",
+                            "library_name": "day0_BbSQE-I",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "194930",
+                            "read_count": "965",
+                            "tax_id": "1202541",
+                            "scientific_name": "Botryococcus braunii Showa",
+                            "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
+                            "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
+                            "sample_description": "Liquid culture",
+                            "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
+                            "fastq_bytes": "60275;61610",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                            "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
+                            "md5_2": "941c9998d746416dad53c94c480ddf30",
+                            "single_end": false
+                        },
+                        [
+                            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
+                            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "ERX1188904_ERR1109373",
+                            "run_accession": "ERR1109373",
+                            "experiment_accession": "ERX1188904",
+                            "sample_accession": "SAMEA3643867",
+                            "secondary_sample_accession": "ERS951016",
+                            "study_accession": "PRJEB11633",
+                            "secondary_study_accession": "ERP013030",
+                            "submission_accession": "ERA528939",
+                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
+                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
+                            "sample_alias": "sample_56",
+                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
+                            "library_layout": "PAIRED",
+                            "library_selection": "RT-PCR",
+                            "library_source": "TRANSCRIPTOMIC",
+                            "library_strategy": "RNA-Seq",
+                            "library_name": "unspecified",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "29700",
+                            "read_count": "169",
+                            "tax_id": "63433",
+                            "scientific_name": "Leptopilina boulardi",
+                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
+                            "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
+                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
+                            "fastq_bytes": "3221;8151;8118",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
+                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
+                            "single_end": false
+                        },
+                        [
+                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
+                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "ERX1234253_ERR1160846",
+                            "run_accession": "ERR1160846",
+                            "experiment_accession": "ERX1234253",
+                            "sample_accession": "SAMEA3687214",
+                            "secondary_sample_accession": "ERS994363",
+                            "study_accession": "PRJEB11419",
+                            "secondary_study_accession": "ERP012803",
+                            "submission_accession": "ERA541392",
+                            "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                            "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                            "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                            "study_alias": "qiita_sid_10317",
+                            "library_layout": "SINGLE",
+                            "library_selection": "PCR",
+                            "library_source": "METAGENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "10317.BLANK.93.3E.r22",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "35658",
+                            "read_count": "283",
+                            "tax_id": "256318",
+                            "scientific_name": "metagenome",
+                            "sample_title": "10317.BLANK.93.3E.r22",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                            "study_title": "American Gut Project",
+                            "sample_description": "American Gut control",
+                            "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                            "fastq_bytes": "18077",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                            "fastq_2": "",
+                            "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                            "md5_2": "",
+                            "single_end": true
+                        },
+                        "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6"
+                    ],
+                    [
+                        {
+                            "id": "SRX10940790_SRR14593545",
+                            "run_accession": "SRR14593545",
+                            "experiment_accession": "SRX10940790",
+                            "sample_accession": "SAMN19097423",
+                            "secondary_sample_accession": "SRS9020442",
+                            "study_accession": "PRJNA728650",
+                            "secondary_study_accession": "SRP319413",
+                            "submission_accession": "SRA1234280",
+                            "run_alias": "577-6_530058_19-037147 Goat_F.ab1",
+                            "experiment_alias": "PRNP_2765",
+                            "sample_alias": "prp_2765",
+                            "study_alias": "PRJNA728650",
+                            "library_layout": "PAIRED",
+                            "library_selection": "PCR",
+                            "library_source": "GENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "PRNP_2765",
+                            "instrument_model": "AB 3500xL Genetic Analyzer",
+                            "instrument_platform": "CAPILLARY",
+                            "base_count": "828",
+                            "read_count": "1",
+                            "tax_id": "9925",
+                            "scientific_name": "Capra hircus",
+                            "sample_title": "MIGS Eukaryotic sample from Capra hircus",
+                            "experiment_title": "AB 3500xL Genetic Analyzer sequencing: prp_2765",
+                            "study_title": "Capra hircus Raw sequence reads",
+                            "sample_description": "Keywords: GSC:MIxS MIGS:5.0",
+                            "fastq_md5": "",
+                            "fastq_bytes": "",
+                            "fastq_ftp": "",
+                            "fastq_galaxy": "",
+                            "fastq_aspera": "",
+                            "fastq_1": "",
+                            "fastq_2": "",
+                            "md5_1": "",
+                            "md5_2": "",
+                            "single_end": false
+                        },
+                        [
+                            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
+                            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX11047067_SRR14709033",
+                            "run_accession": "SRR14709033",
+                            "experiment_accession": "SRX11047067",
+                            "sample_accession": "SAMN19373034",
+                            "secondary_sample_accession": "SRS9115923",
+                            "study_accession": "PRJNA733285",
+                            "secondary_study_accession": "SRP322267",
+                            "submission_accession": "SRA1239521",
+                            "run_alias": "Sebastes_levis-2.fastq",
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+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
+                            "md5_1": "795d460abff6009c7f5ff7c14b773fbe",
+                            "md5_2": "c3f34379356b28d6dac7212abc1a0a04",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
+                            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "run_accession": "SRR13191702",
+                            "experiment_accession": "SRX9626017",
+                            "sample_accession": "SAMN16980141",
+                            "secondary_sample_accession": "SRS7827211",
+                            "study_accession": "PRJNA682076",
+                            "secondary_study_accession": "SRP295653",
+                            "submission_accession": "SRA1166126",
+                            "run_alias": "S.170804.00784_662_L001_R1_001.fastq.gz",
+                            "experiment_alias": "S.170804.00784",
+                            "sample_alias": "S.170804.00784_662",
+                            "study_alias": "PRJNA682076",
+                            "library_layout": "PAIRED",
+                            "library_selection": "PCR",
+                            "library_source": "METAGENOMIC",
+                            "library_strategy": "AMPLICON",
+                            "library_name": "S.170804.00784",
+                            "instrument_model": "Illumina HiSeq 2500",
+                            "instrument_platform": "ILLUMINA",
+                            "base_count": "45682",
+                            "read_count": "91",
+                            "tax_id": "408170",
+                            "scientific_name": "human gut metagenome",
+                            "sample_title": "Metagenome or environmental sample from human gut metagenome",
+                            "experiment_title": "Illumina HiSeq 2500 sequencing: Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
+                            "study_title": "Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
+                            "sample_description": "Metagenome or environmental sample from human gut metagenome",
+                            "fastq_md5": "89c5be920021a035084d8aeb74f32df7;56271be38a80db78ef3bdfc5d9909b98",
+                            "fastq_bytes": "15420;16324",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz",
+                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98",
+                            "single_end": false
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
+                        ]
+                    ]
+                ],
+                "mappings": [
+                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                ],
+                "samplesheet": [
+                    "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556"
+                ],
+                "versions": [
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                ]
+            }
+        ],
+        "timestamp": "2023-09-11T18:34:25.049818"
+    }
+}
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
new file mode 100644
index 00000000..67abee3b
--- /dev/null
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -0,0 +1,31 @@
+nextflow_workflow {
+
+    name "Test workflow: sra/main.nf"
+    script "workflows/sra/main.nf"
+    workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
+    tag "sra_skip_fastq_download"
+
+    test("Parameters: --skip_fastq_download") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                """
+            }
+            params {
+                outdir = "results"
+                skip_fastq_download = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
new file mode 100644
index 00000000..3b04b917
--- /dev/null
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
@@ -0,0 +1,37 @@
+{
+    "Parameters: --skip_fastq_download": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    "samplesheet.csv:md5,7cf3503b651fe016bc1e5fb3c2e996d5"
+                ],
+                "2": [
+                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                ],
+                "3": [
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                ],
+                "fastq": [
+                    
+                ],
+                "mappings": [
+                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                ],
+                "samplesheet": [
+                    "samplesheet.csv:md5,7cf3503b651fe016bc1e5fb3c2e996d5"
+                ],
+                "versions": [
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                ]
+            }
+        ],
+        "timestamp": "2023-09-11T18:56:34.175665"
+    }
+}
\ No newline at end of file

From 23b75bc70aa22c2d1dd66ce0d1ff3c0ed1a4ff6c Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 21 Sep 2023 19:21:10 +0200
Subject: [PATCH 454/852] restore module tests

---
 .../tests/main.nf.test                        |  31 ++++
 .../tests/main.nf.test.snap                   |  52 +++++++
 .../local/sra_fastq_ftp/tests/main.nf.test    |  34 +++++
 .../sra_fastq_ftp/tests/main.nf.test.snap     | 140 ++++++++++++++++++
 .../sra_ids_to_runinfo/tests/main.nf.test     |  32 ++++
 .../tests/main.nf.test.snap                   |  21 +++
 .../sra_merge_samplesheet/tests/main.nf.test  |  32 ++++
 .../tests/main.nf.test.snap                   |  27 ++++
 .../sra_runinfo_to_ftp/tests/main.nf.test     |  31 ++++
 .../tests/main.nf.test.snap                   |  21 +++
 .../sra_to_samplesheet/tests/main.nf.test     |  34 +++++
 .../tests/main.nf.test.snap                   | 113 ++++++++++++++
 12 files changed, 568 insertions(+)
 create mode 100644 modules/local/multiqc_mappings_config/tests/main.nf.test
 create mode 100644 modules/local/multiqc_mappings_config/tests/main.nf.test.snap
 create mode 100644 modules/local/sra_fastq_ftp/tests/main.nf.test
 create mode 100644 modules/local/sra_fastq_ftp/tests/main.nf.test.snap
 create mode 100644 modules/local/sra_ids_to_runinfo/tests/main.nf.test
 create mode 100644 modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap
 create mode 100644 modules/local/sra_merge_samplesheet/tests/main.nf.test
 create mode 100644 modules/local/sra_merge_samplesheet/tests/main.nf.test.snap
 create mode 100644 modules/local/sra_runinfo_to_ftp/tests/main.nf.test
 create mode 100644 modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap
 create mode 100644 modules/local/sra_to_samplesheet/tests/main.nf.test
 create mode 100644 modules/local/sra_to_samplesheet/tests/main.nf.test.snap

diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test
new file mode 100644
index 00000000..3bf79537
--- /dev/null
+++ b/modules/local/multiqc_mappings_config/tests/main.nf.test
@@ -0,0 +1,31 @@
+nextflow_process {
+
+    name "Test process: MULTIQC_MAPPINGS_CONFIG"
+    script "modules/local/multiqc_mappings_config/main.nf"
+    process "MULTIQC_MAPPINGS_CONFIG"
+    tag "modules"
+    tag "modules_local"
+    tag "multiqc_mappings_config"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+
+            process {
+                """
+                input[0] = file(params.test_data['modules_local']['multiqc_mappings_config'], checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap
new file mode 100644
index 00000000..9cf7fb38
--- /dev/null
+++ b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap
@@ -0,0 +1,52 @@
+{
+    "SRX9626017_SRR13191702": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
+                        "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                ],
+                "versions": [
+                    "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                ],
+                "yml": [
+                    [
+                        "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
+                        "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2023-08-17T12:02:35+0000"
+    },
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
+                        "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                ],
+                "versions": [
+                    "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                ],
+                "yml": [
+                    [
+                        "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
+                        "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2023-08-17T12:02:35+0000"
+    }
+}
\ No newline at end of file
diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test
new file mode 100644
index 00000000..7892d156
--- /dev/null
+++ b/modules/local/sra_fastq_ftp/tests/main.nf.test
@@ -0,0 +1,34 @@
+nextflow_process {
+
+    name "Test process: SRA_FASTQ_FTP"
+    script "modules/local/sra_fastq_ftp/main.nf"
+    process "SRA_FASTQ_FTP"
+    tag "modules"
+    tag "modules_local"
+    tag "sra_fastq_ftp"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+
+            process {
+                """
+                input[0] = [
+                    [ id:'SRX9626017_SRR13191702', single_end:false, md5_1: '89c5be920021a035084d8aeb74f32df7', md5_2: '56271be38a80db78ef3bdfc5d9909b98' ], // meta map
+                    params.test_data['modules_local']['sra_fastq_ftp']
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap
new file mode 100644
index 00000000..c0d5ffdc
--- /dev/null
+++ b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap
@@ -0,0 +1,140 @@
+{
+    "SRX9626017_SRR13191702": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
+                            "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
+                        ]
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b"
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
+                        ]
+                    ]
+                ],
+                "md5": [
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
+                            "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b"
+                ]
+            }
+        ],
+        "timestamp": "2023-08-06T23:31:57+0000"
+    },
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
+                            "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
+                        ]
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b"
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
+                        ]
+                    ]
+                ],
+                "md5": [
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
+                            "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b"
+                ]
+            }
+        ],
+        "timestamp": "2023-08-06T23:31:57+0000"
+    }
+}
\ No newline at end of file
diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test
new file mode 100644
index 00000000..f8a44086
--- /dev/null
+++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test
@@ -0,0 +1,32 @@
+nextflow_process {
+
+    name "Test process: SRA_IDS_TO_RUNINFO"
+    script "modules/local/sra_ids_to_runinfo/main.nf"
+    process "SRA_IDS_TO_RUNINFO"
+    tag "modules"
+    tag "modules_local"
+    tag "sra_ids_to_runinfo"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+
+            process {
+                """
+                input[0] = 'SRR13191702'
+                input[1] = ''
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap
new file mode 100644
index 00000000..dbca931f
--- /dev/null
+++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap
@@ -0,0 +1,21 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    "SRR13191702.runinfo.tsv:md5,3a1be35781ca6e8a28d8fd4d2f3bbe85"
+                ],
+                "1": [
+                    "versions.yml:md5,1c14442e9b494b586eafe41e77300fae"
+                ],
+                "tsv": [
+                    "SRR13191702.runinfo.tsv:md5,3a1be35781ca6e8a28d8fd4d2f3bbe85"
+                ],
+                "versions": [
+                    "versions.yml:md5,1c14442e9b494b586eafe41e77300fae"
+                ]
+            }
+        ],
+        "timestamp": "2023-08-06T23:30:51+0000"
+    }
+}
\ No newline at end of file
diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test b/modules/local/sra_merge_samplesheet/tests/main.nf.test
new file mode 100644
index 00000000..e37039bd
--- /dev/null
+++ b/modules/local/sra_merge_samplesheet/tests/main.nf.test
@@ -0,0 +1,32 @@
+nextflow_process {
+
+    name "Test process: SRA_MERGE_SAMPLESHEET"
+    script "modules/local/sra_merge_samplesheet/main.nf"
+    process "SRA_MERGE_SAMPLESHEET"
+    tag "modules"
+    tag "modules_local"
+    tag "sra_merge_samplesheet"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+
+            process {
+                """
+                input[0] = params.test_data['modules_local']['sra_merge_samplesheet_samplesheets'].collect { file(it, checkIfExists: true) }
+                input[1] = params.test_data['modules_local']['sra_merge_samplesheet_mappings'].collect { file(it, checkIfExists: true) }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap b/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap
new file mode 100644
index 00000000..c5f06aac
--- /dev/null
+++ b/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap
@@ -0,0 +1,27 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    "samplesheet.csv:md5,ef756557b0735becd2574c2a3f5840b2"
+                ],
+                "1": [
+                    "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253"
+                ],
+                "2": [
+                    "versions.yml:md5,410006679d5e496d8c55e58e78ca6b34"
+                ],
+                "mappings": [
+                    "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253"
+                ],
+                "samplesheet": [
+                    "samplesheet.csv:md5,ef756557b0735becd2574c2a3f5840b2"
+                ],
+                "versions": [
+                    "versions.yml:md5,410006679d5e496d8c55e58e78ca6b34"
+                ]
+            }
+        ],
+        "timestamp": "2023-07-06T13:16:36+0000"
+    }
+}
\ No newline at end of file
diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
new file mode 100644
index 00000000..1558ff39
--- /dev/null
+++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
@@ -0,0 +1,31 @@
+nextflow_process {
+
+    name "Test process: SRA_RUNINFO_TO_FTP"
+    script "modules/local/sra_runinfo_to_ftp/main.nf"
+    process "SRA_RUNINFO_TO_FTP"
+    tag "modules"
+    tag "modules_local"
+    tag "sra_runinfo_to_ftp"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+
+            process {
+                """
+                input[0] = file(params.test_data['modules_local']['sra_runinfo_to_ftp'], checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap
new file mode 100644
index 00000000..71a25f99
--- /dev/null
+++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap
@@ -0,0 +1,21 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e"
+                ],
+                "1": [
+                    "versions.yml:md5,e95f8185f665127a73622a19d321bcca"
+                ],
+                "tsv": [
+                    "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e"
+                ],
+                "versions": [
+                    "versions.yml:md5,e95f8185f665127a73622a19d321bcca"
+                ]
+            }
+        ],
+        "timestamp": "2023-08-06T23:13:20+0000"
+    }
+}
\ No newline at end of file
diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test
new file mode 100644
index 00000000..b2ec5b11
--- /dev/null
+++ b/modules/local/sra_to_samplesheet/tests/main.nf.test
@@ -0,0 +1,34 @@
+nextflow_process {
+
+    name "Test process: SRA_TO_SAMPLESHEET"
+    script "modules/local/sra_to_samplesheet/main.nf"
+    process "SRA_TO_SAMPLESHEET"
+    tag "modules"
+    tag "modules_local"
+    tag "sra_to_samplesheet"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+
+            process {
+                """
+                input[0] = [id:'ERX1188904_ERR1109373', run_accession:'ERR1109373', experiment_accession:'ERX1188904', sample_accession:'SAMEA3643867',  experiment_alias:'ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7', run_alias:'ena-RUN-CAM-03-11-2015-17:01:52:847-7',  sample_alias:'sample_56', study_alias:'ena-STUDY-CAM-02-11-2015-17:42:24:189-13', library_layout:'PAIRED', experiment_title:'Illumina HiSeq 2500 paired end sequencing', sample_title:'RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome', sample_description:'RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome', fastq_md5:'8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9', fastq_ftp:'ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz', fastq_1:'./results/fastq/ERX1188904_ERR1109373_1.fastq.gz', fastq_2:'./results/fastq/ERX1188904_ERR1109373_2.fastq.gz', md5_1:'9fd57225d6c07a31843276d6df9b15c0', md5_2:'5a62e8f785687dce890cfb4fe3e607f9', single_end:false]
+                input[1] = 'rnaseq'
+                input[2] = 'auto'
+                input[3] = 'experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap
new file mode 100644
index 00000000..e60c646a
--- /dev/null
+++ b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap
@@ -0,0 +1,113 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "ERX1188904_ERR1109373",
+                            "run_accession": "ERR1109373",
+                            "experiment_accession": "ERX1188904",
+                            "sample_accession": "SAMEA3643867",
+                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
+                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
+                            "sample_alias": "sample_56",
+                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
+                            "library_layout": "PAIRED",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
+                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz",
+                            "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz",
+                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
+                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
+                            "single_end": false
+                        },
+                        "ERX1188904_ERR1109373.samplesheet.csv:md5,e7898191d57258e049ee7129d36f5c08"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "ERX1188904_ERR1109373",
+                            "run_accession": "ERR1109373",
+                            "experiment_accession": "ERX1188904",
+                            "sample_accession": "SAMEA3643867",
+                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
+                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
+                            "sample_alias": "sample_56",
+                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
+                            "library_layout": "PAIRED",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
+                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz",
+                            "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz",
+                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
+                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
+                            "single_end": false
+                        },
+                        "ERX1188904_ERR1109373.mappings.csv:md5,d09ddb4f0709675e5dfe1eadf12c608f"
+                    ]
+                ],
+                "mappings": [
+                    [
+                        {
+                            "id": "ERX1188904_ERR1109373",
+                            "run_accession": "ERR1109373",
+                            "experiment_accession": "ERX1188904",
+                            "sample_accession": "SAMEA3643867",
+                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
+                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
+                            "sample_alias": "sample_56",
+                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
+                            "library_layout": "PAIRED",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
+                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz",
+                            "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz",
+                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
+                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
+                            "single_end": false
+                        },
+                        "ERX1188904_ERR1109373.mappings.csv:md5,d09ddb4f0709675e5dfe1eadf12c608f"
+                    ]
+                ],
+                "samplesheet": [
+                    [
+                        {
+                            "id": "ERX1188904_ERR1109373",
+                            "run_accession": "ERR1109373",
+                            "experiment_accession": "ERX1188904",
+                            "sample_accession": "SAMEA3643867",
+                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
+                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
+                            "sample_alias": "sample_56",
+                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
+                            "library_layout": "PAIRED",
+                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
+                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
+                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
+                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
+                            "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz",
+                            "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz",
+                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
+                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
+                            "single_end": false
+                        },
+                        "ERX1188904_ERR1109373.samplesheet.csv:md5,e7898191d57258e049ee7129d36f5c08"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2023-08-23T09:38:15+0000"
+    }
+}
\ No newline at end of file

From c95793e1e82b144ffb16ba8703e8072e80929aa5 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 21 Sep 2023 19:22:53 +0200
Subject: [PATCH 455/852] restore CI

---
 .github/workflows/ci.yml | 89 +++++++++++++++++++++++++++-------------
 1 file changed, 61 insertions(+), 28 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 566ef509..7b7070e7 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,28 +1,67 @@
+# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 name: nf-core CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on:
   pull_request:
   release:
     types: [published]
+  merge_group:
+    types:
+      - checks_requested
+    branches:
+      - master
+      - dev
+      - refactor
 
 env:
   NXF_ANSI_LOG: false
+  NFTEST_VER: "0.8.0-rc1"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
 
 jobs:
+  changes:
+    name: Check for changes
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose matched filters as job 'tags' output variable
+      tags: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: ".github/tags.yml"
+
+  define_nxf_versions:
+    name: Choose nextflow versions to test against depending on target branch
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.nxf_versions.outputs.matrix }}
+    steps:
+      - id: nxf_versions
+        run: |
+          if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
+            echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT
+          else
+            echo matrix='["latest-everything", "22.10.1"]' | tee -a $GITHUB_OUTPUT
+          fi
+
   test:
-    name: Run pipeline with test data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}"
+    name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }}
+    needs: [changes, define_nxf_versions]
+    if: needs.changes.outputs.tags != '[]'
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
+        NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
+        tags: ["${{ fromJson(needs.changes.outputs.tags) }}"]
+        profile:
+          - "docker"
+
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v3
@@ -32,29 +71,23 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Run pipeline with test data
+      - name: Install nf-test
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
+          sudo mv nf-test /usr/local/bin/
 
-  parameters:
-    name: Test workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        parameters:
-          - "--nf_core_pipeline rnaseq"
-          - "--ena_metadata_fields run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5 --sample_mapping_fields run_accession,library_layout"
-          - "--skip_fastq_download"
-          - "--force_sratools_download"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Install Nextflow
+      - name: Run nf-test
         run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-      - name: Run pipeline with various parameters
+          nf-test test --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml
+
+      - name: Output log on failure
+        if: failure()
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: test.xml

From 7e935bbbd1705853fd5f8858d9ca50dea4f466fa Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 21 Sep 2023 19:26:37 +0200
Subject: [PATCH 456/852] forgot some files

---
 .gitattributes |  1 +
 .gitignore     |  3 +++
 nf-test.config | 16 ++++++++++++++++
 3 files changed, 20 insertions(+)
 create mode 100644 nf-test.config

diff --git a/.gitattributes b/.gitattributes
index 7a2dabc2..c1c17000 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1,4 +1,5 @@
 *.config linguist-language=nextflow
 *.nf.test linguist-language=nextflow
+tests/**/*nf.test.snap linguist-generated
 modules/nf-core/** linguist-generated
 subworkflows/nf-core/** linguist-generated
diff --git a/.gitignore b/.gitignore
index 5124c9ac..b1b5890a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,6 @@ results/
 testing/
 testing*
 *.pyc
+.nf-test/
+nf-test
+.nf-test.log
diff --git a/nf-test.config b/nf-test.config
new file mode 100644
index 00000000..0799cb40
--- /dev/null
+++ b/nf-test.config
@@ -0,0 +1,16 @@
+config {
+    // location for all nf-tests
+    testsDir "."
+
+    // nf-test directory including temporary files for each test
+    workDir ".nf-test"
+
+    // location of library folder that is added automatically to the classpath
+    libDir "lib/"
+
+    // location of an optional nextflow.config file specific for executing tests
+    configFile "nextflow.config"
+
+    // run all test with the defined docker profile from the main nextflow.config
+    profile ""
+}

From e43e5f178e3812d000db3739f5f2c55a981e0e15 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 22 Sep 2023 09:39:50 +0200
Subject: [PATCH 457/852] fix NXF_VER

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 7b7070e7..59011a37 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -46,7 +46,7 @@ jobs:
           if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
             echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT
           else
-            echo matrix='["latest-everything", "22.10.1"]' | tee -a $GITHUB_OUTPUT
+            echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT
           fi
 
   test:

From eb11d0b2a54ea8b31411f3d5e5a9ca52bd833a81 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Fri, 22 Sep 2023 09:42:37 +0200
Subject: [PATCH 458/852] Delete .github/tags.yml

this should happen in the `nf-test` branch
---
 .github/tags.yml | 79 ------------------------------------------------
 1 file changed, 79 deletions(-)
 delete mode 100644 .github/tags.yml

diff --git a/.github/tags.yml b/.github/tags.yml
deleted file mode 100644
index 9fc74a2c..00000000
--- a/.github/tags.yml
+++ /dev/null
@@ -1,79 +0,0 @@
-# local modules
-multiqc_mappings_config:
-  - modules/local/multiqc_mappings_config/*
-sra_fastq_ftp:
-  - modules/local/sra_fastq_ftp/*
-sra_ids_to_runinfo:
-  - modules/local/sra_ids_to_runinfo/*
-sra_merge_samplesheet:
-  - modules/local/sra_merge_samplesheet/*
-sra_runinfo_to_ftp:
-  - modules/local/sra_runinfo_to_ftp/*
-sra_to_samplesheet:
-  - modules/local/sra_to_samplesheet/*
-
-# workflow: sra
-sra_custom_ena_metadata_fields:
-  - modules/local/sra_ids_to_runinfo/*
-  - modules/local/sra_runinfo_to_ftp/*
-  - modules/local/sra_fastq_ftp/*
-  - modules/local/sra_to_samplesheet/*
-  - modules/local/sra_merge_samplesheet/*
-  - workflows/sra/*
-  - workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
-sra_default_parameters:
-  - modules/local/sra_ids_to_runinfo/*
-  - modules/local/sra_runinfo_to_ftp/*
-  - modules/local/sra_fastq_ftp/*
-  - modules/local/sra_to_samplesheet/*
-  - modules/local/sra_merge_samplesheet/*
-  - workflows/sra/*
-  - workflows/sra/tests/sra_default_parameters.nf.test
-sra_force_sratools_download:
-  - modules/local/sra_ids_to_runinfo/*
-  - modules/local/sra_runinfo_to_ftp/*
-  - modules/local/sra_fastq_ftp/*
-  - modules/local/sra_to_samplesheet/*
-  - modules/local/sra_merge_samplesheet/*
-  - workflows/sra/*
-  - workflows/sra/tests/sra_force_sratools_download.nf.test
-sra_nf_core_pipeline_atacseq:
-  - modules/local/sra_ids_to_runinfo/*
-  - modules/local/sra_runinfo_to_ftp/*
-  - modules/local/sra_fastq_ftp/*
-  - modules/local/sra_to_samplesheet/*
-  - modules/local/sra_merge_samplesheet/*
-  - workflows/sra/*
-  - workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
-sra_nf_core_pipeline_rnaseq:
-  - modules/local/sra_ids_to_runinfo/*
-  - modules/local/sra_runinfo_to_ftp/*
-  - modules/local/sra_fastq_ftp/*
-  - modules/local/sra_to_samplesheet/*
-  - modules/local/sra_merge_samplesheet/*
-  - workflows/sra/*
-  - workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
-sra_nf_core_pipeline_taxprofiler:
-  - modules/local/sra_ids_to_runinfo/*
-  - modules/local/sra_runinfo_to_ftp/*
-  - modules/local/sra_fastq_ftp/*
-  - modules/local/sra_to_samplesheet/*
-  - modules/local/sra_merge_samplesheet/*
-  - workflows/sra/*
-  - workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
-sra_nf_core_pipeline_viralrecon:
-  - modules/local/sra_ids_to_runinfo/*
-  - modules/local/sra_runinfo_to_ftp/*
-  - modules/local/sra_fastq_ftp/*
-  - modules/local/sra_to_samplesheet/*
-  - modules/local/sra_merge_samplesheet/*
-  - workflows/sra/*
-  - workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
-sra_skip_fastq_download:
-  - modules/local/sra_ids_to_runinfo/*
-  - modules/local/sra_runinfo_to_ftp/*
-  - modules/local/sra_fastq_ftp/*
-  - modules/local/sra_to_samplesheet/*
-  - modules/local/sra_merge_samplesheet/*
-  - workflows/sra/*
-  - workflows/sra/tests/sra_skip_fastq_download.nf.test

From 185e930ca70cc3af853865b24af9f2ce893a1685 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 22 Sep 2023 09:45:59 +0200
Subject: [PATCH 459/852] fix linting

---
 .nf-core.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.nf-core.yml b/.nf-core.yml
index 9975ac5b..d617b3a3 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -6,3 +6,4 @@ lint:
   files_unchanged:
     - assets/sendmail_template.txt
     - lib/NfcoreTemplate.groovy
+    - .gitattributes

From 71e1a319dd342e7ecf5a810a9671e321cb9accce Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Fri, 22 Sep 2023 10:09:15 +0200
Subject: [PATCH 460/852] Delete conf/modules/base.config

No need for this file anymore
---
 conf/modules/base.config | 33 ---------------------------------
 1 file changed, 33 deletions(-)
 delete mode 100644 conf/modules/base.config

diff --git a/conf/modules/base.config b/conf/modules/base.config
deleted file mode 100644
index 035487c5..00000000
--- a/conf/modules/base.config
+++ /dev/null
@@ -1,33 +0,0 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Config file for defining DSL2 per module options and publishing paths
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Available keys to override module options:
-        ext.args   = Additional arguments appended to command in module.
-        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
-        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
-        ext.prefix = File name prefix for output files.
-----------------------------------------------------------------------------------------
-*/
-
-//
-// Generic process options for all workflows
-//
-process {
-
-    publishDir = [
-        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-    ]
-
-    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            pattern: '*_versions.yml'
-        ]
-    }
-
-}

From 07b25b300fb424f8b7cebefd53edccfa8c42b0df Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Fri, 22 Sep 2023 10:10:58 +0200
Subject: [PATCH 461/852] Apply suggestions from code review

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 1e8bea6e..01da14f6 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -162,7 +162,7 @@ profiles {
         executor.cpus          = 16
         executor.memory        = 60.GB
     }
-    test         { includeConfig 'conf/test.config' }
+    test         { includeConfig 'conf/test.config'         }
     test_synapse { includeConfig 'conf/test_synapse.config' }
     test_full    { includeConfig 'conf/test_full.config'    }
 }

From b11c1d8da1e0d68e5b80641690b3d0e5590990c1 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 22 Sep 2023 10:21:03 +0200
Subject: [PATCH 462/852] restore file

---
 .github/tags.yml | 71 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 71 insertions(+)
 create mode 100644 .github/tags.yml

diff --git a/.github/tags.yml b/.github/tags.yml
new file mode 100644
index 00000000..a5914ccf
--- /dev/null
+++ b/.github/tags.yml
@@ -0,0 +1,71 @@
+# local modules
+multiqc_mappings_config:
+  - modules/local/multiqc_mappings_config/*
+sra_fastq_ftp:
+  - modules/local/sra_fastq_ftp/*
+sra_ids_to_runinfo:
+  - modules/local/sra_ids_to_runinfo/*
+sra_merge_samplesheet:
+  - modules/local/sra_merge_samplesheet/*
+sra_runinfo_to_ftp:
+  - modules/local/sra_runinfo_to_ftp/*
+sra_to_samplesheet:
+  - modules/local/sra_to_samplesheet/*
+
+# workflow: sra
+sra_custom_ena_metadata_fields:
+  - modules/local/sra_ids_to_runinfo/*
+  - modules/local/sra_runinfo_to_ftp/*
+  - modules/local/sra_fastq_ftp/*
+  - modules/local/sra_to_samplesheet/*
+  - modules/local/sra_merge_samplesheet/*
+  - workflows/sra/*
+sra_default_parameters:
+  - modules/local/sra_ids_to_runinfo/*
+  - modules/local/sra_runinfo_to_ftp/*
+  - modules/local/sra_fastq_ftp/*
+  - modules/local/sra_to_samplesheet/*
+  - modules/local/sra_merge_samplesheet/*
+  - workflows/sra/*
+sra_force_sratools_download:
+  - modules/local/sra_ids_to_runinfo/*
+  - modules/local/sra_runinfo_to_ftp/*
+  - modules/local/sra_fastq_ftp/*
+  - modules/local/sra_to_samplesheet/*
+  - modules/local/sra_merge_samplesheet/*
+  - workflows/sra/*
+sra_nf_core_pipeline_atacseq:
+  - modules/local/sra_ids_to_runinfo/*
+  - modules/local/sra_runinfo_to_ftp/*
+  - modules/local/sra_fastq_ftp/*
+  - modules/local/sra_to_samplesheet/*
+  - modules/local/sra_merge_samplesheet/*
+  - workflows/sra/*
+sra_nf_core_pipeline_rnaseq:
+  - modules/local/sra_ids_to_runinfo/*
+  - modules/local/sra_runinfo_to_ftp/*
+  - modules/local/sra_fastq_ftp/*
+  - modules/local/sra_to_samplesheet/*
+  - modules/local/sra_merge_samplesheet/*
+  - workflows/sra/*
+sra_nf_core_pipeline_taxprofiler:
+  - modules/local/sra_ids_to_runinfo/*
+  - modules/local/sra_runinfo_to_ftp/*
+  - modules/local/sra_fastq_ftp/*
+  - modules/local/sra_to_samplesheet/*
+  - modules/local/sra_merge_samplesheet/*
+  - workflows/sra/*
+sra_nf_core_pipeline_viralrecon:
+  - modules/local/sra_ids_to_runinfo/*
+  - modules/local/sra_runinfo_to_ftp/*
+  - modules/local/sra_fastq_ftp/*
+  - modules/local/sra_to_samplesheet/*
+  - modules/local/sra_merge_samplesheet/*
+  - workflows/sra/*
+sra_skip_fastq_download:
+  - modules/local/sra_ids_to_runinfo/*
+  - modules/local/sra_runinfo_to_ftp/*
+  - modules/local/sra_fastq_ftp/*
+  - modules/local/sra_to_samplesheet/*
+  - modules/local/sra_merge_samplesheet/*
+  - workflows/sra/*

From b0dd0a3c27a88371fa9ef5cdf6c42d334c845bb1 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 22 Sep 2023 10:23:07 +0200
Subject: [PATCH 463/852] do some tests

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 59011a37..5642602b 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,6 +1,5 @@
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 name: nf-core CI
-# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on:
   pull_request:
   release:
@@ -12,6 +11,7 @@ on:
       - master
       - dev
       - refactor
+      - nf-test
 
 env:
   NXF_ANSI_LOG: false

From aad776b1166eeea52eeba789c9558233f4e7a4f7 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 22 Sep 2023 10:35:23 +0200
Subject: [PATCH 464/852] 2 *

---
 .github/tags.yml | 108 +++++++++++++++++++++++------------------------
 1 file changed, 54 insertions(+), 54 deletions(-)

diff --git a/.github/tags.yml b/.github/tags.yml
index a5914ccf..03569f78 100644
--- a/.github/tags.yml
+++ b/.github/tags.yml
@@ -1,71 +1,71 @@
 # local modules
 multiqc_mappings_config:
-  - modules/local/multiqc_mappings_config/*
+  - modules/local/multiqc_mappings_config/**
 sra_fastq_ftp:
-  - modules/local/sra_fastq_ftp/*
+  - modules/local/sra_fastq_ftp/**
 sra_ids_to_runinfo:
-  - modules/local/sra_ids_to_runinfo/*
+  - modules/local/sra_ids_to_runinfo/**
 sra_merge_samplesheet:
-  - modules/local/sra_merge_samplesheet/*
+  - modules/local/sra_merge_samplesheet/**
 sra_runinfo_to_ftp:
-  - modules/local/sra_runinfo_to_ftp/*
+  - modules/local/sra_runinfo_to_ftp/**
 sra_to_samplesheet:
-  - modules/local/sra_to_samplesheet/*
+  - modules/local/sra_to_samplesheet/**
 
 # workflow: sra
 sra_custom_ena_metadata_fields:
-  - modules/local/sra_ids_to_runinfo/*
-  - modules/local/sra_runinfo_to_ftp/*
-  - modules/local/sra_fastq_ftp/*
-  - modules/local/sra_to_samplesheet/*
-  - modules/local/sra_merge_samplesheet/*
-  - workflows/sra/*
+  - modules/local/sra_ids_to_runinfo/**
+  - modules/local/sra_runinfo_to_ftp/**
+  - modules/local/sra_fastq_ftp/**
+  - modules/local/sra_to_samplesheet/**
+  - modules/local/sra_merge_samplesheet/**
+  - workflows/sra/**
 sra_default_parameters:
-  - modules/local/sra_ids_to_runinfo/*
-  - modules/local/sra_runinfo_to_ftp/*
-  - modules/local/sra_fastq_ftp/*
-  - modules/local/sra_to_samplesheet/*
-  - modules/local/sra_merge_samplesheet/*
-  - workflows/sra/*
+  - modules/local/sra_ids_to_runinfo/**
+  - modules/local/sra_runinfo_to_ftp/**
+  - modules/local/sra_fastq_ftp/**
+  - modules/local/sra_to_samplesheet/**
+  - modules/local/sra_merge_samplesheet/**
+  - workflows/sra/**
 sra_force_sratools_download:
-  - modules/local/sra_ids_to_runinfo/*
-  - modules/local/sra_runinfo_to_ftp/*
-  - modules/local/sra_fastq_ftp/*
-  - modules/local/sra_to_samplesheet/*
-  - modules/local/sra_merge_samplesheet/*
-  - workflows/sra/*
+  - modules/local/sra_ids_to_runinfo/**
+  - modules/local/sra_runinfo_to_ftp/**
+  - modules/local/sra_fastq_ftp/**
+  - modules/local/sra_to_samplesheet/**
+  - modules/local/sra_merge_samplesheet/**
+  - workflows/sra/**
 sra_nf_core_pipeline_atacseq:
-  - modules/local/sra_ids_to_runinfo/*
-  - modules/local/sra_runinfo_to_ftp/*
-  - modules/local/sra_fastq_ftp/*
-  - modules/local/sra_to_samplesheet/*
-  - modules/local/sra_merge_samplesheet/*
-  - workflows/sra/*
+  - modules/local/sra_ids_to_runinfo/**
+  - modules/local/sra_runinfo_to_ftp/**
+  - modules/local/sra_fastq_ftp/**
+  - modules/local/sra_to_samplesheet/**
+  - modules/local/sra_merge_samplesheet/**
+  - workflows/sra/**
 sra_nf_core_pipeline_rnaseq:
-  - modules/local/sra_ids_to_runinfo/*
-  - modules/local/sra_runinfo_to_ftp/*
-  - modules/local/sra_fastq_ftp/*
-  - modules/local/sra_to_samplesheet/*
-  - modules/local/sra_merge_samplesheet/*
-  - workflows/sra/*
+  - modules/local/sra_ids_to_runinfo/**
+  - modules/local/sra_runinfo_to_ftp/**
+  - modules/local/sra_fastq_ftp/**
+  - modules/local/sra_to_samplesheet/**
+  - modules/local/sra_merge_samplesheet/**
+  - workflows/sra/**
 sra_nf_core_pipeline_taxprofiler:
-  - modules/local/sra_ids_to_runinfo/*
-  - modules/local/sra_runinfo_to_ftp/*
-  - modules/local/sra_fastq_ftp/*
-  - modules/local/sra_to_samplesheet/*
-  - modules/local/sra_merge_samplesheet/*
-  - workflows/sra/*
+  - modules/local/sra_ids_to_runinfo/**
+  - modules/local/sra_runinfo_to_ftp/**
+  - modules/local/sra_fastq_ftp/**
+  - modules/local/sra_to_samplesheet/**
+  - modules/local/sra_merge_samplesheet/**
+  - workflows/sra/**
 sra_nf_core_pipeline_viralrecon:
-  - modules/local/sra_ids_to_runinfo/*
-  - modules/local/sra_runinfo_to_ftp/*
-  - modules/local/sra_fastq_ftp/*
-  - modules/local/sra_to_samplesheet/*
-  - modules/local/sra_merge_samplesheet/*
-  - workflows/sra/*
+  - modules/local/sra_ids_to_runinfo/**
+  - modules/local/sra_runinfo_to_ftp/**
+  - modules/local/sra_fastq_ftp/**
+  - modules/local/sra_to_samplesheet/**
+  - modules/local/sra_merge_samplesheet/**
+  - workflows/sra/**
 sra_skip_fastq_download:
-  - modules/local/sra_ids_to_runinfo/*
-  - modules/local/sra_runinfo_to_ftp/*
-  - modules/local/sra_fastq_ftp/*
-  - modules/local/sra_to_samplesheet/*
-  - modules/local/sra_merge_samplesheet/*
-  - workflows/sra/*
+  - modules/local/sra_ids_to_runinfo/**
+  - modules/local/sra_runinfo_to_ftp/**
+  - modules/local/sra_fastq_ftp/**
+  - modules/local/sra_to_samplesheet/**
+  - modules/local/sra_merge_samplesheet/**
+  - workflows/sra/**

From 89d39e98727f7f0c8beb868b243f726a27a8bbd5 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 22 Sep 2023 10:49:40 +0200
Subject: [PATCH 465/852] forgot this file

---
 conf/test_data.config | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 conf/test_data.config

diff --git a/conf/test_data.config b/conf/test_data.config
new file mode 100644
index 00000000..42d3d818
--- /dev/null
+++ b/conf/test_data.config
@@ -0,0 +1,36 @@
+params {
+    // Base directory for test data
+    test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs"
+
+    merge_samplesheet_ids = [ "DRX024467_DRR026872", "SRX11047067_SRR14709033", "SRX9504942_SRR13055517", "DRX026011_DRR028935", "SRX17709227_SRR21711856", "SRX9504942_SRR13055518", "ERX1188904_ERR1109373", "SRX17709228_SRR21711855", "SRX9504942_SRR13055519", "ERX1234253_ERR1160846", "SRX6725035_SRR9984183", "SRX9504942_SRR13055520", "SRX10940790_SRR14593545", "SRX9315476_SRR12848126", "SRX9626017_SRR13191702" ]
+
+    def merge_samplesheet_url  = "${params.test_data_base}/modules/local/sra_merge_samplesheet/samplesheets/"
+    def merge_mappings_url     = "${params.test_data_base}/modules/local/sra_merge_samplesheet/mappings/"
+    def merge_samplesheet_urls = []
+    def merge_mappings_urls    = []
+
+    merge_samplesheet_ids.each { id ->
+        merge_samplesheet_urls += "${merge_samplesheet_url}${id}.samplesheet.csv"
+        merge_mappings_urls    += "${merge_mappings_url}/${id}.mappings.csv"
+    }
+
+    fastq_ftp_ids      = ["SRR13191702"]
+    def fastq_ftp_url  = "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/"
+    def fastq_ftp_urls = []
+
+    fastq_ftp_ids.each { id ->
+        fastq_ftp_urls += "${fastq_ftp_url}${id}_1.fastq.gz"
+        fastq_ftp_urls += "${fastq_ftp_url}${id}_2.fastq.gz"
+    }
+
+    test_data {
+        'modules_local' {
+                multiqc_mappings_config             = "${params.test_data_base}/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv"
+                sra_merge_samplesheet_samplesheets  = merge_samplesheet_urls
+                sra_merge_samplesheet_mappings      = merge_mappings_urls
+                sra_to_samplesheet                  = "${params.test_data_base}/modules/local/sra_to_samplesheet/SRX9626017_SRR13191702.mappings.csv"
+                sra_fastq_ftp                       = fastq_ftp_urls
+                sra_runinfo_to_ftp                  = "${params.test_data_base}/modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv"
+        }
+    }
+}

From d456c208def2bf4e046b520ab9a72e91c27c0b2e Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 22 Sep 2023 11:00:43 +0200
Subject: [PATCH 466/852] fix path to file to include and update snapshots

---
 .../tests/main.nf.test.snap                   | 27 +------
 .../sra_fastq_ftp/tests/main.nf.test.snap     | 71 +------------------
 .../tests/main.nf.test.snap                   |  2 +-
 .../tests/main.nf.test.snap                   |  2 +-
 .../tests/main.nf.test.snap                   |  2 +-
 .../tests/main.nf.test.snap                   |  2 +-
 nextflow.config                               |  5 +-
 7 files changed, 10 insertions(+), 101 deletions(-)

diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap
index 9cf7fb38..1a4d16c4 100644
--- a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap
+++ b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap
@@ -1,29 +1,4 @@
 {
-    "SRX9626017_SRR13191702": {
-        "content": [
-            {
-                "0": [
-                    [
-                        "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
-                        "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
-                ],
-                "versions": [
-                    "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
-                ],
-                "yml": [
-                    [
-                        "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
-                        "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
-                    ]
-                ]
-            }
-        ],
-        "timestamp": "2023-08-17T12:02:35+0000"
-    },
     "Should run without failures": {
         "content": [
             {
@@ -47,6 +22,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-08-17T12:02:35+0000"
+        "timestamp": "2023-09-22T10:58:18.132284"
     }
 }
\ No newline at end of file
diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap
index c0d5ffdc..fb815455 100644
--- a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap
+++ b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap
@@ -1,73 +1,4 @@
 {
-    "SRX9626017_SRR13191702": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "SRX9626017_SRR13191702",
-                            "single_end": false,
-                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
-                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
-                        },
-                        [
-                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
-                        ]
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "SRX9626017_SRR13191702",
-                            "single_end": false,
-                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
-                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
-                        },
-                        [
-                            "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
-                            "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
-                        ]
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b"
-                ],
-                "fastq": [
-                    [
-                        {
-                            "id": "SRX9626017_SRR13191702",
-                            "single_end": false,
-                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
-                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
-                        },
-                        [
-                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
-                        ]
-                    ]
-                ],
-                "md5": [
-                    [
-                        {
-                            "id": "SRX9626017_SRR13191702",
-                            "single_end": false,
-                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
-                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
-                        },
-                        [
-                            "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
-                            "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
-                        ]
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b"
-                ]
-            }
-        ],
-        "timestamp": "2023-08-06T23:31:57+0000"
-    },
     "Should run without failures": {
         "content": [
             {
@@ -135,6 +66,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-08-06T23:31:57+0000"
+        "timestamp": "2023-09-22T10:58:46.998421"
     }
 }
\ No newline at end of file
diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap
index dbca931f..241efe2a 100644
--- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap
+++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap
@@ -16,6 +16,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-08-06T23:30:51+0000"
+        "timestamp": "2023-09-22T10:58:56.721948"
     }
 }
\ No newline at end of file
diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap b/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap
index c5f06aac..203395ae 100644
--- a/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap
+++ b/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap
@@ -22,6 +22,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-07-06T13:16:36+0000"
+        "timestamp": "2023-09-22T10:59:14.022116"
     }
 }
\ No newline at end of file
diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap
index 71a25f99..cd246303 100644
--- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap
+++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap
@@ -16,6 +16,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-08-06T23:13:20+0000"
+        "timestamp": "2023-09-22T10:58:36.16611"
     }
 }
\ No newline at end of file
diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap
index e60c646a..8cc8686a 100644
--- a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap
+++ b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap
@@ -108,6 +108,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-08-23T09:38:15+0000"
+        "timestamp": "2023-09-22T10:58:27.169349"
     }
 }
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 01da14f6..28fb66a0 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -162,7 +162,10 @@ profiles {
         executor.cpus          = 16
         executor.memory        = 60.GB
     }
-    test         { includeConfig 'conf/test.config'         }
+    test         {
+        includeConfig 'conf/test.config'
+        includeConfig 'conf/test_data.config'
+    }
     test_synapse { includeConfig 'conf/test_synapse.config' }
     test_full    { includeConfig 'conf/test_full.config'    }
 }

From 938e7b99742aba5a285f77989ed839618a72f50b Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 22 Sep 2023 11:30:43 +0200
Subject: [PATCH 467/852] use initialise subworkflows

---
 main.nf                                  | 22 +-------
 modules.json                             |  5 ++
 subworkflows/nf-core/initialise/main.nf  | 68 ++++++++++++++++++++++++
 subworkflows/nf-core/initialise/meta.yml | 33 ++++++++++++
 4 files changed, 108 insertions(+), 20 deletions(-)
 create mode 100644 subworkflows/nf-core/initialise/main.nf
 create mode 100644 subworkflows/nf-core/initialise/meta.yml

diff --git a/main.nf b/main.nf
index 355898d0..a5011951 100644
--- a/main.nf
+++ b/main.nf
@@ -17,26 +17,6 @@ nextflow.enable.dsl = 2
 ========================================================================================
 */
 
-include { paramsHelp; paramsSummaryLog; validateParameters } from 'plugin/nf-validation'
-
-def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
-def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
-
-// Print parameter summary log to screen
-log.info logo + paramsSummaryLog(workflow) + citation
-
-// Print help message if needed
-if (params.help) {
-    def String command = "nextflow run ${workflow.manifest.name} --input id.csv -profile docker"
-    log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
-    System.exit(0)
-}
-
-// Validate input parameters
-if (params.validate_params) {
-    validateParameters()
-}
-
 // Check if --input file is empty
 ch_input = file(params.input, checkIfExists: true)
 if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") }
@@ -88,6 +68,7 @@ if (params.input_type == 'synapse') {
 
 include { MULTIQC_MAPPINGS_CONFIG     } from './modules/local/multiqc_mappings_config'
 include { CUSTOM_DUMPSOFTWAREVERSIONS } from './modules/nf-core/custom/dumpsoftwareversions'
+include { INITIALISE                  } from './subworkflows/nf-core/initialise/main'
 
 /*
 ========================================================================================
@@ -108,6 +89,7 @@ if (params.input_type == 'synapse') include { SYNAPSE } from './workflows/synaps
 // WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided
 //
 workflow NFCORE_FETCHNGS {
+    INITIALISE(params.version, params.help, params.valid_params)
 
     ch_versions = Channel.empty()
 
diff --git a/modules.json b/modules.json
index ab610dfb..46dc80ef 100644
--- a/modules.json
+++ b/modules.json
@@ -33,6 +33,11 @@
                         "branch": "master",
                         "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca",
                         "installed_by": ["subworkflows"]
+                    },
+                    "initialise": {
+                        "branch": "master",
+                        "git_sha": "7b55a4631bebd1cf827a448d0b70386681fea475",
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }
diff --git a/subworkflows/nf-core/initialise/main.nf b/subworkflows/nf-core/initialise/main.nf
new file mode 100644
index 00000000..0cbd3799
--- /dev/null
+++ b/subworkflows/nf-core/initialise/main.nf
@@ -0,0 +1,68 @@
+// This is a reimplementation of the basic initialise methods in the nf-core template
+// The role of this subworkflow is to check the input parameters and print help messages
+// Use this to start your nf-core pipeline
+
+include { paramsHelp; paramsSummaryLog; paramsSummaryMap; validateParameters } from 'plugin/nf-validation'
+
+workflow INITIALISE {
+
+    take:
+        version         // bool
+        help            // bool
+        validate_params // bool
+
+    main:
+
+        // Print workflow version and exit on --version
+        if (version) {
+            String version_string = ""
+
+            if (workflow.manifest.version) {
+                def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
+                version_string += "${prefix_v}${workflow.manifest.version}"
+            }
+
+            if (workflow.commitId) {
+                def git_shortsha = workflow.commitId.substring(0, 7)
+                version_string += "-g${git_shortsha}"
+            }
+            log.info "${workflow.manifest.name} ${version_string}"
+            System.exit(0)
+        }
+
+        // Print citation for nf-core
+        def citation = "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
+            "* The nf-core framework\n" +
+            "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
+            "* Software dependencies\n" +
+            "  ${workflow.manifest.homePage}/blob/master/CITATIONS.md"
+        log.info citation
+
+        // Print help message if needed
+        if (params.help) {
+            def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv -profile docker"
+            log.info paramsHelp(command)
+            System.exit(0)
+        }
+
+        if ( params.validate_params != false ){
+            validateParameters()
+        }
+
+        if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
+            log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
+                    "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
+                    "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
+                    "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
+                    "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
+                    "Please refer to the quick start section and usage docs for the pipeline.\n "
+        }
+
+        log.info paramsSummaryLog(workflow)
+
+        summary_params = paramsSummaryMap(workflow)
+
+    emit:
+        summary_params
+
+}
diff --git a/subworkflows/nf-core/initialise/meta.yml b/subworkflows/nf-core/initialise/meta.yml
new file mode 100644
index 00000000..69596bb5
--- /dev/null
+++ b/subworkflows/nf-core/initialise/meta.yml
@@ -0,0 +1,33 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "initialise"
+description: Validate input parameters and print help messages
+keywords:
+  - admin
+  - check
+  - help
+  - version
+modules:
+input:
+  - version:
+    type: boolean
+    description: |
+      Structure: val(version)
+      Boolean to show the pipeline version and exit.
+  - help:
+    type: boolean
+    description: |
+      Structure: val(help)
+      Boolean to show the pipeline help message and exit.
+  - validate_params:
+    type: boolean
+    description: |
+      Structure: val(validate_params)
+      Whether to validate the parameters prior to starting the pipeline.
+output:
+  - summary_params:
+    type: value
+    description: |
+      Structure: val(summary_params)
+      A map of the parameters used in the pipeline.
+authors:
+  - "@adamrtalbot"

From ad25a22c03268c42dc72c3fad8a22ba61589b45a Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 22 Sep 2023 12:00:32 +0200
Subject: [PATCH 468/852] move scripts

---
 .../main.nf}                                     |  0
 .../{sra_fastq_ftp.nf => sra_fastq_ftp/main.nf}  |  0
 .../main.nf}                                     |  0
 .../main.nf}                                     |  0
 .../main.nf}                                     |  0
 .../main.nf}                                     |  0
 .../{synapse_get.nf => synapse_get/main.nf}      |  0
 .../{synapse_list.nf => synapse_list/main.nf}    |  0
 .../main.nf}                                     |  0
 .../{synapse_show.nf => synapse_show/main.nf}    |  0
 .../main.nf}                                     |  0
 workflows/{sra.nf => sra/main.nf}                | 16 ++++++++--------
 workflows/{synapse.nf => synapse/main.nf}        | 12 ++++++------
 13 files changed, 14 insertions(+), 14 deletions(-)
 rename modules/local/{multiqc_mappings_config.nf => multiqc_mappings_config/main.nf} (100%)
 rename modules/local/{sra_fastq_ftp.nf => sra_fastq_ftp/main.nf} (100%)
 rename modules/local/{sra_ids_to_runinfo.nf => sra_ids_to_runinfo/main.nf} (100%)
 rename modules/local/{sra_merge_samplesheet.nf => sra_merge_samplesheet/main.nf} (100%)
 rename modules/local/{sra_runinfo_to_ftp.nf => sra_runinfo_to_ftp/main.nf} (100%)
 rename modules/local/{sra_to_samplesheet.nf => sra_to_samplesheet/main.nf} (100%)
 rename modules/local/{synapse_get.nf => synapse_get/main.nf} (100%)
 rename modules/local/{synapse_list.nf => synapse_list/main.nf} (100%)
 rename modules/local/{synapse_merge_samplesheet.nf => synapse_merge_samplesheet/main.nf} (100%)
 rename modules/local/{synapse_show.nf => synapse_show/main.nf} (100%)
 rename modules/local/{synapse_to_samplesheet.nf => synapse_to_samplesheet/main.nf} (100%)
 rename workflows/{sra.nf => sra/main.nf} (89%)
 rename workflows/{synapse.nf => synapse/main.nf} (89%)

diff --git a/modules/local/multiqc_mappings_config.nf b/modules/local/multiqc_mappings_config/main.nf
similarity index 100%
rename from modules/local/multiqc_mappings_config.nf
rename to modules/local/multiqc_mappings_config/main.nf
diff --git a/modules/local/sra_fastq_ftp.nf b/modules/local/sra_fastq_ftp/main.nf
similarity index 100%
rename from modules/local/sra_fastq_ftp.nf
rename to modules/local/sra_fastq_ftp/main.nf
diff --git a/modules/local/sra_ids_to_runinfo.nf b/modules/local/sra_ids_to_runinfo/main.nf
similarity index 100%
rename from modules/local/sra_ids_to_runinfo.nf
rename to modules/local/sra_ids_to_runinfo/main.nf
diff --git a/modules/local/sra_merge_samplesheet.nf b/modules/local/sra_merge_samplesheet/main.nf
similarity index 100%
rename from modules/local/sra_merge_samplesheet.nf
rename to modules/local/sra_merge_samplesheet/main.nf
diff --git a/modules/local/sra_runinfo_to_ftp.nf b/modules/local/sra_runinfo_to_ftp/main.nf
similarity index 100%
rename from modules/local/sra_runinfo_to_ftp.nf
rename to modules/local/sra_runinfo_to_ftp/main.nf
diff --git a/modules/local/sra_to_samplesheet.nf b/modules/local/sra_to_samplesheet/main.nf
similarity index 100%
rename from modules/local/sra_to_samplesheet.nf
rename to modules/local/sra_to_samplesheet/main.nf
diff --git a/modules/local/synapse_get.nf b/modules/local/synapse_get/main.nf
similarity index 100%
rename from modules/local/synapse_get.nf
rename to modules/local/synapse_get/main.nf
diff --git a/modules/local/synapse_list.nf b/modules/local/synapse_list/main.nf
similarity index 100%
rename from modules/local/synapse_list.nf
rename to modules/local/synapse_list/main.nf
diff --git a/modules/local/synapse_merge_samplesheet.nf b/modules/local/synapse_merge_samplesheet/main.nf
similarity index 100%
rename from modules/local/synapse_merge_samplesheet.nf
rename to modules/local/synapse_merge_samplesheet/main.nf
diff --git a/modules/local/synapse_show.nf b/modules/local/synapse_show/main.nf
similarity index 100%
rename from modules/local/synapse_show.nf
rename to modules/local/synapse_show/main.nf
diff --git a/modules/local/synapse_to_samplesheet.nf b/modules/local/synapse_to_samplesheet/main.nf
similarity index 100%
rename from modules/local/synapse_to_samplesheet.nf
rename to modules/local/synapse_to_samplesheet/main.nf
diff --git a/workflows/sra.nf b/workflows/sra/main.nf
similarity index 89%
rename from workflows/sra.nf
rename to workflows/sra/main.nf
index 8d396ca1..366e4b28 100644
--- a/workflows/sra.nf
+++ b/workflows/sra/main.nf
@@ -19,12 +19,12 @@ log.info logo + paramsSummaryLog(workflow) + citation
 ========================================================================================
 */
 
-include { SRA_IDS_TO_RUNINFO      } from '../modules/local/sra_ids_to_runinfo'
-include { SRA_RUNINFO_TO_FTP      } from '../modules/local/sra_runinfo_to_ftp'
-include { SRA_FASTQ_FTP           } from '../modules/local/sra_fastq_ftp'
-include { SRA_TO_SAMPLESHEET      } from '../modules/local/sra_to_samplesheet'
-include { SRA_MERGE_SAMPLESHEET   } from '../modules/local/sra_merge_samplesheet'
-include { MULTIQC_MAPPINGS_CONFIG } from '../modules/local/multiqc_mappings_config'
+include { SRA_IDS_TO_RUNINFO      } from '../../modules/local/sra_ids_to_runinfo'
+include { SRA_RUNINFO_TO_FTP      } from '../../modules/local/sra_runinfo_to_ftp'
+include { SRA_FASTQ_FTP           } from '../../modules/local/sra_fastq_ftp'
+include { SRA_TO_SAMPLESHEET      } from '../../modules/local/sra_to_samplesheet'
+include { SRA_MERGE_SAMPLESHEET   } from '../../modules/local/sra_merge_samplesheet'
+include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_config'
 
 /*
 ========================================================================================
@@ -32,9 +32,9 @@ include { MULTIQC_MAPPINGS_CONFIG } from '../modules/local/multiqc_mappings_conf
 ========================================================================================
 */
 
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
+include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions/main'
 
-include { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS } from '../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main'
+include { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS } from '../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main'
 
 /*
 ========================================================================================
diff --git a/workflows/synapse.nf b/workflows/synapse/main.nf
similarity index 89%
rename from workflows/synapse.nf
rename to workflows/synapse/main.nf
index f2138a60..7d871659 100644
--- a/workflows/synapse.nf
+++ b/workflows/synapse/main.nf
@@ -19,11 +19,11 @@ if (params.synapse_config) {
 ========================================================================================
 */
 
-include { SYNAPSE_LIST              } from '../modules/local/synapse_list'
-include { SYNAPSE_SHOW              } from '../modules/local/synapse_show'
-include { SYNAPSE_GET               } from '../modules/local/synapse_get'
-include { SYNAPSE_TO_SAMPLESHEET    } from '../modules/local/synapse_to_samplesheet'
-include { SYNAPSE_MERGE_SAMPLESHEET } from '../modules/local/synapse_merge_samplesheet'
+include { SYNAPSE_LIST              } from '../../modules/local/synapse_list'
+include { SYNAPSE_SHOW              } from '../../modules/local/synapse_show'
+include { SYNAPSE_GET               } from '../../modules/local/synapse_get'
+include { SYNAPSE_TO_SAMPLESHEET    } from '../../modules/local/synapse_to_samplesheet'
+include { SYNAPSE_MERGE_SAMPLESHEET } from '../../modules/local/synapse_merge_samplesheet'
 
 /*
 ========================================================================================
@@ -31,7 +31,7 @@ include { SYNAPSE_MERGE_SAMPLESHEET } from '../modules/local/synapse_merge_sampl
 ========================================================================================
 */
 
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
+include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions/main'
 
 /*
 ========================================================================================

From a86f54ffe094133f3f26d25fe4d2f76b148ee796 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 22 Sep 2023 12:36:19 +0200
Subject: [PATCH 469/852] remove public_aws_ecr profile

---
 .github/workflows/cloud_tests_full.yml  |  2 +-
 .github/workflows/cloud_tests_small.yml |  2 +-
 conf/public_aws_ecr.config              | 33 -------------------------
 nextflow.config                         |  3 ---
 4 files changed, 2 insertions(+), 38 deletions(-)
 delete mode 100644 conf/public_aws_ecr.config

diff --git a/.github/workflows/cloud_tests_full.yml b/.github/workflows/cloud_tests_full.yml
index e25a97aa..d0ed0552 100644
--- a/.github/workflows/cloud_tests_full.yml
+++ b/.github/workflows/cloud_tests_full.yml
@@ -27,7 +27,7 @@ jobs:
           compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
           workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/fetchngs/work-${{ github.sha }}"
           run_name: "aws_fetchngs_full"
-          profiles: test_full,public_aws_ecr
+          profiles: test_full
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
diff --git a/.github/workflows/cloud_tests_small.yml b/.github/workflows/cloud_tests_small.yml
index e7636fdc..12b8daab 100644
--- a/.github/workflows/cloud_tests_small.yml
+++ b/.github/workflows/cloud_tests_small.yml
@@ -25,7 +25,7 @@ jobs:
           compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
           workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/fetchngs/work-${{ github.sha }}"
           run_name: "aws_fetchngs_small"
-          profiles: test,public_aws_ecr
+          profiles: test
           parameters: |
             {
                 "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/fetchngs/results-test-${{ github.sha }}"
diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config
deleted file mode 100644
index 14b577d7..00000000
--- a/conf/public_aws_ecr.config
+++ /dev/null
@@ -1,33 +0,0 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    AWS ECR Config
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Config to set public AWS ECR images wherever possible
-    This improves speed when running on AWS infrastructure.
-    Use this as an example template when using your own private registry.
-----------------------------------------------------------------------------------------
-*/
-
-docker.registry = 'public.ecr.aws'
-podman.registry = 'public.ecr.aws'
-
-process {
-    withName: '.*:SRA_IDS_TO_RUNINFO' {
-        container = 'quay.io/biocontainers/python:3.9--1'
-    }
-    withName: '.*:SRA_RUNINFO_TO_FTP' {
-        container = 'quay.io/biocontainers/python:3.9--1'
-    }
-    withName: '.*:MULTIQC_MAPPINGS_CONFIG' {
-        container = 'quay.io/biocontainers/python:3.9--1'
-    }
-    withName: '.*:SRATOOLS_FASTERQDUMP' {
-        container = 'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0'
-    }
-    withName: '.*:SRA_MERGE_SAMPLESHEET' {
-        container = 'quay.io/nf-core/ubuntu:20.04'
-    }
-    withName: '.*:SYNAPSE_MERGE_SAMPLESHEET' {
-        container = 'quay.io/nf-core/ubuntu:20.04'
-    }
-}
diff --git a/nextflow.config b/nextflow.config
index 2a8e9bcc..62c60dd0 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -162,9 +162,6 @@ profiles {
         executor.cpus          = 16
         executor.memory        = 60.GB
     }
-    public_aws_ecr {
-        includeConfig 'conf/public_aws_ecr.config'
-    }
     test         { includeConfig 'conf/test.config'         }
     test_synapse { includeConfig 'conf/test_synapse.config' }
     test_full    { includeConfig 'conf/test_full.config'    }

From e89691d10ed1ab576c5d1e2babc33e59a86d2e8d Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 22 Sep 2023 17:59:55 +0200
Subject: [PATCH 470/852] no need to test on push on dev, pr are enough

---
 .github/workflows/ci.yml | 3 ---
 .nf-core.yml             | 6 ++++++
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index ac382c1e..566ef509 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,9 +1,6 @@
 name: nf-core CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on:
-  push:
-    branches:
-      - dev
   pull_request:
   release:
     types: [published]
diff --git a/.nf-core.yml b/.nf-core.yml
index cafd671c..cad7f3e2 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,5 +1,11 @@
 repository_type: pipeline
 lint:
+  actions_ci: false
+  files_exist:
+    - .github/workflows/awsfulltest.yml
+    - .github/workflows/awstest.yml
+    - conf/igenomes.config
+    - lib/WorkflowFetchngs.groovy
   files_unchanged:
     - assets/sendmail_template.txt
     - lib/NfcoreTemplate.groovy

From a434c4616c976fbcd109d4c49fcd70f5934545c2 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 22 Sep 2023 18:08:35 +0200
Subject: [PATCH 471/852] more code polish

---
 main.nf | 55 ++++++++++++++++++++++++++++++++-----------------------
 1 file changed, 32 insertions(+), 23 deletions(-)

diff --git a/main.nf b/main.nf
index b600e82f..ed4f6877 100644
--- a/main.nf
+++ b/main.nf
@@ -1,28 +1,33 @@
 #!/usr/bin/env nextflow
+
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
     nf-core/fetchngs
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
     Github : https://github.com/nf-core/fetchngs
     Website: https://nf-co.re/fetchngs
     Slack  : https://nfcore.slack.com/channels/fetchngs
-----------------------------------------------------------------------------------------
+========================================================================================
 */
 
 nextflow.enable.dsl = 2
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
     VALIDATE & PRINT PARAMETER SUMMARY
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
 */
 
-include { validateParameters; paramsHelp } from 'plugin/nf-validation'
+include { paramsHelp; paramsSummaryLog; validateParameters } from 'plugin/nf-validation'
+
+def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
+def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
+
+// Print parameter summary log to screen
+log.info logo + paramsSummaryLog(workflow) + citation
 
 // Print help message if needed
 if (params.help) {
-    def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
-    def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
     def String command = "nextflow run ${workflow.manifest.name} --input id.csv -profile docker"
     log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
     System.exit(0)
@@ -33,11 +38,9 @@ if (params.validate_params) {
     validateParameters()
 }
 
-WorkflowMain.initialise(workflow, params, log)
-
 // Check if --input file is empty
 ch_input = file(params.input, checkIfExists: true)
-if (ch_input.isEmpty()) {exit 1, "File provided with --input is empty: ${ch_input.getName()}!"}
+if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") }
 
 // Read in ids from --input file
 Channel
@@ -47,12 +50,6 @@ Channel
     .unique()
     .set { ch_ids }
 
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    NAMED WORKFLOW FOR PIPELINE
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
 // Auto-detect input id type
 def input_type = ''
 if (WorkflowMain.isSraId(ch_input)) {
@@ -60,9 +57,15 @@ if (WorkflowMain.isSraId(ch_input)) {
 } else if (WorkflowMain.isSynapseId(ch_input)) {
     input_type = 'synapse'
 } else {
-    exit 1, 'Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!'
+    error('Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!')
 }
 
+/*
+========================================================================================
+    VALIDATE INPUTS
+========================================================================================
+*/
+
 if (params.input_type == input_type) {
     if (params.input_type == 'sra') {
         include { SRA } from './workflows/sra'
@@ -70,9 +73,15 @@ if (params.input_type == input_type) {
         include { SYNAPSE } from './workflows/synapse'
     }
 } else {
-    exit 1, "Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!"
+    error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!")
 }
 
+/*
+========================================================================================
+    NAMED WORKFLOW FOR PIPELINE
+========================================================================================
+*/
+
 //
 // WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided
 //
@@ -93,9 +102,9 @@ workflow NFCORE_FETCHNGS {
 }
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
     RUN ALL WORKFLOWS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
 */
 
 //
@@ -107,7 +116,7 @@ workflow {
 }
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
     THE END
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
 */

From 5fcb97d2d260d971b9080b17aa070fab3316778b Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 22 Sep 2023 18:12:08 +0200
Subject: [PATCH 472/852] nf-core bump-version 1.10.1

---
 assets/multiqc_config.yml | 4 ++--
 nextflow.config           | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 5e3d9889..70cc1fc7 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/fetchngs/1.10.1dev" target="_blank">nf-core/fetchngs</a>
+  This report has been generated by the <a href="https://github.com/nf-core/fetchngs/1.10.1" target="_blank">nf-core/fetchngs</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/fetchngs/1.10.1dev/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/fetchngs/1.10.1/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-fetchngs-methods-description":
     order: -1000
diff --git a/nextflow.config b/nextflow.config
index 62c60dd0..9eb454f4 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -219,7 +219,7 @@ manifest {
     description     = """Pipeline to fetch metadata and raw FastQ files from public databases"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.10.1dev'
+    version         = '1.10.1'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
 

From 89d0cc8aaae7d24ebf983014cc782440249fcbc3 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 22 Sep 2023 18:36:41 +0200
Subject: [PATCH 473/852] update CHANGELOG

---
 CHANGELOG.md | 26 +++++++++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index daf474c0..c9dfa84d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,31 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## dev - [date]
+## [[1.10.1](https://github.com/nf-core/fetchngs/releases/tag/1.10.1)] - 2023-09-25
+
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Adam Talbot](https://github.com/adamrtalbot)
+- [Harshil Patel](https://github.com/drpatelh)
+- [Maxime Garcia](https://github.com/maxulysse)
+
+Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
+
+### Enhancements & fixes
+
+- [#177](https://github.com/nf-core/fetchngs/pull/177) - Template update with nf-core/tools 2.9
+- [#205](https://github.com/nf-core/fetchngs/pull/205) - Rename all local modules, workflows and remove public_aws_ecr profile
+- [#206](https://github.com/nf-core/fetchngs/pull/206) - CI improvments and code cleanup
+
+### Software dependencies
+
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+>
+> **NB:** Dependency has been **added** if just the new version information is present.
+>
+> **NB:** Dependency has been **removed** if new version information isn't present.
 
 ## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-16
 

From 8b8ed2f1642872c7abbaf86929d9d42f41e963f9 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 25 Sep 2023 09:42:52 +0200
Subject: [PATCH 474/852] code polish

---
 main.nf | 21 ++++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/main.nf b/main.nf
index b7254a45..339eedd6 100644
--- a/main.nf
+++ b/main.nf
@@ -43,17 +43,24 @@ ch_input = file(params.input, checkIfExists: true)
 if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") }
 
 // Read in ids from --input file
-ch_ids = Channel.from(file(params.input, checkIfExists: true))
+Channel.from(file(params.input, checkIfExists: true))
     .splitCsv(header:false, sep:'', strip:true)
     .map { it[0] }
     .unique()
+    .set { ch_ids }
 
-// Auto-detect input type
+// Auto-detect input id type
 def input_type = ''
-if (WorkflowMain.isSraId(ch_input))          { input_type = 'sra' }
-else if (WorkflowMain.isSynapseId(ch_input)) { input_type = 'synapse' }
-else                                         { error('Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!') }
-if (params.input_type != input_type)         { error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!") }
+if (WorkflowMain.isSraId(ch_input)) {
+    input_type = 'sra'
+} else if (WorkflowMain.isSynapseId(ch_input)) {
+    input_type = 'synapse'
+} else {
+    error('Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!')
+}
+if (params.input_type != input_type) {
+    error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!")
+}
 
 /*
 ========================================================================================
@@ -83,7 +90,7 @@ if (params.input_type == 'synapse') {
 
 /*
 ========================================================================================
-    IMPORT MODULES
+    IMPORT MODULES/SUBWORKFLOWS
 ========================================================================================
 */
 

From aa3339953f4e203730bcf4c47f794479e6ab7b07 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 25 Sep 2023 09:57:09 +0200
Subject: [PATCH 475/852] more code polish

---
 main.nf | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/main.nf b/main.nf
index 339eedd6..34f6d9ce 100644
--- a/main.nf
+++ b/main.nf
@@ -43,7 +43,8 @@ ch_input = file(params.input, checkIfExists: true)
 if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") }
 
 // Read in ids from --input file
-Channel.from(file(params.input, checkIfExists: true))
+Channel
+    .from(file(params.input, checkIfExists: true))
     .splitCsv(header:false, sep:'', strip:true)
     .map { it[0] }
     .unique()
@@ -75,9 +76,7 @@ if (params.input_type == 'sra') {
 
     // Validate input parameters
     WorkflowSra.initialise(params, valid_params)
-}
-
-if (params.input_type == 'synapse') {
+} else if (params.input_type == 'synapse') {
 
     // Create channel for synapse config
     if (params.synapse_config) {
@@ -120,12 +119,16 @@ workflow NFCORE_FETCHNGS {
 
     ch_versions = Channel.empty()
 
+    //
     // WORKFLOW: Download FastQ files for SRA / ENA / GEO / DDBJ ids
+    //
     if (params.input_type == 'sra') {
         SRA(ch_ids, params.sample_mapping_fields)
         ch_versions = ch_versions.mix(SRA.out.versions)
 
+    //
     // WORKFLOW: Download FastQ files for Synapse ids
+    //
     } else if (params.input_type == 'synapse') {
         SYNAPSE(ch_ids, ch_synapse_config)
         ch_versions = ch_versions.mix(SYNAPSE.out.versions)

From 8ccf26a95c42c1dcbd2494be3ea1f4e1f2f0785e Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 25 Sep 2023 10:00:34 +0200
Subject: [PATCH 476/852] params

---
 main.nf               | 2 +-
 workflows/sra/main.nf | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/main.nf b/main.nf
index 34f6d9ce..9617f85e 100644
--- a/main.nf
+++ b/main.nf
@@ -123,7 +123,7 @@ workflow NFCORE_FETCHNGS {
     // WORKFLOW: Download FastQ files for SRA / ENA / GEO / DDBJ ids
     //
     if (params.input_type == 'sra') {
-        SRA(ch_ids, params.sample_mapping_fields)
+        SRA(ch_ids)
         ch_versions = ch_versions.mix(SRA.out.versions)
 
     //
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index e7e56b93..e92ae283 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -22,7 +22,6 @@ workflow SRA {
 
     take:
     ids // channel: [ ids ]
-    sample_mapping_fields
 
     main:
     ch_versions = Channel.empty()
@@ -124,7 +123,7 @@ workflow SRA {
     )
     ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions)
 
-    if (sample_mapping_fields) {
+    if (params.sample_mapping_fields) {
         MULTIQC_MAPPINGS_CONFIG(SRA_MERGE_SAMPLESHEET.out.mappings)
         ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions)
     }

From 6f0189a6395f3d2cdb362fc5c8d9baf8c90044cd Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 25 Sep 2023 10:27:52 +0200
Subject: [PATCH 477/852] more code polish

---
 lib/WorkflowMain.groovy    | 111 +++++++++++++++++++++++++++++++++++++
 lib/WorkflowSra.groovy     |  33 -----------
 lib/WorkflowSynapse.groovy |  92 ------------------------------
 main.nf                    |  12 ++--
 workflows/sra/main.nf      |  14 +++--
 workflows/synapse/main.nf  |   6 +-
 6 files changed, 128 insertions(+), 140 deletions(-)
 delete mode 100755 lib/WorkflowSra.groovy
 delete mode 100755 lib/WorkflowSynapse.groovy

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index f9469941..4ec4029a 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -102,4 +102,115 @@ class WorkflowMain {
         }
         return is_synapse
     }
+
+    //
+    // Check and validate parameters
+    //
+    public static void sraInitialise(params, valid_params) {
+        // Check minimal ENA fields are provided to download FastQ files
+        def ena_metadata_fields = params.ena_metadata_fields ? params.ena_metadata_fields.split(',').collect{ it.trim().toLowerCase() } : valid_params['ena_metadata_fields']
+        if (!ena_metadata_fields.containsAll(valid_params['ena_metadata_fields'])) {
+            Nextflow.error("Invalid option: '${params.ena_metadata_fields}'. Minimally required fields for '--ena_metadata_fields': '${valid_params['ena_metadata_fields'].join(',')}'")
+        }
+    }
+
+    //
+    // Print a warning after pipeline has completed
+    //
+    public static void sraCurateSamplesheetWarn(log) {
+        log.warn "=============================================================================\n" +
+            "  Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" +
+            "  Public databases don't reliably hold information such as strandedness\n" +
+            "  information, controls etc\n\n" +
+            "  All of the sample metadata obtained from the ENA has been appended\n" +
+            "  as additional columns to help you manually curate the samplesheet before\n" +
+            "  running nf-core/other pipelines.\n" +
+            "==================================================================================="
+    }
+
+    //
+    // Convert metadata obtained from the 'synapse show' command to a Groovy map
+    //
+    public static Map synapseShowToMap(synapse_file) {
+        def meta = [:]
+        def category = ''
+        synapse_file.eachLine { line ->
+            def entries = [null, null]
+            if (!line.startsWith(' ') && !line.trim().isEmpty()) {
+                category = line.tokenize(':')[0]
+            } else {
+                entries = line.trim().tokenize('=')
+            }
+            meta["${category}|${entries[0]}"] = entries[1]
+        }
+        meta.id = meta['properties|id']
+        meta.name = meta['properties|name']
+        meta.md5 = meta['File|md5']
+        return meta.findAll{ it.value != null }
+    }
+
+    //
+    // Print a warning after pipeline has completed
+    //
+    public static void synapseCurateSamplesheetWarn(log) {
+        log.warn "=============================================================================\n" +
+            "  Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" +
+            "  Where applicable, default values will be used for sample-specific metadata\n" +
+            "  such as strandedness, controls etc as this information is not provided\n" +
+            "  in a standardised manner when uploading data to Synapse.\n" +
+            "==================================================================================="
+    }
+
+    //
+    // Obtain Sample ID from File Name
+    //
+    public static String synapseSampleNameFromFastQ(input_file, pattern) {
+
+        def sampleids = ""
+
+        def filePattern = pattern.toString()
+        int p = filePattern.lastIndexOf('/')
+            if( p != -1 )
+                filePattern = filePattern.substring(p+1)
+
+        input_file.each {
+            String fileName = input_file.getFileName().toString()
+
+            String indexOfWildcards = filePattern.findIndexOf { it=='*' || it=='?' }
+            String indexOfBrackets = filePattern.findIndexOf { it=='{' || it=='[' }
+            if( indexOfWildcards==-1 && indexOfBrackets==-1 ) {
+                if( fileName == filePattern )
+                    return actual.getSimpleName()
+                throw new IllegalArgumentException("Not a valid file pair globbing pattern: pattern=$filePattern file=$fileName")
+            }
+
+            int groupCount = 0
+            for( int i=0; i<filePattern.size(); i++ ) {
+                def ch = filePattern[i]
+                if( ch=='?' || ch=='*' )
+                    groupCount++
+                else if( ch=='{' || ch=='[' )
+                    break
+            }
+
+            def regex = filePattern
+                    .replace('.','\\.')
+                    .replace('*','(.*)')
+                    .replace('?','(.?)')
+                    .replace('{','(?:')
+                    .replace('}',')')
+                    .replace(',','|')
+
+            def matcher = (fileName =~ /$regex/)
+            if( matcher.matches() ) {
+                int c=Math.min(groupCount, matcher.groupCount())
+                int end = c ? matcher.end(c) : ( indexOfBrackets != -1 ? indexOfBrackets : fileName.size() )
+                def prefix = fileName.substring(0,end)
+                while(prefix.endsWith('-') || prefix.endsWith('_') || prefix.endsWith('.') )
+                    prefix=prefix[0..-2]
+                sampleids = prefix
+            }
+        }
+        return sampleids
+    }
 }
diff --git a/lib/WorkflowSra.groovy b/lib/WorkflowSra.groovy
deleted file mode 100755
index 3c092a6f..00000000
--- a/lib/WorkflowSra.groovy
+++ /dev/null
@@ -1,33 +0,0 @@
-//
-// This file holds several functions specific to the workflow/sra.nf in the nf-core/fetchngs pipeline
-//
-
-import nextflow.Nextflow
-
-class WorkflowSra {
-
-    //
-    // Check and validate parameters
-    //
-    public static void initialise(params, valid_params) {
-        // Check minimal ENA fields are provided to download FastQ files
-        def ena_metadata_fields = params.ena_metadata_fields ? params.ena_metadata_fields.split(',').collect{ it.trim().toLowerCase() } : valid_params['ena_metadata_fields']
-        if (!ena_metadata_fields.containsAll(valid_params['ena_metadata_fields'])) {
-            Nextflow.error("Invalid option: '${params.ena_metadata_fields}'. Minimally required fields for '--ena_metadata_fields': '${valid_params['ena_metadata_fields'].join(',')}'")
-        }
-    }
-
-    //
-    // Print a warning after pipeline has completed
-    //
-    public static void curateSamplesheetWarn(log) {
-        log.warn "=============================================================================\n" +
-            "  Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" +
-            "  Public databases don't reliably hold information such as strandedness\n" +
-            "  information, controls etc\n\n" +
-            "  All of the sample metadata obtained from the ENA has been appended\n" +
-            "  as additional columns to help you manually curate the samplesheet before\n" +
-            "  running nf-core/other pipelines.\n" +
-            "==================================================================================="
-    }
-}
diff --git a/lib/WorkflowSynapse.groovy b/lib/WorkflowSynapse.groovy
deleted file mode 100755
index 8a79c6a6..00000000
--- a/lib/WorkflowSynapse.groovy
+++ /dev/null
@@ -1,92 +0,0 @@
-//
-// This file holds several functions specific to the workflow/synapse.nf in the nf-core/fetchngs pipeline
-//
-
-class WorkflowSynapse {
-
-    //
-    // Convert metadata obtained from the 'synapse show' command to a Groovy map
-    //
-    public static Map synapseShowToMap(synapse_file) {
-        def meta = [:]
-        def category = ''
-        synapse_file.eachLine { line ->
-            def entries = [null, null]
-            if (!line.startsWith(' ') && !line.trim().isEmpty()) {
-                category = line.tokenize(':')[0]
-            } else {
-                entries = line.trim().tokenize('=')
-            }
-            meta["${category}|${entries[0]}"] = entries[1]
-        }
-        meta.id = meta['properties|id']
-        meta.name = meta['properties|name']
-        meta.md5 = meta['File|md5']
-        return meta.findAll{ it.value != null }
-    }
-
-    //
-    // Print a warning after pipeline has completed
-    //
-    public static void curateSamplesheetWarn(log) {
-        log.warn "=============================================================================\n" +
-            "  Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" +
-            "  Where applicable, default values will be used for sample-specific metadata\n" +
-            "  such as strandedness, controls etc as this information is not provided\n" +
-            "  in a standardised manner when uploading data to Synapse.\n" +
-            "==================================================================================="
-    }
-
-    //
-    // Obtain Sample ID from File Name
-    //
-    public static String sampleNameFromFastQ(input_file, pattern) {
-
-        def sampleids = ""
-
-        def filePattern = pattern.toString()
-        int p = filePattern.lastIndexOf('/')
-            if( p != -1 )
-                filePattern = filePattern.substring(p+1)
-
-        input_file.each {
-            String fileName = input_file.getFileName().toString()
-
-            String indexOfWildcards = filePattern.findIndexOf { it=='*' || it=='?' }
-            String indexOfBrackets = filePattern.findIndexOf { it=='{' || it=='[' }
-            if( indexOfWildcards==-1 && indexOfBrackets==-1 ) {
-                if( fileName == filePattern )
-                    return actual.getSimpleName()
-                throw new IllegalArgumentException("Not a valid file pair globbing pattern: pattern=$filePattern file=$fileName")
-            }
-
-            int groupCount = 0
-            for( int i=0; i<filePattern.size(); i++ ) {
-                def ch = filePattern[i]
-                if( ch=='?' || ch=='*' )
-                    groupCount++
-                else if( ch=='{' || ch=='[' )
-                    break
-            }
-
-            def regex = filePattern
-                    .replace('.','\\.')
-                    .replace('*','(.*)')
-                    .replace('?','(.?)')
-                    .replace('{','(?:')
-                    .replace('}',')')
-                    .replace(',','|')
-
-            def matcher = (fileName =~ /$regex/)
-            if( matcher.matches() ) {
-                int c=Math.min(groupCount, matcher.groupCount())
-                int end = c ? matcher.end(c) : ( indexOfBrackets != -1 ? indexOfBrackets : fileName.size() )
-                def prefix = fileName.substring(0,end)
-                while(prefix.endsWith('-') || prefix.endsWith('_') || prefix.endsWith('.') )
-                    prefix=prefix[0..-2]
-                sampleids = prefix
-            }
-        }
-        return sampleids
-    }
-}
diff --git a/main.nf b/main.nf
index 9617f85e..f0f40588 100644
--- a/main.nf
+++ b/main.nf
@@ -75,7 +75,7 @@ if (params.input_type == 'sra') {
     ]
 
     // Validate input parameters
-    WorkflowSra.initialise(params, valid_params)
+    Workflow.sraInitialise(params, valid_params)
 } else if (params.input_type == 'synapse') {
 
     // Create channel for synapse config
@@ -115,7 +115,7 @@ if (params.input_type == 'synapse') include { SYNAPSE } from './workflows/synaps
 // WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided
 //
 workflow NFCORE_FETCHNGS {
-    INITIALISE(params.version, params.help, params.valid_params)
+    INITIALISE ( params.version, params.help, params.valid_params )
 
     ch_versions = Channel.empty()
 
@@ -123,14 +123,14 @@ workflow NFCORE_FETCHNGS {
     // WORKFLOW: Download FastQ files for SRA / ENA / GEO / DDBJ ids
     //
     if (params.input_type == 'sra') {
-        SRA(ch_ids)
+        SRA ( ch_ids )
         ch_versions = ch_versions.mix(SRA.out.versions)
 
     //
     // WORKFLOW: Download FastQ files for Synapse ids
     //
     } else if (params.input_type == 'synapse') {
-        SYNAPSE(ch_ids, ch_synapse_config)
+        SYNAPSE ( ch_ids, ch_synapse_config )
         ch_versions = ch_versions.mix(SYNAPSE.out.versions)
     }
 
@@ -163,8 +163,8 @@ workflow.onComplete {
         NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)
     }
     NfcoreTemplate.summary(workflow, params, log)
-    if (params.input_type == 'sra')     { WorkflowSra.curateSamplesheetWarn(log) }
-    if (params.input_type == 'synapse') { WorkflowSynapse.curateSamplesheetWarn(log) }
+    if (params.input_type == 'sra')     { Workflow.sraCurateSamplesheetWarn(log) }
+    if (params.input_type == 'synapse') { Workflow.synapseCurateSamplesheetWarn(log) }
 }
 
 /*
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index e92ae283..d59b1908 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -43,7 +43,7 @@ workflow SRA {
     )
     ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first())
 
-    ch_sra_metadata = SRA_RUNINFO_TO_FTP
+    SRA_RUNINFO_TO_FTP
         .out
         .tsv
         .splitCsv(header:true, sep:'\t')
@@ -53,6 +53,7 @@ workflow SRA {
             return meta_clone
         }
         .unique()
+        .set{ ch_sra_metadata }
 
     ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first())
 
@@ -60,7 +61,7 @@ workflow SRA {
 
     if (!params.skip_fastq_download) {
 
-        ch_sra_reads = ch_sra_metadata
+        ch_sra_metadata
             .map {
                 meta ->
                     [ meta, [ meta.fastq_1, meta.fastq_2 ] ]
@@ -69,6 +70,7 @@ workflow SRA {
                 ftp: it[0].fastq_1  && !params.force_sratools_download
                 sra: !it[0].fastq_1 || params.force_sratools_download
             }
+            .set { ch_sra_reads }
 
         //
         // MODULE: If FTP link is provided in run information then download FastQ directly via FTP and validate with md5sums
@@ -88,12 +90,12 @@ workflow SRA {
         ch_versions = ch_versions.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.versions.first())
 
         // Isolate FASTQ channel which will be added to emit block
-        fastq_files = fastq_files.mix(
+        fastq_files.mix(
             SRA_FASTQ_FTP.out.fastq,
             FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads
-        )
+        ).set { fastq_files }
 
-        ch_sra_metadata = fastq_files.map { meta, fastq ->
+        fastq_files.map { meta, fastq ->
             def reads = fastq instanceof List ? fastq.flatten() : [ fastq ]
             def meta_clone = meta.clone()
 
@@ -101,7 +103,7 @@ workflow SRA {
             meta_clone.fastq_2 = reads[1] && !meta.single_end ? "${params.outdir}/fastq/${reads[1].getName()}" : ''
 
             return meta_clone
-        }
+        }.set { ch_sra_metadata }
     }
 
     //
diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf
index 30d05f4f..785877ac 100644
--- a/workflows/synapse/main.nf
+++ b/workflows/synapse/main.nf
@@ -56,7 +56,7 @@ workflow SYNAPSE {
     SYNAPSE_SHOW
         .out
         .metadata
-        .map { it -> WorkflowSynapse.synapseShowToMap(it) }
+        .map { it -> Workflow.synapseShowToMap(it) }
         .set { ch_samples_meta }
 
     //
@@ -72,14 +72,14 @@ workflow SYNAPSE {
     SYNAPSE_GET
         .out
         .fastq
-        .map { meta, fastq -> [ WorkflowSynapse.sampleNameFromFastQ( fastq , "*{1,2}*"), fastq ] }
+        .map { meta, fastq -> [ Workflow.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), fastq ] }
         .groupTuple(sort: { it -> it.baseName })
         .set { ch_fastq }
 
     SYNAPSE_GET
         .out
         .fastq
-        .map { meta, fastq -> [ WorkflowSynapse.sampleNameFromFastQ( fastq , "*{1,2}*"), meta.id ] }
+        .map { meta, fastq -> [ Workflow.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), meta.id ] }
         .groupTuple()
         .join(ch_fastq)
         .map { id, synids, fastq ->

From 37229aba32279f5fcb1107215847431362b7bdb6 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 25 Sep 2023 10:32:24 +0200
Subject: [PATCH 478/852] typo

---
 main.nf                   | 8 ++++----
 workflows/synapse/main.nf | 6 +++---
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/main.nf b/main.nf
index f0f40588..95cc5fbc 100644
--- a/main.nf
+++ b/main.nf
@@ -28,7 +28,7 @@ log.info logo + paramsSummaryLog(workflow) + citation
 
 // Print help message if needed
 if (params.help) {
-    def String command = "nextflow run ${workflow.manifest.name} --input id.csv -profile docker"
+    def String command = "nextflow run ${WorkflowMain.manifest.name} --input id.csv -profile docker"
     log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
     System.exit(0)
 }
@@ -75,7 +75,7 @@ if (params.input_type == 'sra') {
     ]
 
     // Validate input parameters
-    Workflow.sraInitialise(params, valid_params)
+    WorkflowMain.sraInitialise(params, valid_params)
 } else if (params.input_type == 'synapse') {
 
     // Create channel for synapse config
@@ -163,8 +163,8 @@ workflow.onComplete {
         NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)
     }
     NfcoreTemplate.summary(workflow, params, log)
-    if (params.input_type == 'sra')     { Workflow.sraCurateSamplesheetWarn(log) }
-    if (params.input_type == 'synapse') { Workflow.synapseCurateSamplesheetWarn(log) }
+    if (params.input_type == 'sra')     { WorkflowMain.sraCurateSamplesheetWarn(log) }
+    if (params.input_type == 'synapse') { WorkflowMain.synapseCurateSamplesheetWarn(log) }
 }
 
 /*
diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf
index 785877ac..0fc46ed4 100644
--- a/workflows/synapse/main.nf
+++ b/workflows/synapse/main.nf
@@ -56,7 +56,7 @@ workflow SYNAPSE {
     SYNAPSE_SHOW
         .out
         .metadata
-        .map { it -> Workflow.synapseShowToMap(it) }
+        .map { it -> WorkflowMain.synapseShowToMap(it) }
         .set { ch_samples_meta }
 
     //
@@ -72,14 +72,14 @@ workflow SYNAPSE {
     SYNAPSE_GET
         .out
         .fastq
-        .map { meta, fastq -> [ Workflow.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), fastq ] }
+        .map { meta, fastq -> [ WorkflowMain.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), fastq ] }
         .groupTuple(sort: { it -> it.baseName })
         .set { ch_fastq }
 
     SYNAPSE_GET
         .out
         .fastq
-        .map { meta, fastq -> [ Workflow.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), meta.id ] }
+        .map { meta, fastq -> [ WorkflowMain.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), meta.id ] }
         .groupTuple()
         .join(ch_fastq)
         .map { id, synids, fastq ->

From ef3a5cfd3ee6f093ed99b5e535e0d94c747b0c46 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Mon, 25 Sep 2023 10:45:28 +0200
Subject: [PATCH 479/852] Apply suggestions from code review

---
 main.nf               |  2 +-
 workflows/sra/main.nf | 10 +++++-----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/main.nf b/main.nf
index 95cc5fbc..70e8ff27 100644
--- a/main.nf
+++ b/main.nf
@@ -28,7 +28,7 @@ log.info logo + paramsSummaryLog(workflow) + citation
 
 // Print help message if needed
 if (params.help) {
-    def String command = "nextflow run ${WorkflowMain.manifest.name} --input id.csv -profile docker"
+    def String command = "nextflow run ${workflow.manifest.name} --input id.csv -profile docker"
     log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
     System.exit(0)
 }
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index d59b1908..45efa9c9 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -53,7 +53,7 @@ workflow SRA {
             return meta_clone
         }
         .unique()
-        .set{ ch_sra_metadata }
+        .set { ch_sra_metadata }
 
     ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first())
 
@@ -93,9 +93,7 @@ workflow SRA {
         fastq_files.mix(
             SRA_FASTQ_FTP.out.fastq,
             FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads
-        ).set { fastq_files }
-
-        fastq_files.map { meta, fastq ->
+        ).map { meta, fastq ->
             def reads = fastq instanceof List ? fastq.flatten() : [ fastq ]
             def meta_clone = meta.clone()
 
@@ -126,7 +124,9 @@ workflow SRA {
     ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions)
 
     if (params.sample_mapping_fields) {
-        MULTIQC_MAPPINGS_CONFIG(SRA_MERGE_SAMPLESHEET.out.mappings)
+        MULTIQC_MAPPINGS_CONFIG (
+            SRA_MERGE_SAMPLESHEET.out.mappings
+        )
         ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions)
     }
 

From cdaf06fa7150f2f994d9214d132f3e83b9e141b5 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 22 Sep 2023 11:30:43 +0200
Subject: [PATCH 480/852] use initialise subworkflows

---
 main.nf                                  | 22 +-------
 modules.json                             |  5 ++
 subworkflows/nf-core/initialise/main.nf  | 68 ++++++++++++++++++++++++
 subworkflows/nf-core/initialise/meta.yml | 33 ++++++++++++
 4 files changed, 108 insertions(+), 20 deletions(-)
 create mode 100644 subworkflows/nf-core/initialise/main.nf
 create mode 100644 subworkflows/nf-core/initialise/meta.yml

diff --git a/main.nf b/main.nf
index 355898d0..a5011951 100644
--- a/main.nf
+++ b/main.nf
@@ -17,26 +17,6 @@ nextflow.enable.dsl = 2
 ========================================================================================
 */
 
-include { paramsHelp; paramsSummaryLog; validateParameters } from 'plugin/nf-validation'
-
-def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
-def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
-
-// Print parameter summary log to screen
-log.info logo + paramsSummaryLog(workflow) + citation
-
-// Print help message if needed
-if (params.help) {
-    def String command = "nextflow run ${workflow.manifest.name} --input id.csv -profile docker"
-    log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
-    System.exit(0)
-}
-
-// Validate input parameters
-if (params.validate_params) {
-    validateParameters()
-}
-
 // Check if --input file is empty
 ch_input = file(params.input, checkIfExists: true)
 if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") }
@@ -88,6 +68,7 @@ if (params.input_type == 'synapse') {
 
 include { MULTIQC_MAPPINGS_CONFIG     } from './modules/local/multiqc_mappings_config'
 include { CUSTOM_DUMPSOFTWAREVERSIONS } from './modules/nf-core/custom/dumpsoftwareversions'
+include { INITIALISE                  } from './subworkflows/nf-core/initialise/main'
 
 /*
 ========================================================================================
@@ -108,6 +89,7 @@ if (params.input_type == 'synapse') include { SYNAPSE } from './workflows/synaps
 // WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided
 //
 workflow NFCORE_FETCHNGS {
+    INITIALISE(params.version, params.help, params.valid_params)
 
     ch_versions = Channel.empty()
 
diff --git a/modules.json b/modules.json
index ab610dfb..46dc80ef 100644
--- a/modules.json
+++ b/modules.json
@@ -33,6 +33,11 @@
                         "branch": "master",
                         "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca",
                         "installed_by": ["subworkflows"]
+                    },
+                    "initialise": {
+                        "branch": "master",
+                        "git_sha": "7b55a4631bebd1cf827a448d0b70386681fea475",
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }
diff --git a/subworkflows/nf-core/initialise/main.nf b/subworkflows/nf-core/initialise/main.nf
new file mode 100644
index 00000000..0cbd3799
--- /dev/null
+++ b/subworkflows/nf-core/initialise/main.nf
@@ -0,0 +1,68 @@
+// This is a reimplementation of the basic initialise methods in the nf-core template
+// The role of this subworkflow is to check the input parameters and print help messages
+// Use this to start your nf-core pipeline
+
+include { paramsHelp; paramsSummaryLog; paramsSummaryMap; validateParameters } from 'plugin/nf-validation'
+
+workflow INITIALISE {
+
+    take:
+        version         // bool
+        help            // bool
+        validate_params // bool
+
+    main:
+
+        // Print workflow version and exit on --version
+        if (version) {
+            String version_string = ""
+
+            if (workflow.manifest.version) {
+                def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
+                version_string += "${prefix_v}${workflow.manifest.version}"
+            }
+
+            if (workflow.commitId) {
+                def git_shortsha = workflow.commitId.substring(0, 7)
+                version_string += "-g${git_shortsha}"
+            }
+            log.info "${workflow.manifest.name} ${version_string}"
+            System.exit(0)
+        }
+
+        // Print citation for nf-core
+        def citation = "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
+            "* The nf-core framework\n" +
+            "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
+            "* Software dependencies\n" +
+            "  ${workflow.manifest.homePage}/blob/master/CITATIONS.md"
+        log.info citation
+
+        // Print help message if needed
+        if (params.help) {
+            def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv -profile docker"
+            log.info paramsHelp(command)
+            System.exit(0)
+        }
+
+        if ( params.validate_params != false ){
+            validateParameters()
+        }
+
+        if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
+            log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
+                    "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
+                    "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
+                    "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
+                    "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
+                    "Please refer to the quick start section and usage docs for the pipeline.\n "
+        }
+
+        log.info paramsSummaryLog(workflow)
+
+        summary_params = paramsSummaryMap(workflow)
+
+    emit:
+        summary_params
+
+}
diff --git a/subworkflows/nf-core/initialise/meta.yml b/subworkflows/nf-core/initialise/meta.yml
new file mode 100644
index 00000000..69596bb5
--- /dev/null
+++ b/subworkflows/nf-core/initialise/meta.yml
@@ -0,0 +1,33 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "initialise"
+description: Validate input parameters and print help messages
+keywords:
+  - admin
+  - check
+  - help
+  - version
+modules:
+input:
+  - version:
+    type: boolean
+    description: |
+      Structure: val(version)
+      Boolean to show the pipeline version and exit.
+  - help:
+    type: boolean
+    description: |
+      Structure: val(help)
+      Boolean to show the pipeline help message and exit.
+  - validate_params:
+    type: boolean
+    description: |
+      Structure: val(validate_params)
+      Whether to validate the parameters prior to starting the pipeline.
+output:
+  - summary_params:
+    type: value
+    description: |
+      Structure: val(summary_params)
+      A map of the parameters used in the pipeline.
+authors:
+  - "@adamrtalbot"

From b8b15903aa71378d9357ab61c7e3c2f93a9d4d51 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 22 Sep 2023 12:00:32 +0200
Subject: [PATCH 481/852] move scripts

---
 workflows/sra/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 8d5149d2..8b5f649e 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -9,6 +9,7 @@ include { SRA_RUNINFO_TO_FTP      } from '../../modules/local/sra_runinfo_to_ftp
 include { SRA_FASTQ_FTP           } from '../../modules/local/sra_fastq_ftp'
 include { SRA_TO_SAMPLESHEET      } from '../../modules/local/sra_to_samplesheet'
 include { SRA_MERGE_SAMPLESHEET   } from '../../modules/local/sra_merge_samplesheet'
+include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_config'
 
 /*
 ========================================================================================

From b6c71a112e971d918c048bc4899dbfe131dab923 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 22 Sep 2023 17:59:55 +0200
Subject: [PATCH 482/852] no need to test on push on dev, pr are enough

---
 .nf-core.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.nf-core.yml b/.nf-core.yml
index d617b3a3..78f1faff 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -2,7 +2,11 @@ repository_type: pipeline
 lint:
   actions_ci: false
   files_exist:
+    - .github/workflows/awsfulltest.yml
+    - .github/workflows/awstest.yml
+    - conf/igenomes.config
     - conf/modules.config
+    - lib/WorkflowFetchngs.groovy
   files_unchanged:
     - assets/sendmail_template.txt
     - lib/NfcoreTemplate.groovy

From d6f8971a23c7432cc8a5655340ba627323b2410e Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 22 Sep 2023 18:08:35 +0200
Subject: [PATCH 483/852] more code polish

---
 main.nf | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/main.nf b/main.nf
index a5011951..aa24ed36 100644
--- a/main.nf
+++ b/main.nf
@@ -1,4 +1,5 @@
 #!/usr/bin/env nextflow
+
 /*
 ========================================================================================
     nf-core/fetchngs
@@ -66,7 +67,6 @@ if (params.input_type == 'synapse') {
 ========================================================================================
 */
 
-include { MULTIQC_MAPPINGS_CONFIG     } from './modules/local/multiqc_mappings_config'
 include { CUSTOM_DUMPSOFTWAREVERSIONS } from './modules/nf-core/custom/dumpsoftwareversions'
 include { INITIALISE                  } from './subworkflows/nf-core/initialise/main'
 
@@ -98,12 +98,6 @@ workflow NFCORE_FETCHNGS {
         SRA(ch_ids)
         ch_versions = ch_versions.mix(SRA.out.versions)
 
-        // MODULE: Create a MultiQC config file with sample name mappings
-        if (params.sample_mapping_fields) {
-            MULTIQC_MAPPINGS_CONFIG(SRA.out.mappings)
-            ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions)
-        }
-
     // WORKFLOW: Download FastQ files for Synapse ids
     } else if (params.input_type == 'synapse') {
         SYNAPSE(ch_ids, ch_synapse_config)
@@ -115,9 +109,9 @@ workflow NFCORE_FETCHNGS {
 }
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
     RUN ALL WORKFLOWS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
 */
 
 //

From a968fcb29bb5791199f921f2823f7f6c848539e3 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 25 Sep 2023 09:42:52 +0200
Subject: [PATCH 484/852] code polish

---
 main.nf | 21 ++++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/main.nf b/main.nf
index aa24ed36..a67acf26 100644
--- a/main.nf
+++ b/main.nf
@@ -23,17 +23,24 @@ ch_input = file(params.input, checkIfExists: true)
 if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") }
 
 // Read in ids from --input file
-ch_ids = Channel.from(file(params.input, checkIfExists: true))
+Channel.from(file(params.input, checkIfExists: true))
     .splitCsv(header:false, sep:'', strip:true)
     .map { it[0] }
     .unique()
+    .set { ch_ids }
 
-// Auto-detect input type
+// Auto-detect input id type
 def input_type = ''
-if (WorkflowMain.isSraId(ch_input))          { input_type = 'sra' }
-else if (WorkflowMain.isSynapseId(ch_input)) { input_type = 'synapse' }
-else                                         { error('Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!') }
-if (params.input_type != input_type)         { error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!") }
+if (WorkflowMain.isSraId(ch_input)) {
+    input_type = 'sra'
+} else if (WorkflowMain.isSynapseId(ch_input)) {
+    input_type = 'synapse'
+} else {
+    error('Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!')
+}
+if (params.input_type != input_type) {
+    error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!")
+}
 
 /*
 ========================================================================================
@@ -63,7 +70,7 @@ if (params.input_type == 'synapse') {
 
 /*
 ========================================================================================
-    IMPORT MODULES
+    IMPORT MODULES/SUBWORKFLOWS
 ========================================================================================
 */
 

From 58f92b086478fabcb1a106678c34e15f42a6e40d Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 25 Sep 2023 09:57:09 +0200
Subject: [PATCH 485/852] more code polish

---
 main.nf | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/main.nf b/main.nf
index a67acf26..22977145 100644
--- a/main.nf
+++ b/main.nf
@@ -23,7 +23,8 @@ ch_input = file(params.input, checkIfExists: true)
 if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") }
 
 // Read in ids from --input file
-Channel.from(file(params.input, checkIfExists: true))
+Channel
+    .from(file(params.input, checkIfExists: true))
     .splitCsv(header:false, sep:'', strip:true)
     .map { it[0] }
     .unique()
@@ -55,9 +56,7 @@ if (params.input_type == 'sra') {
 
     // Validate input parameters
     WorkflowSra.initialise(params, valid_params)
-}
-
-if (params.input_type == 'synapse') {
+} else if (params.input_type == 'synapse') {
 
     // Create channel for synapse config
     if (params.synapse_config) {
@@ -100,12 +99,16 @@ workflow NFCORE_FETCHNGS {
 
     ch_versions = Channel.empty()
 
+    //
     // WORKFLOW: Download FastQ files for SRA / ENA / GEO / DDBJ ids
+    //
     if (params.input_type == 'sra') {
         SRA(ch_ids)
         ch_versions = ch_versions.mix(SRA.out.versions)
 
+    //
     // WORKFLOW: Download FastQ files for Synapse ids
+    //
     } else if (params.input_type == 'synapse') {
         SYNAPSE(ch_ids, ch_synapse_config)
         ch_versions = ch_versions.mix(SYNAPSE.out.versions)

From c98917663793ea5af43afcf85d8b75a7f83e16af Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 25 Sep 2023 10:00:34 +0200
Subject: [PATCH 486/852] params

---
 workflows/sra/main.nf | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 8b5f649e..de3eaf8b 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -130,6 +130,11 @@ workflow SRA {
     )
     ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions)
 
+    if (params.sample_mapping_fields) {
+        MULTIQC_MAPPINGS_CONFIG(SRA_MERGE_SAMPLESHEET.out.mappings)
+        ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions)
+    }
+
     emit:
     fastq         = fastq_files
     samplesheet   = SRA_MERGE_SAMPLESHEET.out.samplesheet

From 131fd1b6fa42679d8cd779039e8f40de333d4e95 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 25 Sep 2023 10:27:52 +0200
Subject: [PATCH 487/852] more code polish

---
 lib/WorkflowMain.groovy    | 111 +++++++++++++++++++++++++++++++++++++
 lib/WorkflowSra.groovy     |  33 -----------
 lib/WorkflowSynapse.groovy |  92 ------------------------------
 main.nf                    |  12 ++--
 workflows/sra/main.nf      |  14 +++--
 workflows/synapse/main.nf  |   6 +-
 6 files changed, 128 insertions(+), 140 deletions(-)
 delete mode 100755 lib/WorkflowSra.groovy
 delete mode 100755 lib/WorkflowSynapse.groovy

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index f9469941..4ec4029a 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -102,4 +102,115 @@ class WorkflowMain {
         }
         return is_synapse
     }
+
+    //
+    // Check and validate parameters
+    //
+    public static void sraInitialise(params, valid_params) {
+        // Check minimal ENA fields are provided to download FastQ files
+        def ena_metadata_fields = params.ena_metadata_fields ? params.ena_metadata_fields.split(',').collect{ it.trim().toLowerCase() } : valid_params['ena_metadata_fields']
+        if (!ena_metadata_fields.containsAll(valid_params['ena_metadata_fields'])) {
+            Nextflow.error("Invalid option: '${params.ena_metadata_fields}'. Minimally required fields for '--ena_metadata_fields': '${valid_params['ena_metadata_fields'].join(',')}'")
+        }
+    }
+
+    //
+    // Print a warning after pipeline has completed
+    //
+    public static void sraCurateSamplesheetWarn(log) {
+        log.warn "=============================================================================\n" +
+            "  Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" +
+            "  Public databases don't reliably hold information such as strandedness\n" +
+            "  information, controls etc\n\n" +
+            "  All of the sample metadata obtained from the ENA has been appended\n" +
+            "  as additional columns to help you manually curate the samplesheet before\n" +
+            "  running nf-core/other pipelines.\n" +
+            "==================================================================================="
+    }
+
+    //
+    // Convert metadata obtained from the 'synapse show' command to a Groovy map
+    //
+    public static Map synapseShowToMap(synapse_file) {
+        def meta = [:]
+        def category = ''
+        synapse_file.eachLine { line ->
+            def entries = [null, null]
+            if (!line.startsWith(' ') && !line.trim().isEmpty()) {
+                category = line.tokenize(':')[0]
+            } else {
+                entries = line.trim().tokenize('=')
+            }
+            meta["${category}|${entries[0]}"] = entries[1]
+        }
+        meta.id = meta['properties|id']
+        meta.name = meta['properties|name']
+        meta.md5 = meta['File|md5']
+        return meta.findAll{ it.value != null }
+    }
+
+    //
+    // Print a warning after pipeline has completed
+    //
+    public static void synapseCurateSamplesheetWarn(log) {
+        log.warn "=============================================================================\n" +
+            "  Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" +
+            "  Where applicable, default values will be used for sample-specific metadata\n" +
+            "  such as strandedness, controls etc as this information is not provided\n" +
+            "  in a standardised manner when uploading data to Synapse.\n" +
+            "==================================================================================="
+    }
+
+    //
+    // Obtain Sample ID from File Name
+    //
+    public static String synapseSampleNameFromFastQ(input_file, pattern) {
+
+        def sampleids = ""
+
+        def filePattern = pattern.toString()
+        int p = filePattern.lastIndexOf('/')
+            if( p != -1 )
+                filePattern = filePattern.substring(p+1)
+
+        input_file.each {
+            String fileName = input_file.getFileName().toString()
+
+            String indexOfWildcards = filePattern.findIndexOf { it=='*' || it=='?' }
+            String indexOfBrackets = filePattern.findIndexOf { it=='{' || it=='[' }
+            if( indexOfWildcards==-1 && indexOfBrackets==-1 ) {
+                if( fileName == filePattern )
+                    return actual.getSimpleName()
+                throw new IllegalArgumentException("Not a valid file pair globbing pattern: pattern=$filePattern file=$fileName")
+            }
+
+            int groupCount = 0
+            for( int i=0; i<filePattern.size(); i++ ) {
+                def ch = filePattern[i]
+                if( ch=='?' || ch=='*' )
+                    groupCount++
+                else if( ch=='{' || ch=='[' )
+                    break
+            }
+
+            def regex = filePattern
+                    .replace('.','\\.')
+                    .replace('*','(.*)')
+                    .replace('?','(.?)')
+                    .replace('{','(?:')
+                    .replace('}',')')
+                    .replace(',','|')
+
+            def matcher = (fileName =~ /$regex/)
+            if( matcher.matches() ) {
+                int c=Math.min(groupCount, matcher.groupCount())
+                int end = c ? matcher.end(c) : ( indexOfBrackets != -1 ? indexOfBrackets : fileName.size() )
+                def prefix = fileName.substring(0,end)
+                while(prefix.endsWith('-') || prefix.endsWith('_') || prefix.endsWith('.') )
+                    prefix=prefix[0..-2]
+                sampleids = prefix
+            }
+        }
+        return sampleids
+    }
 }
diff --git a/lib/WorkflowSra.groovy b/lib/WorkflowSra.groovy
deleted file mode 100755
index 3c092a6f..00000000
--- a/lib/WorkflowSra.groovy
+++ /dev/null
@@ -1,33 +0,0 @@
-//
-// This file holds several functions specific to the workflow/sra.nf in the nf-core/fetchngs pipeline
-//
-
-import nextflow.Nextflow
-
-class WorkflowSra {
-
-    //
-    // Check and validate parameters
-    //
-    public static void initialise(params, valid_params) {
-        // Check minimal ENA fields are provided to download FastQ files
-        def ena_metadata_fields = params.ena_metadata_fields ? params.ena_metadata_fields.split(',').collect{ it.trim().toLowerCase() } : valid_params['ena_metadata_fields']
-        if (!ena_metadata_fields.containsAll(valid_params['ena_metadata_fields'])) {
-            Nextflow.error("Invalid option: '${params.ena_metadata_fields}'. Minimally required fields for '--ena_metadata_fields': '${valid_params['ena_metadata_fields'].join(',')}'")
-        }
-    }
-
-    //
-    // Print a warning after pipeline has completed
-    //
-    public static void curateSamplesheetWarn(log) {
-        log.warn "=============================================================================\n" +
-            "  Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" +
-            "  Public databases don't reliably hold information such as strandedness\n" +
-            "  information, controls etc\n\n" +
-            "  All of the sample metadata obtained from the ENA has been appended\n" +
-            "  as additional columns to help you manually curate the samplesheet before\n" +
-            "  running nf-core/other pipelines.\n" +
-            "==================================================================================="
-    }
-}
diff --git a/lib/WorkflowSynapse.groovy b/lib/WorkflowSynapse.groovy
deleted file mode 100755
index 8a79c6a6..00000000
--- a/lib/WorkflowSynapse.groovy
+++ /dev/null
@@ -1,92 +0,0 @@
-//
-// This file holds several functions specific to the workflow/synapse.nf in the nf-core/fetchngs pipeline
-//
-
-class WorkflowSynapse {
-
-    //
-    // Convert metadata obtained from the 'synapse show' command to a Groovy map
-    //
-    public static Map synapseShowToMap(synapse_file) {
-        def meta = [:]
-        def category = ''
-        synapse_file.eachLine { line ->
-            def entries = [null, null]
-            if (!line.startsWith(' ') && !line.trim().isEmpty()) {
-                category = line.tokenize(':')[0]
-            } else {
-                entries = line.trim().tokenize('=')
-            }
-            meta["${category}|${entries[0]}"] = entries[1]
-        }
-        meta.id = meta['properties|id']
-        meta.name = meta['properties|name']
-        meta.md5 = meta['File|md5']
-        return meta.findAll{ it.value != null }
-    }
-
-    //
-    // Print a warning after pipeline has completed
-    //
-    public static void curateSamplesheetWarn(log) {
-        log.warn "=============================================================================\n" +
-            "  Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" +
-            "  Where applicable, default values will be used for sample-specific metadata\n" +
-            "  such as strandedness, controls etc as this information is not provided\n" +
-            "  in a standardised manner when uploading data to Synapse.\n" +
-            "==================================================================================="
-    }
-
-    //
-    // Obtain Sample ID from File Name
-    //
-    public static String sampleNameFromFastQ(input_file, pattern) {
-
-        def sampleids = ""
-
-        def filePattern = pattern.toString()
-        int p = filePattern.lastIndexOf('/')
-            if( p != -1 )
-                filePattern = filePattern.substring(p+1)
-
-        input_file.each {
-            String fileName = input_file.getFileName().toString()
-
-            String indexOfWildcards = filePattern.findIndexOf { it=='*' || it=='?' }
-            String indexOfBrackets = filePattern.findIndexOf { it=='{' || it=='[' }
-            if( indexOfWildcards==-1 && indexOfBrackets==-1 ) {
-                if( fileName == filePattern )
-                    return actual.getSimpleName()
-                throw new IllegalArgumentException("Not a valid file pair globbing pattern: pattern=$filePattern file=$fileName")
-            }
-
-            int groupCount = 0
-            for( int i=0; i<filePattern.size(); i++ ) {
-                def ch = filePattern[i]
-                if( ch=='?' || ch=='*' )
-                    groupCount++
-                else if( ch=='{' || ch=='[' )
-                    break
-            }
-
-            def regex = filePattern
-                    .replace('.','\\.')
-                    .replace('*','(.*)')
-                    .replace('?','(.?)')
-                    .replace('{','(?:')
-                    .replace('}',')')
-                    .replace(',','|')
-
-            def matcher = (fileName =~ /$regex/)
-            if( matcher.matches() ) {
-                int c=Math.min(groupCount, matcher.groupCount())
-                int end = c ? matcher.end(c) : ( indexOfBrackets != -1 ? indexOfBrackets : fileName.size() )
-                def prefix = fileName.substring(0,end)
-                while(prefix.endsWith('-') || prefix.endsWith('_') || prefix.endsWith('.') )
-                    prefix=prefix[0..-2]
-                sampleids = prefix
-            }
-        }
-        return sampleids
-    }
-}
diff --git a/main.nf b/main.nf
index 22977145..91aa6601 100644
--- a/main.nf
+++ b/main.nf
@@ -55,7 +55,7 @@ if (params.input_type == 'sra') {
     ]
 
     // Validate input parameters
-    WorkflowSra.initialise(params, valid_params)
+    Workflow.sraInitialise(params, valid_params)
 } else if (params.input_type == 'synapse') {
 
     // Create channel for synapse config
@@ -95,7 +95,7 @@ if (params.input_type == 'synapse') include { SYNAPSE } from './workflows/synaps
 // WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided
 //
 workflow NFCORE_FETCHNGS {
-    INITIALISE(params.version, params.help, params.valid_params)
+    INITIALISE ( params.version, params.help, params.valid_params )
 
     ch_versions = Channel.empty()
 
@@ -103,14 +103,14 @@ workflow NFCORE_FETCHNGS {
     // WORKFLOW: Download FastQ files for SRA / ENA / GEO / DDBJ ids
     //
     if (params.input_type == 'sra') {
-        SRA(ch_ids)
+        SRA ( ch_ids )
         ch_versions = ch_versions.mix(SRA.out.versions)
 
     //
     // WORKFLOW: Download FastQ files for Synapse ids
     //
     } else if (params.input_type == 'synapse') {
-        SYNAPSE(ch_ids, ch_synapse_config)
+        SYNAPSE ( ch_ids, ch_synapse_config )
         ch_versions = ch_versions.mix(SYNAPSE.out.versions)
     }
 
@@ -143,8 +143,8 @@ workflow.onComplete {
         NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)
     }
     NfcoreTemplate.summary(workflow, params, log)
-    if (params.input_type == 'sra')     { WorkflowSra.curateSamplesheetWarn(log) }
-    if (params.input_type == 'synapse') { WorkflowSynapse.curateSamplesheetWarn(log) }
+    if (params.input_type == 'sra')     { Workflow.sraCurateSamplesheetWarn(log) }
+    if (params.input_type == 'synapse') { Workflow.synapseCurateSamplesheetWarn(log) }
 }
 
 /*
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index de3eaf8b..46a2c809 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -50,7 +50,7 @@ workflow SRA {
     )
     ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first())
 
-    ch_sra_metadata = SRA_RUNINFO_TO_FTP
+    SRA_RUNINFO_TO_FTP
         .out
         .tsv
         .splitCsv(header:true, sep:'\t')
@@ -60,6 +60,7 @@ workflow SRA {
             return meta_clone
         }
         .unique()
+        .set{ ch_sra_metadata }
 
     ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first())
 
@@ -67,7 +68,7 @@ workflow SRA {
 
     if (!params.skip_fastq_download) {
 
-        ch_sra_reads = ch_sra_metadata
+        ch_sra_metadata
             .map {
                 meta ->
                     [ meta, [ meta.fastq_1, meta.fastq_2 ] ]
@@ -76,6 +77,7 @@ workflow SRA {
                 ftp: it[0].fastq_1  && !params.force_sratools_download
                 sra: !it[0].fastq_1 || params.force_sratools_download
             }
+            .set { ch_sra_reads }
 
         //
         // MODULE: If FTP link is provided in run information then download FastQ directly via FTP and validate with md5sums
@@ -95,12 +97,12 @@ workflow SRA {
         ch_versions = ch_versions.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.versions.first())
 
         // Isolate FASTQ channel which will be added to emit block
-        fastq_files = fastq_files.mix(
+        fastq_files.mix(
             SRA_FASTQ_FTP.out.fastq,
             FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads
-        )
+        ).set { fastq_files }
 
-        ch_sra_metadata = fastq_files.map { meta, fastq ->
+        fastq_files.map { meta, fastq ->
             def reads = fastq instanceof List ? fastq.flatten() : [ fastq ]
             def meta_clone = meta.clone()
 
@@ -108,7 +110,7 @@ workflow SRA {
             meta_clone.fastq_2 = reads[1] && !meta.single_end ? "${params.outdir}/fastq/${reads[1].getName()}" : ''
 
             return meta_clone
-        }
+        }.set { ch_sra_metadata }
     }
 
     //
diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf
index 30d05f4f..785877ac 100644
--- a/workflows/synapse/main.nf
+++ b/workflows/synapse/main.nf
@@ -56,7 +56,7 @@ workflow SYNAPSE {
     SYNAPSE_SHOW
         .out
         .metadata
-        .map { it -> WorkflowSynapse.synapseShowToMap(it) }
+        .map { it -> Workflow.synapseShowToMap(it) }
         .set { ch_samples_meta }
 
     //
@@ -72,14 +72,14 @@ workflow SYNAPSE {
     SYNAPSE_GET
         .out
         .fastq
-        .map { meta, fastq -> [ WorkflowSynapse.sampleNameFromFastQ( fastq , "*{1,2}*"), fastq ] }
+        .map { meta, fastq -> [ Workflow.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), fastq ] }
         .groupTuple(sort: { it -> it.baseName })
         .set { ch_fastq }
 
     SYNAPSE_GET
         .out
         .fastq
-        .map { meta, fastq -> [ WorkflowSynapse.sampleNameFromFastQ( fastq , "*{1,2}*"), meta.id ] }
+        .map { meta, fastq -> [ Workflow.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), meta.id ] }
         .groupTuple()
         .join(ch_fastq)
         .map { id, synids, fastq ->

From 08d30eb30dad60108b780517a2bb70540b1090d8 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 25 Sep 2023 10:32:24 +0200
Subject: [PATCH 488/852] typo

---
 main.nf                   | 6 +++---
 workflows/synapse/main.nf | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/main.nf b/main.nf
index 91aa6601..d74b62f8 100644
--- a/main.nf
+++ b/main.nf
@@ -55,7 +55,7 @@ if (params.input_type == 'sra') {
     ]
 
     // Validate input parameters
-    Workflow.sraInitialise(params, valid_params)
+    WorkflowMain.sraInitialise(params, valid_params)
 } else if (params.input_type == 'synapse') {
 
     // Create channel for synapse config
@@ -143,8 +143,8 @@ workflow.onComplete {
         NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)
     }
     NfcoreTemplate.summary(workflow, params, log)
-    if (params.input_type == 'sra')     { Workflow.sraCurateSamplesheetWarn(log) }
-    if (params.input_type == 'synapse') { Workflow.synapseCurateSamplesheetWarn(log) }
+    if (params.input_type == 'sra')     { WorkflowMain.sraCurateSamplesheetWarn(log) }
+    if (params.input_type == 'synapse') { WorkflowMain.synapseCurateSamplesheetWarn(log) }
 }
 
 /*
diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf
index 785877ac..0fc46ed4 100644
--- a/workflows/synapse/main.nf
+++ b/workflows/synapse/main.nf
@@ -56,7 +56,7 @@ workflow SYNAPSE {
     SYNAPSE_SHOW
         .out
         .metadata
-        .map { it -> Workflow.synapseShowToMap(it) }
+        .map { it -> WorkflowMain.synapseShowToMap(it) }
         .set { ch_samples_meta }
 
     //
@@ -72,14 +72,14 @@ workflow SYNAPSE {
     SYNAPSE_GET
         .out
         .fastq
-        .map { meta, fastq -> [ Workflow.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), fastq ] }
+        .map { meta, fastq -> [ WorkflowMain.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), fastq ] }
         .groupTuple(sort: { it -> it.baseName })
         .set { ch_fastq }
 
     SYNAPSE_GET
         .out
         .fastq
-        .map { meta, fastq -> [ Workflow.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), meta.id ] }
+        .map { meta, fastq -> [ WorkflowMain.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), meta.id ] }
         .groupTuple()
         .join(ch_fastq)
         .map { id, synids, fastq ->

From 034a52023931d1bcdd07cef94e1bff8fa1e2b0fe Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 25 Sep 2023 11:11:07 +0200
Subject: [PATCH 489/852] use rc2

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 5642602b..30656e1a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -15,7 +15,7 @@ on:
 
 env:
   NXF_ANSI_LOG: false
-  NFTEST_VER: "0.8.0-rc1"
+  NFTEST_VER: "0.8.0-rc2"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"

From 45c9020c2d24e669ed2f9b8a5e30dbb56018bc51 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 25 Sep 2023 11:11:25 +0200
Subject: [PATCH 490/852] regenerate tests and snapshots

---
 .../sra_custom_ena_metadata_fields.nf.test    |   2 +-
 ...ra_custom_ena_metadata_fields.nf.test.snap |  62 ++--------
 .../sra/tests/sra_default_parameters.nf.test  |   2 +-
 .../tests/sra_default_parameters.nf.test.snap | 114 ++----------------
 .../tests/sra_force_sratools_download.nf.test |   2 +-
 .../sra_force_sratools_download.nf.test.snap  | 110 ++---------------
 .../sra_nf_core_pipeline_atacseq.nf.test      |   2 +-
 .../sra_nf_core_pipeline_atacseq.nf.test.snap | 114 ++----------------
 .../tests/sra_nf_core_pipeline_rnaseq.nf.test |   2 +-
 .../sra_nf_core_pipeline_rnaseq.nf.test.snap  | 114 ++----------------
 .../sra_nf_core_pipeline_taxprofiler.nf.test  |   2 +-
 ..._nf_core_pipeline_taxprofiler.nf.test.snap | 114 ++----------------
 .../sra_nf_core_pipeline_viralrecon.nf.test   |   2 +-
 ...a_nf_core_pipeline_viralrecon.nf.test.snap | 114 ++----------------
 .../sra/tests/sra_skip_fastq_download.nf.test |   2 +-
 .../sra_skip_fastq_download.nf.test.snap      |  20 +--
 16 files changed, 108 insertions(+), 670 deletions(-)

diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index 45280ab0..7c9df9d9 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -12,7 +12,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
                 """
             }
             params {
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
index a2537a95..29feb896 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
@@ -38,25 +38,6 @@
                             "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
                         ]
                     ],
-                    [
-                        {
-                            "id": "ERX1188904_ERR1109373",
-                            "run_accession": "ERR1109373",
-                            "experiment_accession": "ERX1188904",
-                            "library_layout": "PAIRED",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
-                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
-                            "single_end": false
-                        },
-                        [
-                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
-                        ]
-                    ],
                     [
                         {
                             "id": "ERX1234253_ERR1160846",
@@ -272,17 +253,18 @@
                     ]
                 ],
                 "1": [
-                    "samplesheet.csv:md5,be5465f34924356e136c804d63e1b562"
+                    "samplesheet.csv:md5,d161b1a26b415a61064d8c558c9695c5"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f"
+                    "id_mappings.csv:md5,e8a7d8effe4af1d999dc26cf92cf6621"
                 ],
                 "3": [
+                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
                 ],
                 "fastq": [
                     [
@@ -320,25 +302,6 @@
                             "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
                         ]
                     ],
-                    [
-                        {
-                            "id": "ERX1188904_ERR1109373",
-                            "run_accession": "ERR1109373",
-                            "experiment_accession": "ERX1188904",
-                            "library_layout": "PAIRED",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
-                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
-                            "single_end": false
-                        },
-                        [
-                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
-                        ]
-                    ],
                     [
                         {
                             "id": "ERX1234253_ERR1160846",
@@ -554,20 +517,21 @@
                     ]
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f"
+                    "id_mappings.csv:md5,e8a7d8effe4af1d999dc26cf92cf6621"
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,be5465f34924356e136c804d63e1b562"
+                    "samplesheet.csv:md5,d161b1a26b415a61064d8c558c9695c5"
                 ],
                 "versions": [
+                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
                 ]
             }
         ],
-        "timestamp": "2023-09-11T18:48:18.757655"
+        "timestamp": "2023-09-25T10:51:46.450639"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_default_parameters.nf.test b/workflows/sra/tests/sra_default_parameters.nf.test
index ef35c80a..b525bec5 100644
--- a/workflows/sra/tests/sra_default_parameters.nf.test
+++ b/workflows/sra/tests/sra_default_parameters.nf.test
@@ -12,7 +12,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
                 """
             }
             params {
diff --git a/workflows/sra/tests/sra_default_parameters.nf.test.snap b/workflows/sra/tests/sra_default_parameters.nf.test.snap
index b8dc88ca..ea2b868a 100644
--- a/workflows/sra/tests/sra_default_parameters.nf.test.snap
+++ b/workflows/sra/tests/sra_default_parameters.nf.test.snap
@@ -90,51 +90,6 @@
                             "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
                         ]
                     ],
-                    [
-                        {
-                            "id": "ERX1188904_ERR1109373",
-                            "run_accession": "ERR1109373",
-                            "experiment_accession": "ERX1188904",
-                            "sample_accession": "SAMEA3643867",
-                            "secondary_sample_accession": "ERS951016",
-                            "study_accession": "PRJEB11633",
-                            "secondary_study_accession": "ERP013030",
-                            "submission_accession": "ERA528939",
-                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
-                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
-                            "sample_alias": "sample_56",
-                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
-                            "library_layout": "PAIRED",
-                            "library_selection": "RT-PCR",
-                            "library_source": "TRANSCRIPTOMIC",
-                            "library_strategy": "RNA-Seq",
-                            "library_name": "unspecified",
-                            "instrument_model": "Illumina HiSeq 2500",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "29700",
-                            "read_count": "169",
-                            "tax_id": "63433",
-                            "scientific_name": "Leptopilina boulardi",
-                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
-                            "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
-                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
-                            "fastq_bytes": "3221;8151;8118",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
-                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
-                            "single_end": false
-                        },
-                        [
-                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
-                        ]
-                    ],
                     [
                         {
                             "id": "ERX1234253_ERR1160846",
@@ -662,17 +617,18 @@
                     ]
                 ],
                 "1": [
-                    "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556"
+                    "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
                 "3": [
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
                 ],
                 "fastq": [
                     [
@@ -762,51 +718,6 @@
                             "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
                         ]
                     ],
-                    [
-                        {
-                            "id": "ERX1188904_ERR1109373",
-                            "run_accession": "ERR1109373",
-                            "experiment_accession": "ERX1188904",
-                            "sample_accession": "SAMEA3643867",
-                            "secondary_sample_accession": "ERS951016",
-                            "study_accession": "PRJEB11633",
-                            "secondary_study_accession": "ERP013030",
-                            "submission_accession": "ERA528939",
-                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
-                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
-                            "sample_alias": "sample_56",
-                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
-                            "library_layout": "PAIRED",
-                            "library_selection": "RT-PCR",
-                            "library_source": "TRANSCRIPTOMIC",
-                            "library_strategy": "RNA-Seq",
-                            "library_name": "unspecified",
-                            "instrument_model": "Illumina HiSeq 2500",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "29700",
-                            "read_count": "169",
-                            "tax_id": "63433",
-                            "scientific_name": "Leptopilina boulardi",
-                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
-                            "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
-                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
-                            "fastq_bytes": "3221;8151;8118",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
-                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
-                            "single_end": false
-                        },
-                        [
-                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
-                        ]
-                    ],
                     [
                         {
                             "id": "ERX1234253_ERR1160846",
@@ -1334,20 +1245,21 @@
                     ]
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556"
+                    "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192"
                 ],
                 "versions": [
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
                 ]
             }
         ],
-        "timestamp": "2023-09-11T18:56:05.693225"
+        "timestamp": "2023-09-25T10:59:42.069791"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index 76ce7cd3..2548689d 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -12,7 +12,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
                 """
             }
             params {
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
index 4e1b8aaf..7fdbbf66 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
@@ -90,51 +90,6 @@
                             "DRX026011_DRR028935_2.fastq.gz:md5,b97b1e0e806bcae10a7443e2f22d6ca2"
                         ]
                     ],
-                    [
-                        {
-                            "id": "ERX1188904_ERR1109373",
-                            "run_accession": "ERR1109373",
-                            "experiment_accession": "ERX1188904",
-                            "sample_accession": "SAMEA3643867",
-                            "secondary_sample_accession": "ERS951016",
-                            "study_accession": "PRJEB11633",
-                            "secondary_study_accession": "ERP013030",
-                            "submission_accession": "ERA528939",
-                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
-                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
-                            "sample_alias": "sample_56",
-                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
-                            "library_layout": "PAIRED",
-                            "library_selection": "RT-PCR",
-                            "library_source": "TRANSCRIPTOMIC",
-                            "library_strategy": "RNA-Seq",
-                            "library_name": "unspecified",
-                            "instrument_model": "Illumina HiSeq 2500",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "29700",
-                            "read_count": "169",
-                            "tax_id": "63433",
-                            "scientific_name": "Leptopilina boulardi",
-                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
-                            "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
-                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
-                            "fastq_bytes": "3221;8151;8118",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
-                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
-                            "single_end": false
-                        },
-                        [
-                            "ERX1188904_ERR1109373_1.fastq.gz:md5,e7edae2715dfaf4c318d37959fd9ae22",
-                            "ERX1188904_ERR1109373_2.fastq.gz:md5,34ab048c92201a5ec4ab36d8dc1c5732"
-                        ]
-                    ],
                     [
                         {
                             "id": "ERX1234253_ERR1160846",
@@ -662,16 +617,17 @@
                     ]
                 ],
                 "1": [
-                    "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556"
+                    "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
                 "3": [
+                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ],
                 "fastq": [
                     [
@@ -761,51 +717,6 @@
                             "DRX026011_DRR028935_2.fastq.gz:md5,b97b1e0e806bcae10a7443e2f22d6ca2"
                         ]
                     ],
-                    [
-                        {
-                            "id": "ERX1188904_ERR1109373",
-                            "run_accession": "ERR1109373",
-                            "experiment_accession": "ERX1188904",
-                            "sample_accession": "SAMEA3643867",
-                            "secondary_sample_accession": "ERS951016",
-                            "study_accession": "PRJEB11633",
-                            "secondary_study_accession": "ERP013030",
-                            "submission_accession": "ERA528939",
-                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
-                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
-                            "sample_alias": "sample_56",
-                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
-                            "library_layout": "PAIRED",
-                            "library_selection": "RT-PCR",
-                            "library_source": "TRANSCRIPTOMIC",
-                            "library_strategy": "RNA-Seq",
-                            "library_name": "unspecified",
-                            "instrument_model": "Illumina HiSeq 2500",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "29700",
-                            "read_count": "169",
-                            "tax_id": "63433",
-                            "scientific_name": "Leptopilina boulardi",
-                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
-                            "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
-                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
-                            "fastq_bytes": "3221;8151;8118",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
-                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
-                            "single_end": false
-                        },
-                        [
-                            "ERX1188904_ERR1109373_1.fastq.gz:md5,e7edae2715dfaf4c318d37959fd9ae22",
-                            "ERX1188904_ERR1109373_2.fastq.gz:md5,34ab048c92201a5ec4ab36d8dc1c5732"
-                        ]
-                    ],
                     [
                         {
                             "id": "ERX1234253_ERR1160846",
@@ -1333,19 +1244,20 @@
                     ]
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556"
+                    "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192"
                 ],
                 "versions": [
+                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ]
             }
         ],
-        "timestamp": "2023-09-11T19:02:05.556134"
+        "timestamp": "2023-09-25T11:09:38.27192"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index 0ce0c230..ad60725c 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -12,7 +12,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
                 """
             }
             params {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
index f6528e52..0cbec631 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
@@ -90,51 +90,6 @@
                             "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
                         ]
                     ],
-                    [
-                        {
-                            "id": "ERX1188904_ERR1109373",
-                            "run_accession": "ERR1109373",
-                            "experiment_accession": "ERX1188904",
-                            "sample_accession": "SAMEA3643867",
-                            "secondary_sample_accession": "ERS951016",
-                            "study_accession": "PRJEB11633",
-                            "secondary_study_accession": "ERP013030",
-                            "submission_accession": "ERA528939",
-                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
-                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
-                            "sample_alias": "sample_56",
-                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
-                            "library_layout": "PAIRED",
-                            "library_selection": "RT-PCR",
-                            "library_source": "TRANSCRIPTOMIC",
-                            "library_strategy": "RNA-Seq",
-                            "library_name": "unspecified",
-                            "instrument_model": "Illumina HiSeq 2500",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "29700",
-                            "read_count": "169",
-                            "tax_id": "63433",
-                            "scientific_name": "Leptopilina boulardi",
-                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
-                            "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
-                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
-                            "fastq_bytes": "3221;8151;8118",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
-                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
-                            "single_end": false
-                        },
-                        [
-                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
-                        ]
-                    ],
                     [
                         {
                             "id": "ERX1234253_ERR1160846",
@@ -662,17 +617,18 @@
                     ]
                 ],
                 "1": [
-                    "samplesheet.csv:md5,16e5161103702777b2d763c1ed660d3c"
+                    "samplesheet.csv:md5,46752dd6abac80b59573910f7ce4babe"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
                 "3": [
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
                 ],
                 "fastq": [
                     [
@@ -762,51 +718,6 @@
                             "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
                         ]
                     ],
-                    [
-                        {
-                            "id": "ERX1188904_ERR1109373",
-                            "run_accession": "ERR1109373",
-                            "experiment_accession": "ERX1188904",
-                            "sample_accession": "SAMEA3643867",
-                            "secondary_sample_accession": "ERS951016",
-                            "study_accession": "PRJEB11633",
-                            "secondary_study_accession": "ERP013030",
-                            "submission_accession": "ERA528939",
-                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
-                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
-                            "sample_alias": "sample_56",
-                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
-                            "library_layout": "PAIRED",
-                            "library_selection": "RT-PCR",
-                            "library_source": "TRANSCRIPTOMIC",
-                            "library_strategy": "RNA-Seq",
-                            "library_name": "unspecified",
-                            "instrument_model": "Illumina HiSeq 2500",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "29700",
-                            "read_count": "169",
-                            "tax_id": "63433",
-                            "scientific_name": "Leptopilina boulardi",
-                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
-                            "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
-                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
-                            "fastq_bytes": "3221;8151;8118",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
-                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
-                            "single_end": false
-                        },
-                        [
-                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
-                        ]
-                    ],
                     [
                         {
                             "id": "ERX1234253_ERR1160846",
@@ -1334,20 +1245,21 @@
                     ]
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,16e5161103702777b2d763c1ed660d3c"
+                    "samplesheet.csv:md5,46752dd6abac80b59573910f7ce4babe"
                 ],
                 "versions": [
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
                 ]
             }
         ],
-        "timestamp": "2023-09-11T18:37:54.607231"
+        "timestamp": "2023-09-25T10:45:48.713699"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index 67c0fbe4..993590ff 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -12,7 +12,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
                 """
             }
             params {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
index 124877ae..c6bd2d32 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
@@ -90,51 +90,6 @@
                             "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
                         ]
                     ],
-                    [
-                        {
-                            "id": "ERX1188904_ERR1109373",
-                            "run_accession": "ERR1109373",
-                            "experiment_accession": "ERX1188904",
-                            "sample_accession": "SAMEA3643867",
-                            "secondary_sample_accession": "ERS951016",
-                            "study_accession": "PRJEB11633",
-                            "secondary_study_accession": "ERP013030",
-                            "submission_accession": "ERA528939",
-                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
-                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
-                            "sample_alias": "sample_56",
-                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
-                            "library_layout": "PAIRED",
-                            "library_selection": "RT-PCR",
-                            "library_source": "TRANSCRIPTOMIC",
-                            "library_strategy": "RNA-Seq",
-                            "library_name": "unspecified",
-                            "instrument_model": "Illumina HiSeq 2500",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "29700",
-                            "read_count": "169",
-                            "tax_id": "63433",
-                            "scientific_name": "Leptopilina boulardi",
-                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
-                            "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
-                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
-                            "fastq_bytes": "3221;8151;8118",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
-                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
-                            "single_end": false
-                        },
-                        [
-                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
-                        ]
-                    ],
                     [
                         {
                             "id": "ERX1234253_ERR1160846",
@@ -662,17 +617,18 @@
                     ]
                 ],
                 "1": [
-                    "samplesheet.csv:md5,fcbb1fbe56dc14561ec83e5f6a70ee80"
+                    "samplesheet.csv:md5,69117245b73776d6e4daecdbfdff9767"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
                 "3": [
+                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
                 ],
                 "fastq": [
                     [
@@ -762,51 +718,6 @@
                             "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
                         ]
                     ],
-                    [
-                        {
-                            "id": "ERX1188904_ERR1109373",
-                            "run_accession": "ERR1109373",
-                            "experiment_accession": "ERX1188904",
-                            "sample_accession": "SAMEA3643867",
-                            "secondary_sample_accession": "ERS951016",
-                            "study_accession": "PRJEB11633",
-                            "secondary_study_accession": "ERP013030",
-                            "submission_accession": "ERA528939",
-                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
-                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
-                            "sample_alias": "sample_56",
-                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
-                            "library_layout": "PAIRED",
-                            "library_selection": "RT-PCR",
-                            "library_source": "TRANSCRIPTOMIC",
-                            "library_strategy": "RNA-Seq",
-                            "library_name": "unspecified",
-                            "instrument_model": "Illumina HiSeq 2500",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "29700",
-                            "read_count": "169",
-                            "tax_id": "63433",
-                            "scientific_name": "Leptopilina boulardi",
-                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
-                            "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
-                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
-                            "fastq_bytes": "3221;8151;8118",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
-                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
-                            "single_end": false
-                        },
-                        [
-                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
-                        ]
-                    ],
                     [
                         {
                             "id": "ERX1234253_ERR1160846",
@@ -1334,20 +1245,21 @@
                     ]
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,fcbb1fbe56dc14561ec83e5f6a70ee80"
+                    "samplesheet.csv:md5,69117245b73776d6e4daecdbfdff9767"
                 ],
                 "versions": [
+                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
                 ]
             }
         ],
-        "timestamp": "2023-09-11T18:51:38.198125"
+        "timestamp": "2023-09-25T11:02:54.001279"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index e00793cd..a5e69da1 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -12,7 +12,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
                 """
             }
             params {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
index b63ad4b7..4d57827d 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
@@ -90,51 +90,6 @@
                             "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
                         ]
                     ],
-                    [
-                        {
-                            "id": "ERX1188904_ERR1109373",
-                            "run_accession": "ERR1109373",
-                            "experiment_accession": "ERX1188904",
-                            "sample_accession": "SAMEA3643867",
-                            "secondary_sample_accession": "ERS951016",
-                            "study_accession": "PRJEB11633",
-                            "secondary_study_accession": "ERP013030",
-                            "submission_accession": "ERA528939",
-                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
-                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
-                            "sample_alias": "sample_56",
-                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
-                            "library_layout": "PAIRED",
-                            "library_selection": "RT-PCR",
-                            "library_source": "TRANSCRIPTOMIC",
-                            "library_strategy": "RNA-Seq",
-                            "library_name": "unspecified",
-                            "instrument_model": "Illumina HiSeq 2500",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "29700",
-                            "read_count": "169",
-                            "tax_id": "63433",
-                            "scientific_name": "Leptopilina boulardi",
-                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
-                            "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
-                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
-                            "fastq_bytes": "3221;8151;8118",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
-                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
-                            "single_end": false
-                        },
-                        [
-                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
-                        ]
-                    ],
                     [
                         {
                             "id": "ERX1234253_ERR1160846",
@@ -662,17 +617,18 @@
                     ]
                 ],
                 "1": [
-                    "samplesheet.csv:md5,0df1f60a9b5bc94f8a85e96edcc90f5c"
+                    "samplesheet.csv:md5,0705e78609390cc464c2fb10051178bc"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
                 "3": [
+                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
                 ],
                 "fastq": [
                     [
@@ -762,51 +718,6 @@
                             "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
                         ]
                     ],
-                    [
-                        {
-                            "id": "ERX1188904_ERR1109373",
-                            "run_accession": "ERR1109373",
-                            "experiment_accession": "ERX1188904",
-                            "sample_accession": "SAMEA3643867",
-                            "secondary_sample_accession": "ERS951016",
-                            "study_accession": "PRJEB11633",
-                            "secondary_study_accession": "ERP013030",
-                            "submission_accession": "ERA528939",
-                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
-                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
-                            "sample_alias": "sample_56",
-                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
-                            "library_layout": "PAIRED",
-                            "library_selection": "RT-PCR",
-                            "library_source": "TRANSCRIPTOMIC",
-                            "library_strategy": "RNA-Seq",
-                            "library_name": "unspecified",
-                            "instrument_model": "Illumina HiSeq 2500",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "29700",
-                            "read_count": "169",
-                            "tax_id": "63433",
-                            "scientific_name": "Leptopilina boulardi",
-                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
-                            "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
-                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
-                            "fastq_bytes": "3221;8151;8118",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
-                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
-                            "single_end": false
-                        },
-                        [
-                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
-                        ]
-                    ],
                     [
                         {
                             "id": "ERX1234253_ERR1160846",
@@ -1334,20 +1245,21 @@
                     ]
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,0df1f60a9b5bc94f8a85e96edcc90f5c"
+                    "samplesheet.csv:md5,0705e78609390cc464c2fb10051178bc"
                 ],
                 "versions": [
+                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
                 ]
             }
         ],
-        "timestamp": "2023-09-11T18:44:02.293186"
+        "timestamp": "2023-09-25T10:48:46.519896"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index 045e0363..f64cf92e 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -12,7 +12,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
                 """
             }
             params {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
index 1387f422..3520d5bf 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
@@ -90,51 +90,6 @@
                             "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
                         ]
                     ],
-                    [
-                        {
-                            "id": "ERX1188904_ERR1109373",
-                            "run_accession": "ERR1109373",
-                            "experiment_accession": "ERX1188904",
-                            "sample_accession": "SAMEA3643867",
-                            "secondary_sample_accession": "ERS951016",
-                            "study_accession": "PRJEB11633",
-                            "secondary_study_accession": "ERP013030",
-                            "submission_accession": "ERA528939",
-                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
-                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
-                            "sample_alias": "sample_56",
-                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
-                            "library_layout": "PAIRED",
-                            "library_selection": "RT-PCR",
-                            "library_source": "TRANSCRIPTOMIC",
-                            "library_strategy": "RNA-Seq",
-                            "library_name": "unspecified",
-                            "instrument_model": "Illumina HiSeq 2500",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "29700",
-                            "read_count": "169",
-                            "tax_id": "63433",
-                            "scientific_name": "Leptopilina boulardi",
-                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
-                            "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
-                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
-                            "fastq_bytes": "3221;8151;8118",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
-                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
-                            "single_end": false
-                        },
-                        [
-                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
-                        ]
-                    ],
                     [
                         {
                             "id": "ERX1234253_ERR1160846",
@@ -662,17 +617,18 @@
                     ]
                 ],
                 "1": [
-                    "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556"
+                    "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
                 "3": [
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
                 ],
                 "fastq": [
                     [
@@ -762,51 +718,6 @@
                             "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
                         ]
                     ],
-                    [
-                        {
-                            "id": "ERX1188904_ERR1109373",
-                            "run_accession": "ERR1109373",
-                            "experiment_accession": "ERX1188904",
-                            "sample_accession": "SAMEA3643867",
-                            "secondary_sample_accession": "ERS951016",
-                            "study_accession": "PRJEB11633",
-                            "secondary_study_accession": "ERP013030",
-                            "submission_accession": "ERA528939",
-                            "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7",
-                            "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7",
-                            "sample_alias": "sample_56",
-                            "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13",
-                            "library_layout": "PAIRED",
-                            "library_selection": "RT-PCR",
-                            "library_source": "TRANSCRIPTOMIC",
-                            "library_strategy": "RNA-Seq",
-                            "library_name": "unspecified",
-                            "instrument_model": "Illumina HiSeq 2500",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "29700",
-                            "read_count": "169",
-                            "tax_id": "63433",
-                            "scientific_name": "Leptopilina boulardi",
-                            "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "experiment_title": "Illumina HiSeq 2500 paired end sequencing",
-                            "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.",
-                            "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome",
-                            "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9",
-                            "fastq_bytes": "3221;8151;8118",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz",
-                            "md5_1": "9fd57225d6c07a31843276d6df9b15c0",
-                            "md5_2": "5a62e8f785687dce890cfb4fe3e607f9",
-                            "single_end": false
-                        },
-                        [
-                            "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0",
-                            "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9"
-                        ]
-                    ],
                     [
                         {
                             "id": "ERX1234253_ERR1160846",
@@ -1334,20 +1245,21 @@
                     ]
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556"
+                    "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192"
                 ],
                 "versions": [
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
                 ]
             }
         ],
-        "timestamp": "2023-09-11T18:34:25.049818"
+        "timestamp": "2023-09-25T10:42:52.035768"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index 67abee3b..aa290c68 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -12,7 +12,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183')
+                input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
                 """
             }
             params {
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
index 3b04b917..91a10c87 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
@@ -6,32 +6,34 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,7cf3503b651fe016bc1e5fb3c2e996d5"
+                    "samplesheet.csv:md5,b1636e896008b96044d352a0757a390b"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
                 "3": [
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ],
                 "fastq": [
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565"
+                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,7cf3503b651fe016bc1e5fb3c2e996d5"
+                    "samplesheet.csv:md5,b1636e896008b96044d352a0757a390b"
                 ],
                 "versions": [
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd"
+                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ]
             }
         ],
-        "timestamp": "2023-09-11T18:56:34.175665"
+        "timestamp": "2023-09-25T11:03:28.968158"
     }
 }
\ No newline at end of file

From 191a8e724285471f8d698ce15eebac3fbdeeb95f Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Mon, 25 Sep 2023 10:45:28 +0200
Subject: [PATCH 491/852] Apply suggestions from code review

---
 workflows/sra/main.nf | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 46a2c809..43beb51d 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -60,7 +60,7 @@ workflow SRA {
             return meta_clone
         }
         .unique()
-        .set{ ch_sra_metadata }
+        .set { ch_sra_metadata }
 
     ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first())
 
@@ -100,9 +100,7 @@ workflow SRA {
         fastq_files.mix(
             SRA_FASTQ_FTP.out.fastq,
             FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads
-        ).set { fastq_files }
-
-        fastq_files.map { meta, fastq ->
+        ).map { meta, fastq ->
             def reads = fastq instanceof List ? fastq.flatten() : [ fastq ]
             def meta_clone = meta.clone()
 
@@ -133,7 +131,9 @@ workflow SRA {
     ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions)
 
     if (params.sample_mapping_fields) {
-        MULTIQC_MAPPINGS_CONFIG(SRA_MERGE_SAMPLESHEET.out.mappings)
+        MULTIQC_MAPPINGS_CONFIG (
+            SRA_MERGE_SAMPLESHEET.out.mappings
+        )
         ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions)
     }
 

From e4fddb4901c935c11fac01ab0efddc5755555be7 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 25 Sep 2023 11:46:06 +0200
Subject: [PATCH 492/852] final code polish

---
 main.nf               | 20 --------------------
 workflows/sra/main.nf | 21 ++++++++++++++-------
 2 files changed, 14 insertions(+), 27 deletions(-)

diff --git a/main.nf b/main.nf
index 70e8ff27..d74b62f8 100644
--- a/main.nf
+++ b/main.nf
@@ -18,26 +18,6 @@ nextflow.enable.dsl = 2
 ========================================================================================
 */
 
-include { paramsHelp; paramsSummaryLog; validateParameters } from 'plugin/nf-validation'
-
-def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
-def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
-
-// Print parameter summary log to screen
-log.info logo + paramsSummaryLog(workflow) + citation
-
-// Print help message if needed
-if (params.help) {
-    def String command = "nextflow run ${workflow.manifest.name} --input id.csv -profile docker"
-    log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
-    System.exit(0)
-}
-
-// Validate input parameters
-if (params.validate_params) {
-    validateParameters()
-}
-
 // Check if --input file is empty
 ch_input = file(params.input, checkIfExists: true)
 if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") }
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 45efa9c9..920579d1 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -1,15 +1,22 @@
 /*
 ========================================================================================
-    IMPORT LOCAL MODULES/SUBWORKFLOWS
+    IMPORT LOCAL MODULES
+========================================================================================
+*/
+
+include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_config'
+include { SRA_FASTQ_FTP           } from '../../modules/local/sra_fastq_ftp'
+include { SRA_IDS_TO_RUNINFO      } from '../../modules/local/sra_ids_to_runinfo'
+include { SRA_MERGE_SAMPLESHEET   } from '../../modules/local/sra_merge_samplesheet'
+include { SRA_RUNINFO_TO_FTP      } from '../../modules/local/sra_runinfo_to_ftp'
+include { SRA_TO_SAMPLESHEET      } from '../../modules/local/sra_to_samplesheet'
+
+/*
+========================================================================================
+    IMPORT NF-CORE SUBWORKFLOWS
 ========================================================================================
 */
 
-include { MULTIQC_MAPPINGS_CONFIG   } from '../../modules/local/multiqc_mappings_config'
-include { SRA_FASTQ_FTP             } from '../../modules/local/sra_fastq_ftp'
-include { SRA_IDS_TO_RUNINFO        } from '../../modules/local/sra_ids_to_runinfo'
-include { SRA_MERGE_SAMPLESHEET     } from '../../modules/local/sra_merge_samplesheet'
-include { SRA_RUNINFO_TO_FTP        } from '../../modules/local/sra_runinfo_to_ftp'
-include { SRA_TO_SAMPLESHEET        } from '../../modules/local/sra_to_samplesheet'
 include { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS } from '../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools'
 
 /*

From 9b850ba02896b4753c7a3c9921616f70a611269c Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Mon, 25 Sep 2023 12:11:13 +0200
Subject: [PATCH 493/852] Apply suggestions from code review

---
 main.nf               | 4 +++-
 workflows/sra/main.nf | 3 +++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index d74b62f8..c6d7d13e 100644
--- a/main.nf
+++ b/main.nf
@@ -115,7 +115,9 @@ workflow NFCORE_FETCHNGS {
     }
 
     // MODULE: Dump software versions for all tools used in the workflow
-    CUSTOM_DUMPSOFTWAREVERSIONS(ch_versions.unique().collectFile(name: 'collated_versions.yml'))
+    //
+    // MODULE: Dump software versions for all tools used in the workflow
+    //
 }
 
 /*
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 920579d1..2b221739 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -130,6 +130,9 @@ workflow SRA {
     )
     ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions)
 
+    //
+    // MODULE: Create a MutiQC config file with sample name mappings
+    //
     if (params.sample_mapping_fields) {
         MULTIQC_MAPPINGS_CONFIG (
             SRA_MERGE_SAMPLESHEET.out.mappings

From 6cf3085c08ab4654cba21ac3bdfccd6d3e7745b5 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 25 Sep 2023 12:12:16 +0200
Subject: [PATCH 494/852] update snapshots

---
 ...ra_custom_ena_metadata_fields.nf.test.snap |  500 +------
 .../tests/sra_default_parameters.nf.test.snap | 1228 +----------------
 .../sra_force_sratools_download.nf.test.snap  | 1228 +----------------
 .../sra_nf_core_pipeline_atacseq.nf.test.snap | 1228 +----------------
 .../sra_nf_core_pipeline_rnaseq.nf.test.snap  | 1228 +----------------
 ..._nf_core_pipeline_taxprofiler.nf.test.snap | 1228 +----------------
 ...a_nf_core_pipeline_viralrecon.nf.test.snap | 1228 +----------------
 7 files changed, 21 insertions(+), 7847 deletions(-)

diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
index 29feb896..7a7df129 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
@@ -3,254 +3,7 @@
         "content": [
             {
                 "0": [
-                    [
-                        {
-                            "id": "DRX024467_DRR026872",
-                            "run_accession": "DRR026872",
-                            "experiment_accession": "DRX024467",
-                            "library_layout": "SINGLE",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
-                            "fastq_md5": "515e5448c55e054113c4a22df5f62791",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz",
-                            "fastq_2": "",
-                            "md5_1": "515e5448c55e054113c4a22df5f62791",
-                            "md5_2": "",
-                            "single_end": true
-                        },
-                        "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791"
-                    ],
-                    [
-                        {
-                            "id": "DRX026011_DRR028935",
-                            "run_accession": "DRR028935",
-                            "experiment_accession": "DRX026011",
-                            "library_layout": "PAIRED",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                            "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                            "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
-                            "md5_2": "941c9998d746416dad53c94c480ddf30",
-                            "single_end": false
-                        },
-                        [
-                            "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a",
-                            "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30"
-                        ]
-                    ],
-                    [
-                        {
-                            "id": "ERX1234253_ERR1160846",
-                            "run_accession": "ERR1160846",
-                            "experiment_accession": "ERX1234253",
-                            "library_layout": "SINGLE",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                            "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                            "fastq_2": "",
-                            "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                            "md5_2": "",
-                            "single_end": true
-                        },
-                        "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6"
-                    ],
-                    [
-                        {
-                            "id": "SRX10940790_SRR14593545",
-                            "run_accession": "SRR14593545",
-                            "experiment_accession": "SRX10940790",
-                            "library_layout": "PAIRED",
-                            "fastq_ftp": "",
-                            "fastq_md5": "",
-                            "fastq_1": "",
-                            "fastq_2": "",
-                            "md5_1": "",
-                            "md5_2": "",
-                            "single_end": false
-                        },
-                        [
-                            "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3",
-                            "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2"
-                        ]
-                    ],
-                    [
-                        {
-                            "id": "SRX11047067_SRR14709033",
-                            "run_accession": "SRR14709033",
-                            "experiment_accession": "SRX11047067",
-                            "library_layout": "SINGLE",
-                            "fastq_ftp": "",
-                            "fastq_md5": "",
-                            "fastq_1": "",
-                            "fastq_2": "",
-                            "md5_1": "",
-                            "md5_2": "",
-                            "single_end": true
-                        },
-                        "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda"
-                    ],
-                    [
-                        {
-                            "id": "SRX17709227_SRR21711856",
-                            "run_accession": "SRR21711856",
-                            "experiment_accession": "SRX17709227",
-                            "library_layout": "SINGLE",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                            "fastq_md5": "7cd1402155befc87be338132d1f31f64",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                            "fastq_2": "",
-                            "md5_1": "7cd1402155befc87be338132d1f31f64",
-                            "md5_2": "",
-                            "single_end": true
-                        },
-                        "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64"
-                    ],
-                    [
-                        {
-                            "id": "SRX17709228_SRR21711855",
-                            "run_accession": "SRR21711855",
-                            "experiment_accession": "SRX17709228",
-                            "library_layout": "SINGLE",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                            "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                            "fastq_2": "",
-                            "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
-                            "md5_2": "",
-                            "single_end": true
-                        },
-                        "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83"
-                    ],
-                    [
-                        {
-                            "id": "SRX6725035_SRR9984183",
-                            "run_accession": "SRR9984183",
-                            "experiment_accession": "SRX6725035",
-                            "library_layout": "SINGLE",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                            "fastq_md5": "0b512d2dc31685983456bd56fd836544",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                            "fastq_2": "",
-                            "md5_1": "0b512d2dc31685983456bd56fd836544",
-                            "md5_2": "",
-                            "single_end": true
-                        },
-                        "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544"
-                    ],
-                    [
-                        {
-                            "id": "SRX9315476_SRR12848126",
-                            "run_accession": "SRR12848126",
-                            "experiment_accession": "SRX9315476",
-                            "library_layout": "PAIRED",
-                            "fastq_ftp": "",
-                            "fastq_md5": "",
-                            "fastq_1": "",
-                            "fastq_2": "",
-                            "md5_1": "",
-                            "md5_2": "",
-                            "single_end": false
-                        },
-                        [
-                            "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665",
-                            "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79"
-                        ]
-                    ],
-                    [
-                        {
-                            "id": "SRX9504942_SRR13055517",
-                            "run_accession": "SRR13055517",
-                            "experiment_accession": "SRX9504942",
-                            "library_layout": "PAIRED",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_2.fastq.gz",
-                            "fastq_md5": "dcf4438c0b682242ee90c5f3a803fb40;18dbe96e7f58b63406d9058938df1962",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/017/SRR13055517/SRR13055517_2.fastq.gz",
-                            "md5_1": "dcf4438c0b682242ee90c5f3a803fb40",
-                            "md5_2": "18dbe96e7f58b63406d9058938df1962",
-                            "single_end": false
-                        },
-                        [
-                            "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40",
-                            "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962"
-                        ]
-                    ],
-                    [
-                        {
-                            "id": "SRX9504942_SRR13055518",
-                            "run_accession": "SRR13055518",
-                            "experiment_accession": "SRX9504942",
-                            "library_layout": "PAIRED",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_2.fastq.gz",
-                            "fastq_md5": "5ec894d863fcefe394470a0925aefde4;aead170df9851773d5202b5760c76d76",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/018/SRR13055518/SRR13055518_2.fastq.gz",
-                            "md5_1": "5ec894d863fcefe394470a0925aefde4",
-                            "md5_2": "aead170df9851773d5202b5760c76d76",
-                            "single_end": false
-                        },
-                        [
-                            "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4",
-                            "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76"
-                        ]
-                    ],
-                    [
-                        {
-                            "id": "SRX9504942_SRR13055519",
-                            "run_accession": "SRR13055519",
-                            "experiment_accession": "SRX9504942",
-                            "library_layout": "PAIRED",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/019/SRR13055519/SRR13055519_2.fastq.gz",
-                            "fastq_md5": "5ad51460c6c4a850dd37a206e2c441c1;a977367bf41dacf4c21bc0c8201b8b88",
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-                        "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791"
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@@ -532,6 +38,6 @@
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-        "timestamp": "2023-09-25T10:51:46.450639"
+        "timestamp": "2023-09-25T11:58:11.85816"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_default_parameters.nf.test.snap b/workflows/sra/tests/sra_default_parameters.nf.test.snap
index ea2b868a..edb662a2 100644
--- a/workflows/sra/tests/sra_default_parameters.nf.test.snap
+++ b/workflows/sra/tests/sra_default_parameters.nf.test.snap
@@ -3,618 +3,7 @@
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@@ -1260,6 +38,6 @@
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-        "timestamp": "2023-09-25T10:59:42.069791"
+        "timestamp": "2023-09-25T12:00:37.501679"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
index 7fdbbf66..91eec432 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
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+                    
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                     "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
@@ -1258,6 +36,6 @@
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-        "timestamp": "2023-09-25T11:09:38.27192"
+        "timestamp": "2023-09-25T12:08:28.465466"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
index 0cbec631..4560b05b 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
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@@ -1260,6 +38,6 @@
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-        "timestamp": "2023-09-25T10:45:48.713699"
+        "timestamp": "2023-09-25T11:53:25.411769"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
index c6bd2d32..26357aa5 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
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@@ -1260,6 +38,6 @@
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-        "timestamp": "2023-09-25T11:02:54.001279"
+        "timestamp": "2023-09-25T12:03:02.485911"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
index 4d57827d..ff4b27df 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
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+        "timestamp": "2023-09-25T11:55:48.759498"
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 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
index 3520d5bf..4b38d6a1 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
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-                            "fastq_md5": "795d460abff6009c7f5ff7c14b773fbe;c3f34379356b28d6dac7212abc1a0a04",
-                            "fastq_bytes": "709867;716862",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz",
-                            "md5_1": "795d460abff6009c7f5ff7c14b773fbe",
-                            "md5_2": "c3f34379356b28d6dac7212abc1a0a04",
-                            "single_end": false
-                        },
-                        [
-                            "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe",
-                            "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04"
-                        ]
-                    ],
-                    [
-                        {
-                            "id": "SRX9626017_SRR13191702",
-                            "run_accession": "SRR13191702",
-                            "experiment_accession": "SRX9626017",
-                            "sample_accession": "SAMN16980141",
-                            "secondary_sample_accession": "SRS7827211",
-                            "study_accession": "PRJNA682076",
-                            "secondary_study_accession": "SRP295653",
-                            "submission_accession": "SRA1166126",
-                            "run_alias": "S.170804.00784_662_L001_R1_001.fastq.gz",
-                            "experiment_alias": "S.170804.00784",
-                            "sample_alias": "S.170804.00784_662",
-                            "study_alias": "PRJNA682076",
-                            "library_layout": "PAIRED",
-                            "library_selection": "PCR",
-                            "library_source": "METAGENOMIC",
-                            "library_strategy": "AMPLICON",
-                            "library_name": "S.170804.00784",
-                            "instrument_model": "Illumina HiSeq 2500",
-                            "instrument_platform": "ILLUMINA",
-                            "base_count": "45682",
-                            "read_count": "91",
-                            "tax_id": "408170",
-                            "scientific_name": "human gut metagenome",
-                            "sample_title": "Metagenome or environmental sample from human gut metagenome",
-                            "experiment_title": "Illumina HiSeq 2500 sequencing: Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
-                            "study_title": "Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection",
-                            "sample_description": "Metagenome or environmental sample from human gut metagenome",
-                            "fastq_md5": "89c5be920021a035084d8aeb74f32df7;56271be38a80db78ef3bdfc5d9909b98",
-                            "fastq_bytes": "15420;16324",
-                            "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
-                            "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
-                            "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
-                            "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz",
-                            "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz",
-                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
-                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98",
-                            "single_end": false
-                        },
-                        [
-                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
-                        ]
-                    ]
+                    
                 ],
                 "mappings": [
                     "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
@@ -1260,6 +38,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-25T10:42:52.035768"
+        "timestamp": "2023-09-25T11:50:52.373496"
     }
 }
\ No newline at end of file

From 41c5a71836b8738d2bb296d3f7b3eed9ebebbebc Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Mon, 25 Sep 2023 12:16:23 +0200
Subject: [PATCH 495/852] Update CHANGELOG.md

---
 CHANGELOG.md | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c9dfa84d..952ff499 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -18,17 +18,9 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 ### Enhancements & fixes
 
 - [#177](https://github.com/nf-core/fetchngs/pull/177) - Template update with nf-core/tools 2.9
-- [#205](https://github.com/nf-core/fetchngs/pull/205) - Rename all local modules, workflows and remove public_aws_ecr profile
+- [#205](https://github.com/nf-core/fetchngs/pull/205) - Rename all local modules, workflows and remove `public_aws_ecr profile`
 - [#206](https://github.com/nf-core/fetchngs/pull/206) - CI improvments and code cleanup
 
-### Software dependencies
-
-> **NB:** Dependency has been **updated** if both old and new version information is present.
->
-> **NB:** Dependency has been **added** if just the new version information is present.
->
-> **NB:** Dependency has been **removed** if new version information isn't present.
-
 ## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-16
 
 ### Credits

From 67ffe73a4eb1270983542fef47823037f2636834 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Mon, 25 Sep 2023 12:32:06 +0200
Subject: [PATCH 496/852] Update main.nf

---
 main.nf | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/main.nf b/main.nf
index c6d7d13e..2733a41a 100644
--- a/main.nf
+++ b/main.nf
@@ -113,11 +113,6 @@ workflow NFCORE_FETCHNGS {
         SYNAPSE ( ch_ids, ch_synapse_config )
         ch_versions = ch_versions.mix(SYNAPSE.out.versions)
     }
-
-    // MODULE: Dump software versions for all tools used in the workflow
-    //
-    // MODULE: Dump software versions for all tools used in the workflow
-    //
 }
 
 /*

From fbe5be6886761d5ae751d82c49c4b3955ee8ed93 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Mon, 25 Sep 2023 13:53:23 +0200
Subject: [PATCH 497/852] Apply suggestions from code review

---
 main.nf | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/main.nf b/main.nf
index ed4f6877..93afa437 100644
--- a/main.nf
+++ b/main.nf
@@ -59,6 +59,9 @@ if (WorkflowMain.isSraId(ch_input)) {
 } else {
     error('Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!')
 }
+if (params.input_type != input_type) {
+    error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!")
+}
 
 /*
 ========================================================================================
@@ -72,8 +75,6 @@ if (params.input_type == input_type) {
     } else if (params.input_type == 'synapse') {
         include { SYNAPSE } from './workflows/synapse'
     }
-} else {
-    error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!")
 }
 
 /*

From 328c387a1a2bcb5247031be67c2e14b3911e98d9 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Mon, 25 Sep 2023 14:04:22 +0200
Subject: [PATCH 498/852] Apply suggestions from code review

---
 main.nf | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/main.nf b/main.nf
index 93afa437..191de3ad 100644
--- a/main.nf
+++ b/main.nf
@@ -65,17 +65,12 @@ if (params.input_type != input_type) {
 
 /*
 ========================================================================================
-    VALIDATE INPUTS
+    IMPORT WORKFLOWS
 ========================================================================================
 */
 
-if (params.input_type == input_type) {
-    if (params.input_type == 'sra') {
-        include { SRA } from './workflows/sra'
-    } else if (params.input_type == 'synapse') {
-        include { SYNAPSE } from './workflows/synapse'
-    }
-}
+if (params.input_type == 'sra')     include { SRA     } from './workflows/sra'
+if (params.input_type == 'synapse') include { SYNAPSE } from './workflows/synapse'
 
 /*
 ========================================================================================

From 84d9aa87663f8e287920bb59cc785057a6d1062a Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Mon, 25 Sep 2023 14:05:26 +0200
Subject: [PATCH 499/852] Update main.nf

---
 main.nf | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/main.nf b/main.nf
index 191de3ad..943aa301 100644
--- a/main.nf
+++ b/main.nf
@@ -72,12 +72,6 @@ if (params.input_type != input_type) {
 if (params.input_type == 'sra')     include { SRA     } from './workflows/sra'
 if (params.input_type == 'synapse') include { SYNAPSE } from './workflows/synapse'
 
-/*
-========================================================================================
-    NAMED WORKFLOW FOR PIPELINE
-========================================================================================
-*/
-
 //
 // WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided
 //

From 6ee945e3555527b86987cc4a94ec5bd115083d40 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Tue, 26 Sep 2023 09:54:29 +0200
Subject: [PATCH 500/852] Apply suggestions from code review

---
 conf/modules.config | 9 ---------
 nextflow.config     | 2 +-
 2 files changed, 1 insertion(+), 10 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 8bffcb2a..f5cb1c77 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -29,15 +29,6 @@ process {
         ]
     }
 
-    withName: 'MULTIQC' {
-        ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
-        publishDir = [
-            path: { "${params.outdir}/multiqc" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
 }
 
 //
diff --git a/nextflow.config b/nextflow.config
index b91e67a5..f6f53063 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -49,7 +49,7 @@ params {
     // Schema validation default options
     validationFailUnrecognisedParams = false
     validationLenientMode            = false
-    validationSchemaIgnoreParams     = 'genomes,igenomes_base'
+    validationSchemaIgnoreParams     = 'genomes'
     validationShowHiddenParams       = false
     validate_params                  = true
 

From 7bc7a5e94eb5a5af3efb8709d54d8fa9124b28fc Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Fri, 29 Sep 2023 17:05:54 +0200
Subject: [PATCH 501/852] Update main.nf

squiggles all the way
---
 main.nf | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/main.nf b/main.nf
index 943aa301..8ab3ae5e 100644
--- a/main.nf
+++ b/main.nf
@@ -1,21 +1,21 @@
 #!/usr/bin/env nextflow
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     nf-core/fetchngs
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Github : https://github.com/nf-core/fetchngs
     Website: https://nf-co.re/fetchngs
     Slack  : https://nfcore.slack.com/channels/fetchngs
-========================================================================================
+----------------------------------------------------------------------------------------
 */
 
 nextflow.enable.dsl = 2
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     VALIDATE & PRINT PARAMETER SUMMARY
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 include { paramsHelp; paramsSummaryLog; validateParameters } from 'plugin/nf-validation'
@@ -64,9 +64,9 @@ if (params.input_type != input_type) {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT WORKFLOWS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 if (params.input_type == 'sra')     include { SRA     } from './workflows/sra'
@@ -92,9 +92,9 @@ workflow NFCORE_FETCHNGS {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     RUN ALL WORKFLOWS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
@@ -106,7 +106,7 @@ workflow {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     THE END
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */

From 9dc4c4e47a1e47853715ee9a27d8314b0154a08f Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Fri, 29 Sep 2023 17:06:16 +0200
Subject: [PATCH 502/852] Apply suggestions from code review

---
 main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/main.nf b/main.nf
index 8ab3ae5e..7de31c2c 100644
--- a/main.nf
+++ b/main.nf
@@ -1,5 +1,4 @@
 #!/usr/bin/env nextflow
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     nf-core/fetchngs

From 3eda77d16a2f24732f52fa68eebe4e60c779ec85 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Fri, 29 Sep 2023 17:07:09 +0200
Subject: [PATCH 503/852] Update main.nf

squiggles all the way
---
 workflows/sra/main.nf | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 366e4b28..e393b726 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -1,7 +1,7 @@
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     VALIDATE INPUTS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'
@@ -14,9 +14,9 @@ def summary_params = paramsSummaryMap(workflow)
 log.info logo + paramsSummaryLog(workflow) + citation
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT LOCAL MODULES/SUBWORKFLOWS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 include { SRA_IDS_TO_RUNINFO      } from '../../modules/local/sra_ids_to_runinfo'
@@ -27,9 +27,9 @@ include { SRA_MERGE_SAMPLESHEET   } from '../../modules/local/sra_merge_samplesh
 include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_config'
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT NF-CORE MODULES/SUBWORKFLOWS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions/main'
@@ -37,9 +37,9 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumps
 include { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS } from '../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main'
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     RUN MAIN WORKFLOW
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow SRA {
@@ -164,9 +164,9 @@ workflow SRA {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     COMPLETION EMAIL AND SUMMARY
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow.onComplete {
@@ -178,7 +178,7 @@ workflow.onComplete {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     THE END
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */

From 907ad76d139ac243fab3a3c135eb80b2e8f21eaf Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Fri, 29 Sep 2023 17:07:46 +0200
Subject: [PATCH 504/852] Update main.nf

squiggles all the way
---
 workflows/synapse/main.nf | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf
index 7d871659..4f015e0e 100644
--- a/workflows/synapse/main.nf
+++ b/workflows/synapse/main.nf
@@ -1,7 +1,7 @@
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     VALIDATE INPUTS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
@@ -14,9 +14,9 @@ if (params.synapse_config) {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT LOCAL MODULES/SUBWORKFLOWS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 include { SYNAPSE_LIST              } from '../../modules/local/synapse_list'
@@ -26,17 +26,17 @@ include { SYNAPSE_TO_SAMPLESHEET    } from '../../modules/local/synapse_to_sampl
 include { SYNAPSE_MERGE_SAMPLESHEET } from '../../modules/local/synapse_merge_samplesheet'
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT NF-CORE MODULES/SUBWORKFLOWS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions/main'
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     RUN MAIN WORKFLOW
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow SYNAPSE {
@@ -136,9 +136,9 @@ workflow SYNAPSE {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     COMPLETION EMAIL AND SUMMARY
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow.onComplete {
@@ -150,7 +150,7 @@ workflow.onComplete {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     THE END
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */

From 2d08cb4b7c52ba59df89d72b13a59a6daead0d83 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Fri, 6 Oct 2023 11:27:49 +0200
Subject: [PATCH 505/852] Update CHANGELOG.md

---
 CHANGELOG.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 952ff499..e85a5564 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[1.10.1](https://github.com/nf-core/fetchngs/releases/tag/1.10.1)] - 2023-09-25
+## [[1.10.1](https://github.com/nf-core/fetchngs/releases/tag/1.10.1)] - 2023-10-09
 
 ### Credits
 
@@ -17,9 +17,9 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 
 ### Enhancements & fixes
 
-- [#177](https://github.com/nf-core/fetchngs/pull/177) - Template update with nf-core/tools 2.9
-- [#205](https://github.com/nf-core/fetchngs/pull/205) - Rename all local modules, workflows and remove `public_aws_ecr profile`
-- [#206](https://github.com/nf-core/fetchngs/pull/206) - CI improvments and code cleanup
+- [PR #205](https://github.com/nf-core/fetchngs/pull/205) - Rename all local modules, workflows and remove `public_aws_ecr profile`
+- [PR #206](https://github.com/nf-core/fetchngs/pull/206) - CI improvments and code cleanup
+- [PR #208](https://github.com/nf-core/fetchngs/pull/208) - Template update with nf-core/tools 2.10
 
 ## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-16
 

From 8114abc1c23c92fc1021fb79dfc27e79b01a3fbc Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Fri, 6 Oct 2023 11:47:54 +0200
Subject: [PATCH 506/852] Update main.nf

---
 workflows/sra/main.nf | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 441430ea..562d1726 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -133,18 +133,21 @@ workflow SRA {
     //
     // MODULE: Create a MutiQC config file with sample name mappings
     //
+    ch_sample_mappings_yml = Channel.empty()
     if (params.sample_mapping_fields) {
         MULTIQC_MAPPINGS_CONFIG (
             SRA_MERGE_SAMPLESHEET.out.mappings
         )
         ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions)
+        ch_sample_mappings_yml = MULTIQC_MAPPINGS_CONFIG.out.yml
     }
 
     emit:
-    fastq         = fastq_files
-    samplesheet   = SRA_MERGE_SAMPLESHEET.out.samplesheet
-    mappings      = SRA_MERGE_SAMPLESHEET.out.mappings
-    versions      = ch_versions.unique()
+    fastq           = fastq_files
+    samplesheet     = SRA_MERGE_SAMPLESHEET.out.samplesheet
+    mappings        = SRA_MERGE_SAMPLESHEET.out.mappings
+    sample_mappings = ch_sample_mappings_yml
+    versions        = ch_versions.unique()    
 }
 
 /*

From 588cef665272ceddd1f27cec8c2f660584c98a18 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Fri, 6 Oct 2023 12:00:10 +0200
Subject: [PATCH 507/852] Update multiqc_config.yml

---
 assets/multiqc_config.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 70cc1fc7..bafbf577 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/fetchngs/1.10.1" target="_blank">nf-core/fetchngs</a>
+  This report has been generated by the <a href="https://github.com/nf-core/fetchngs/releases/tag/1.10.1" target="_blank">nf-core/fetchngs</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/fetchngs/1.10.1/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/fetchngs/1.10.1/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-fetchngs-methods-description":
     order: -1000

From 56e5143fbf3d14b944183df461e5c0903ac7faea Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 6 Oct 2023 12:25:48 +0200
Subject: [PATCH 508/852] update snapshots

---
 .github/workflows/ci.yml                           |  2 +-
 ...sra_default_parameters.nf.test => main.nf.test} |  0
 ...t_parameters.nf.test.snap => main.nf.test.snap} | 14 +++++++++++++-
 .../sra_custom_ena_metadata_fields.nf.test.snap    | 14 +++++++++++++-
 .../tests/sra_force_sratools_download.nf.test.snap | 14 +++++++++++++-
 .../sra_nf_core_pipeline_atacseq.nf.test.snap      | 14 +++++++++++++-
 .../tests/sra_nf_core_pipeline_rnaseq.nf.test.snap | 14 +++++++++++++-
 .../sra_nf_core_pipeline_taxprofiler.nf.test.snap  | 14 +++++++++++++-
 .../sra_nf_core_pipeline_viralrecon.nf.test.snap   | 14 +++++++++++++-
 .../sra/tests/sra_skip_fastq_download.nf.test.snap | 14 +++++++++++++-
 10 files changed, 105 insertions(+), 9 deletions(-)
 rename workflows/sra/tests/{sra_default_parameters.nf.test => main.nf.test} (100%)
 rename workflows/sra/tests/{sra_default_parameters.nf.test.snap => main.nf.test.snap} (75%)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 30656e1a..68e2773c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -15,7 +15,7 @@ on:
 
 env:
   NXF_ANSI_LOG: false
-  NFTEST_VER: "0.8.0-rc2"
+  NFTEST_VER: "0.8.0"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
diff --git a/workflows/sra/tests/sra_default_parameters.nf.test b/workflows/sra/tests/main.nf.test
similarity index 100%
rename from workflows/sra/tests/sra_default_parameters.nf.test
rename to workflows/sra/tests/main.nf.test
diff --git a/workflows/sra/tests/sra_default_parameters.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
similarity index 75%
rename from workflows/sra/tests/sra_default_parameters.nf.test.snap
rename to workflows/sra/tests/main.nf.test.snap
index edb662a2..955dd72a 100644
--- a/workflows/sra/tests/sra_default_parameters.nf.test.snap
+++ b/workflows/sra/tests/main.nf.test.snap
@@ -12,6 +12,12 @@
                     "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
                 "3": [
+                    [
+                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
+                    ]
+                ],
+                "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
@@ -25,6 +31,12 @@
                 "mappings": [
                     "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
+                "sample_mappings": [
+                    [
+                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
+                    ]
+                ],
                 "samplesheet": [
                     "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192"
                 ],
@@ -38,6 +50,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-25T12:00:37.501679"
+        "timestamp": "2023-10-06T12:18:32.149462"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
index 7a7df129..143375ac 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
@@ -12,6 +12,12 @@
                     "id_mappings.csv:md5,e8a7d8effe4af1d999dc26cf92cf6621"
                 ],
                 "3": [
+                    [
+                        "multiqc_config.yml:md5,b1c25951b237552448e878f7c9dc4235",
+                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
+                    ]
+                ],
+                "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
@@ -25,6 +31,12 @@
                 "mappings": [
                     "id_mappings.csv:md5,e8a7d8effe4af1d999dc26cf92cf6621"
                 ],
+                "sample_mappings": [
+                    [
+                        "multiqc_config.yml:md5,b1c25951b237552448e878f7c9dc4235",
+                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
+                    ]
+                ],
                 "samplesheet": [
                     "samplesheet.csv:md5,d161b1a26b415a61064d8c558c9695c5"
                 ],
@@ -38,6 +50,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-25T11:58:11.85816"
+        "timestamp": "2023-10-06T12:10:32.762201"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
index 91eec432..5cb1876c 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
@@ -12,6 +12,12 @@
                     "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
                 "3": [
+                    [
+                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
+                    ]
+                ],
+                "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
@@ -24,6 +30,12 @@
                 "mappings": [
                     "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
+                "sample_mappings": [
+                    [
+                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
+                    ]
+                ],
                 "samplesheet": [
                     "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192"
                 ],
@@ -36,6 +48,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-25T12:08:28.465466"
+        "timestamp": "2023-10-06T12:24:57.695874"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
index 4560b05b..60cd3444 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
@@ -12,6 +12,12 @@
                     "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
                 "3": [
+                    [
+                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
+                    ]
+                ],
+                "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
@@ -25,6 +31,12 @@
                 "mappings": [
                     "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
+                "sample_mappings": [
+                    [
+                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
+                    ]
+                ],
                 "samplesheet": [
                     "samplesheet.csv:md5,46752dd6abac80b59573910f7ce4babe"
                 ],
@@ -38,6 +50,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-25T11:53:25.411769"
+        "timestamp": "2023-10-06T12:03:19.401141"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
index 26357aa5..a0c20a40 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
@@ -12,6 +12,12 @@
                     "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
                 "3": [
+                    [
+                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
+                    ]
+                ],
+                "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
@@ -25,6 +31,12 @@
                 "mappings": [
                     "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
+                "sample_mappings": [
+                    [
+                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
+                    ]
+                ],
                 "samplesheet": [
                     "samplesheet.csv:md5,69117245b73776d6e4daecdbfdff9767"
                 ],
@@ -38,6 +50,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-25T12:03:02.485911"
+        "timestamp": "2023-10-06T12:14:02.500312"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
index ff4b27df..d9d6ddee 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
@@ -12,6 +12,12 @@
                     "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
                 "3": [
+                    [
+                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
+                    ]
+                ],
+                "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
@@ -25,6 +31,12 @@
                 "mappings": [
                     "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
+                "sample_mappings": [
+                    [
+                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
+                    ]
+                ],
                 "samplesheet": [
                     "samplesheet.csv:md5,0705e78609390cc464c2fb10051178bc"
                 ],
@@ -38,6 +50,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-25T11:55:48.759498"
+        "timestamp": "2023-10-06T12:07:01.184728"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
index 4b38d6a1..c3e9ae8b 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
@@ -12,6 +12,12 @@
                     "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
                 "3": [
+                    [
+                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
+                    ]
+                ],
+                "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
@@ -25,6 +31,12 @@
                 "mappings": [
                     "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
+                "sample_mappings": [
+                    [
+                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
+                    ]
+                ],
                 "samplesheet": [
                     "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192"
                 ],
@@ -38,6 +50,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-25T11:50:52.373496"
+        "timestamp": "2023-10-06T11:59:31.7356"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
index 91a10c87..c137d853 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
@@ -12,6 +12,12 @@
                     "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
                 "3": [
+                    [
+                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
+                    ]
+                ],
+                "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
                     "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
@@ -23,6 +29,12 @@
                 "mappings": [
                     "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
                 ],
+                "sample_mappings": [
+                    [
+                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
+                    ]
+                ],
                 "samplesheet": [
                     "samplesheet.csv:md5,b1636e896008b96044d352a0757a390b"
                 ],
@@ -34,6 +46,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-25T11:03:28.968158"
+        "timestamp": "2023-10-06T12:18:48.477246"
     }
 }
\ No newline at end of file

From 3c011b1f580c2f2b4c4748ccbba96e90f2cf5891 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 6 Oct 2023 12:14:14 +0100
Subject: [PATCH 509/852] Minor pre-release tweaks and bug fixes

---
 lib/WorkflowSra.groovy    |  9 +++++----
 main.nf                   | 41 ++++++++++++++++++++++-----------------
 workflows/sra/main.nf     |  8 ++------
 workflows/synapse/main.nf |  4 +++-
 4 files changed, 33 insertions(+), 29 deletions(-)

diff --git a/lib/WorkflowSra.groovy b/lib/WorkflowSra.groovy
index 3c092a6f..8b17a2c1 100755
--- a/lib/WorkflowSra.groovy
+++ b/lib/WorkflowSra.groovy
@@ -9,11 +9,12 @@ class WorkflowSra {
     //
     // Check and validate parameters
     //
-    public static void initialise(params, valid_params) {
+    public static void initialise(params) {
         // Check minimal ENA fields are provided to download FastQ files
-        def ena_metadata_fields = params.ena_metadata_fields ? params.ena_metadata_fields.split(',').collect{ it.trim().toLowerCase() } : valid_params['ena_metadata_fields']
-        if (!ena_metadata_fields.containsAll(valid_params['ena_metadata_fields'])) {
-            Nextflow.error("Invalid option: '${params.ena_metadata_fields}'. Minimally required fields for '--ena_metadata_fields': '${valid_params['ena_metadata_fields'].join(',')}'")
+        def valid_ena_metadata_fields = ['run_accession', 'experiment_accession', 'library_layout', 'fastq_ftp', 'fastq_md5']
+        def ena_metadata_fields = params.ena_metadata_fields ? params.ena_metadata_fields.split(',').collect{ it.trim().toLowerCase() } : valid_ena_metadata_fields
+        if (!ena_metadata_fields.containsAll(valid_ena_metadata_fields)) {
+            Nextflow.error("Invalid option: '${params.ena_metadata_fields}'. Minimally required fields for '--ena_metadata_fields': '${valid_ena_metadata_fields.join(',')}'")
         }
     }
 
diff --git a/main.nf b/main.nf
index 7de31c2c..3afd60db 100644
--- a/main.nf
+++ b/main.nf
@@ -19,35 +19,25 @@ nextflow.enable.dsl = 2
 
 include { paramsHelp; paramsSummaryLog; validateParameters } from 'plugin/nf-validation'
 
+// Print parameter summary log to screen
 def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
 def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
-
-// Print parameter summary log to screen
-log.info logo + paramsSummaryLog(workflow) + citation
-
-// Print help message if needed
+def String command = "nextflow run ${workflow.manifest.name} --input id.csv -profile docker"
 if (params.help) {
-    def String command = "nextflow run ${workflow.manifest.name} --input id.csv -profile docker"
     log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
     System.exit(0)
-}
-
-// Validate input parameters
-if (params.validate_params) {
-    validateParameters()
+} else {
+    log.info logo + paramsSummaryLog(workflow) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
 }
 
 // Check if --input file is empty
 ch_input = file(params.input, checkIfExists: true)
 if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") }
 
-// Read in ids from --input file
-Channel
-    .from(file(params.input, checkIfExists: true))
-    .splitCsv(header:false, sep:'', strip:true)
-    .map { it[0] }
-    .unique()
-    .set { ch_ids }
+// Validate input parameters
+if (params.validate_params) {
+    validateParameters()
+}
 
 // Auto-detect input id type
 def input_type = ''
@@ -58,10 +48,19 @@ if (WorkflowMain.isSraId(ch_input)) {
 } else {
     error('Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!')
 }
+
 if (params.input_type != input_type) {
     error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!")
 }
 
+// Read in ids from --input file
+Channel
+    .from(file(params.input, checkIfExists: true))
+    .splitCsv(header:false, sep:'', strip:true)
+    .map { it[0] }
+    .unique()
+    .set { ch_ids }
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT WORKFLOWS
@@ -71,6 +70,12 @@ if (params.input_type != input_type) {
 if (params.input_type == 'sra')     include { SRA     } from './workflows/sra'
 if (params.input_type == 'synapse') include { SYNAPSE } from './workflows/synapse'
 
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    NAMED WORKFLOWS FOR PIPELINE
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
 //
 // WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided
 //
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index e393b726..6b2ce98b 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -4,14 +4,11 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'
+include { paramsSummaryMap } from 'plugin/nf-validation'
 
-def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
-def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
 def summary_params = paramsSummaryMap(workflow)
 
-// Print parameter summary log to screen
-log.info logo + paramsSummaryLog(workflow) + citation
+WorkflowSra.initialise(params)
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -33,7 +30,6 @@ include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_c
 */
 
 include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions/main'
-
 include { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS } from '../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main'
 
 /*
diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf
index 4f015e0e..abe7cb22 100644
--- a/workflows/synapse/main.nf
+++ b/workflows/synapse/main.nf
@@ -4,7 +4,9 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
+include { paramsSummaryMap } from 'plugin/nf-validation'
+
+def summary_params = paramsSummaryMap(workflow)
 
 // Create channel for synapse config
 if (params.synapse_config) {

From a9e5646e60a24f59346392d7acc657f8efcd29e0 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 6 Oct 2023 17:13:28 +0100
Subject: [PATCH 510/852] Fix #173

---
 CHANGELOG.md                                       | 14 ++++++++++++++
 modules.json                                       |  6 +++---
 modules/nf-core/sratools/fasterqdump/main.nf       |  8 ++++----
 modules/nf-core/sratools/prefetch/main.nf          |  6 +++---
 .../prefetch/templates/retry_with_backoff.sh       |  4 +---
 .../meta.yml                                       |  2 +-
 6 files changed, 26 insertions(+), 14 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e85a5564..019b46bd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,15 +12,29 @@ Special thanks to the following for their contributions to the release:
 - [Adam Talbot](https://github.com/adamrtalbot)
 - [Harshil Patel](https://github.com/drpatelh)
 - [Maxime Garcia](https://github.com/maxulysse)
+- [Rob Syme](https://github.com/robsyme)
 
 Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
 
 ### Enhancements & fixes
 
+- [#173](https://github.com/nf-core/fetchngs/issues/173) - Add compatibility for sralite files
 - [PR #205](https://github.com/nf-core/fetchngs/pull/205) - Rename all local modules, workflows and remove `public_aws_ecr profile`
 - [PR #206](https://github.com/nf-core/fetchngs/pull/206) - CI improvments and code cleanup
 - [PR #208](https://github.com/nf-core/fetchngs/pull/208) - Template update with nf-core/tools 2.10
 
+### Software dependencies
+
+| Dependency      | Old version | New version |
+| --------------- | ----------- | ----------- |
+| `sra-tools`     | 2.11.0      | 3.0.8       |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+>
+> **NB:** Dependency has been **added** if just the new version information is present.
+>
+> **NB:** Dependency has been **removed** if new version information isn't present.
+
 ## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-16
 
 ### Credits
diff --git a/modules.json b/modules.json
index ab610dfb..6dd402db 100644
--- a/modules.json
+++ b/modules.json
@@ -17,12 +17,12 @@
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca",
+                        "git_sha": "4d9951c6c9c4c19ea944bb73149caf9d3cb1f2fc",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/prefetch": {
                         "branch": "master",
-                        "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca",
+                        "git_sha": "4d9951c6c9c4c19ea944bb73149caf9d3cb1f2fc",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     }
                 }
@@ -31,7 +31,7 @@
                 "nf-core": {
                     "fastq_download_prefetch_fasterqdump_sratools": {
                         "branch": "master",
-                        "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca",
+                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf
index 2d9090e2..2c5cc8f6 100644
--- a/modules/nf-core/sratools/fasterqdump/main.nf
+++ b/modules/nf-core/sratools/fasterqdump/main.nf
@@ -2,10 +2,10 @@ process SRATOOLS_FASTERQDUMP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::sra-tools=2.11.0 conda-forge::pigz=2.6"
+    conda "bioconda::sra-tools=3.0.8 conda-forge::pigz=2.6"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' :
-        'biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:2f4a4c900edd6801ff0068c2b3048b4459d119eb-0' :
+        'biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:2f4a4c900edd6801ff0068c2b3048b4459d119eb-0' }"
 
     input:
     tuple val(meta), path(sra)
@@ -33,7 +33,7 @@ process SRATOOLS_FASTERQDUMP {
         --threads $task.cpus \\
         --outfile $outfile \\
         ${key_file} \\
-        ${sra.name}
+        ${sra}
 
     pigz \\
         $args2 \\
diff --git a/modules/nf-core/sratools/prefetch/main.nf b/modules/nf-core/sratools/prefetch/main.nf
index ba7be4bd..fb226962 100644
--- a/modules/nf-core/sratools/prefetch/main.nf
+++ b/modules/nf-core/sratools/prefetch/main.nf
@@ -2,10 +2,10 @@ process SRATOOLS_PREFETCH {
     tag "$id"
     label 'process_low'
 
-    conda "bioconda::sra-tools=2.11.0"
+    conda "bioconda::sra-tools=3.0.8"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' :
-        'biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
+        'https://depot.galaxyproject.org/singularity/sra-tools:3.0.8--h9f5acd7_0' :
+        'biocontainers/sra-tools:3.0.8--h9f5acd7_0' }"
 
     input:
     tuple val(meta), val(id)
diff --git a/modules/nf-core/sratools/prefetch/templates/retry_with_backoff.sh b/modules/nf-core/sratools/prefetch/templates/retry_with_backoff.sh
index e08dbb6a..a72a4bfb 100755
--- a/modules/nf-core/sratools/prefetch/templates/retry_with_backoff.sh
+++ b/modules/nf-core/sratools/prefetch/templates/retry_with_backoff.sh
@@ -47,9 +47,7 @@ retry_with_backoff !{args2} \
     !{args} \
     !{id}
 
-[ -f !{id}.sralite ] && { mkdir -p !{id}; mv "!{id}.sralite" !{id}/; }
-
-vdb-validate !{id}
+[ -f !{id}.sralite ] && vdb-validate !{id}.sralite || vdb-validate !{id}
 
 cat <<-END_VERSIONS > versions.yml
 "!{task.process}":
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml
index 6ff9442b..6a36b225 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml
@@ -8,7 +8,7 @@ keywords:
   - fastq
   - prefetch
   - fasterq-dump
-modules:
+components:
   - custom/sratoolsncbisettings
   - sratools/prefetch
   - sratools/fasterqdump

From ec4c8fef344bcb2893fc0cd84df0ce7ca6b2b2c9 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 6 Oct 2023 17:15:37 +0100
Subject: [PATCH 511/852] Fix prettier

---
 CHANGELOG.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 019b46bd..ce1ddae0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -25,9 +25,9 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 
 ### Software dependencies
 
-| Dependency      | Old version | New version |
-| --------------- | ----------- | ----------- |
-| `sra-tools`     | 2.11.0      | 3.0.8       |
+| Dependency  | Old version | New version |
+| ----------- | ----------- | ----------- |
+| `sra-tools` | 2.11.0      | 3.0.8       |
 
 > **NB:** Dependency has been **updated** if both old and new version information is present.
 >

From f689be7aa466dfdd4842ce5ffcd841fa6c5109cc Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 8 Oct 2023 16:47:06 +0100
Subject: [PATCH 512/852] Bump pipeline version to 1.11.0dev

---
 CHANGELOG.md              | 4 ++++
 assets/multiqc_config.yml | 4 ++--
 nextflow.config           | 2 +-
 3 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4a33776a..c500efcc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unpublished Version / DEV]
+
+### Enhancements & fixes
+
 ## [[1.10.1](https://github.com/nf-core/fetchngs/releases/tag/1.10.1)] - 2023-10-08
 
 ### Credits
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index bafbf577..a8974f98 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/fetchngs/releases/tag/1.10.1" target="_blank">nf-core/fetchngs</a>
+  This report has been generated by the <a href="https://github.com/nf-core/fetchngs/releases/tag/dev" target="_blank">nf-core/fetchngs</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/fetchngs/1.10.1/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/fetchngs/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-fetchngs-methods-description":
     order: -1000
diff --git a/nextflow.config b/nextflow.config
index 3877ed26..912ce43c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -220,7 +220,7 @@ manifest {
     description     = """Pipeline to fetch metadata and raw FastQ files from public databases"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.10.1'
+    version         = '1.11.0dev'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
 

From 524ebe92c5076ae70be4634a503c9593d4d28a00 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Sun, 8 Oct 2023 20:20:24 +0200
Subject: [PATCH 513/852] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ce1ddae0..4a33776a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[1.10.1](https://github.com/nf-core/fetchngs/releases/tag/1.10.1)] - 2023-10-09
+## [[1.10.1](https://github.com/nf-core/fetchngs/releases/tag/1.10.1)] - 2023-10-08
 
 ### Credits
 

From b3d79dfa75875cd518d5bf2d3c93c929737d13d0 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 9 Oct 2023 09:59:25 +0200
Subject: [PATCH 514/852] fix conflicts + update initialise + code polish

---
 .prettierignore                          |   1 +
 README.md                                |   1 +
 conf/test.config                         |   2 +
 main.nf                                  |  13 ++-
 modules.json                             |   2 +-
 nextflow.config                          |   1 -
 subworkflows/nf-core/initialise/main.nf  | 124 +++++++++++++++++++++--
 subworkflows/nf-core/initialise/meta.yml |  34 +++----
 8 files changed, 143 insertions(+), 35 deletions(-)

diff --git a/.prettierignore b/.prettierignore
index 437d763d..bd464e26 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -5,6 +5,7 @@ slackreport.json
 work/
 data/
 results/
+.nf-test/
 .DS_Store
 testing/
 testing*
diff --git a/README.md b/README.md
index de90338a..02be6056 100644
--- a/README.md
+++ b/README.md
@@ -3,6 +3,7 @@
 [![GitHub Actions CI Status](https://github.com/nf-core/fetchngs/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/fetchngs/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/nf-core/fetchngs/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/fetchngs/actions?query=workflow%3A%22nf-core+linting%22)
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/fetchngs/results)
+[![nf-test](https://img.shields.io/badge/tested_with-nf--test-337ab7.svg)](https://github.com/askimed/nf-test)
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.5070524-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.5070524)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
diff --git a/conf/test.config b/conf/test.config
index 3c58e9cf..cb77f578 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -21,4 +21,6 @@ params {
 
     // Input data
     input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv'
+
+    validationSchemaIgnoreParams = 'test_data_base,merge_samplesheet_ids,fastq_ftp_ids,test_data'
 }
diff --git a/main.nf b/main.nf
index 428273c4..b7445e20 100644
--- a/main.nf
+++ b/main.nf
@@ -21,10 +21,13 @@ nextflow.enable.dsl = 2
 ch_input = file(params.input, checkIfExists: true)
 if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") }
 
-// Validate input parameters
-if (params.validate_params) {
-    validateParameters()
-}
+// Read in ids from --input file
+Channel
+    .from(file(params.input, checkIfExists: true))
+    .splitCsv(header:false, sep:'', strip:true)
+    .map { it[0] }
+    .unique()
+    .set { ch_ids }
 
 // Auto-detect input id type
 def input_type = ''
@@ -85,7 +88,7 @@ if (params.input_type == 'synapse') include { SYNAPSE } from './workflows/synaps
 // WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided
 //
 workflow NFCORE_FETCHNGS {
-    INITIALISE ( params.version, params.help, params.valid_params )
+    INITIALISE ( params.version, params.help, params.validate_params, true )
 
     ch_versions = Channel.empty()
 
diff --git a/modules.json b/modules.json
index 7bfa0ad2..aebf22de 100644
--- a/modules.json
+++ b/modules.json
@@ -36,7 +36,7 @@
                     },
                     "initialise": {
                         "branch": "master",
-                        "git_sha": "7b55a4631bebd1cf827a448d0b70386681fea475",
+                        "git_sha": "8340fb3779fe3233a455aeee1f60ceb203434ab6",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/nextflow.config b/nextflow.config
index 8e333cba..8f6f9721 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -49,7 +49,6 @@ params {
     // Schema validation default options
     validationFailUnrecognisedParams = false
     validationLenientMode            = false
-    validationSchemaIgnoreParams     = 'genomes'
     validationShowHiddenParams       = false
     validate_params                  = true
 
diff --git a/subworkflows/nf-core/initialise/main.nf b/subworkflows/nf-core/initialise/main.nf
index 0cbd3799..31fb1b4c 100644
--- a/subworkflows/nf-core/initialise/main.nf
+++ b/subworkflows/nf-core/initialise/main.nf
@@ -10,26 +10,34 @@ workflow INITIALISE {
         version         // bool
         help            // bool
         validate_params // bool
+        logo            // bool
 
     main:
 
-        // Print workflow version and exit on --version
-        if (version) {
-            String version_string = ""
+        // Get version string for use with --version or printing to log when creating
+        String version_string = ""
+
+        if (workflow.manifest.version) {
+            def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
+            version_string += "${prefix_v}${workflow.manifest.version}"
+        }
 
-            if (workflow.manifest.version) {
-                def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
-                version_string += "${prefix_v}${workflow.manifest.version}"
-            }
+        if (workflow.commitId) {
+            def git_shortsha = workflow.commitId.substring(0, 7)
+            version_string += "-g${git_shortsha}"
+        }
 
-            if (workflow.commitId) {
-                def git_shortsha = workflow.commitId.substring(0, 7)
-                version_string += "-g${git_shortsha}"
-            }
+        // Print workflow version and exit on --version
+        if (version) {
             log.info "${workflow.manifest.name} ${version_string}"
             System.exit(0)
         }
 
+        if ( logo ) {
+            log.info logo(workflow, params.monochrome_logs)
+        }
+        log.info "${workflow.manifest.name} ${version_string}"
+
         // Print citation for nf-core
         def citation = "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
             "* The nf-core framework\n" +
@@ -66,3 +74,97 @@ workflow INITIALISE {
         summary_params
 
 }
+
+//
+// ANSII Colours used for terminal logging
+//
+def logColours(Boolean monochrome_logs) {
+    Map colorcodes = [:]
+
+    // Reset / Meta
+    colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
+    colorcodes['bold']       = monochrome_logs ? '' : "\033[1m"
+    colorcodes['dim']        = monochrome_logs ? '' : "\033[2m"
+    colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m"
+    colorcodes['blink']      = monochrome_logs ? '' : "\033[5m"
+    colorcodes['reverse']    = monochrome_logs ? '' : "\033[7m"
+    colorcodes['hidden']     = monochrome_logs ? '' : "\033[8m"
+
+    // Regular Colors
+    colorcodes['black']      = monochrome_logs ? '' : "\033[0;30m"
+    colorcodes['red']        = monochrome_logs ? '' : "\033[0;31m"
+    colorcodes['green']      = monochrome_logs ? '' : "\033[0;32m"
+    colorcodes['yellow']     = monochrome_logs ? '' : "\033[0;33m"
+    colorcodes['blue']       = monochrome_logs ? '' : "\033[0;34m"
+    colorcodes['purple']     = monochrome_logs ? '' : "\033[0;35m"
+    colorcodes['cyan']       = monochrome_logs ? '' : "\033[0;36m"
+    colorcodes['white']      = monochrome_logs ? '' : "\033[0;37m"
+
+    // Bold
+    colorcodes['bblack']     = monochrome_logs ? '' : "\033[1;30m"
+    colorcodes['bred']       = monochrome_logs ? '' : "\033[1;31m"
+    colorcodes['bgreen']     = monochrome_logs ? '' : "\033[1;32m"
+    colorcodes['byellow']    = monochrome_logs ? '' : "\033[1;33m"
+    colorcodes['bblue']      = monochrome_logs ? '' : "\033[1;34m"
+    colorcodes['bpurple']    = monochrome_logs ? '' : "\033[1;35m"
+    colorcodes['bcyan']      = monochrome_logs ? '' : "\033[1;36m"
+    colorcodes['bwhite']     = monochrome_logs ? '' : "\033[1;37m"
+
+    // Underline
+    colorcodes['ublack']     = monochrome_logs ? '' : "\033[4;30m"
+    colorcodes['ured']       = monochrome_logs ? '' : "\033[4;31m"
+    colorcodes['ugreen']     = monochrome_logs ? '' : "\033[4;32m"
+    colorcodes['uyellow']    = monochrome_logs ? '' : "\033[4;33m"
+    colorcodes['ublue']      = monochrome_logs ? '' : "\033[4;34m"
+    colorcodes['upurple']    = monochrome_logs ? '' : "\033[4;35m"
+    colorcodes['ucyan']      = monochrome_logs ? '' : "\033[4;36m"
+    colorcodes['uwhite']     = monochrome_logs ? '' : "\033[4;37m"
+
+    // High Intensity
+    colorcodes['iblack']     = monochrome_logs ? '' : "\033[0;90m"
+    colorcodes['ired']       = monochrome_logs ? '' : "\033[0;91m"
+    colorcodes['igreen']     = monochrome_logs ? '' : "\033[0;92m"
+    colorcodes['iyellow']    = monochrome_logs ? '' : "\033[0;93m"
+    colorcodes['iblue']      = monochrome_logs ? '' : "\033[0;94m"
+    colorcodes['ipurple']    = monochrome_logs ? '' : "\033[0;95m"
+    colorcodes['icyan']      = monochrome_logs ? '' : "\033[0;96m"
+    colorcodes['iwhite']     = monochrome_logs ? '' : "\033[0;97m"
+
+    // Bold High Intensity
+    colorcodes['biblack']    = monochrome_logs ? '' : "\033[1;90m"
+    colorcodes['bired']      = monochrome_logs ? '' : "\033[1;91m"
+    colorcodes['bigreen']    = monochrome_logs ? '' : "\033[1;92m"
+    colorcodes['biyellow']   = monochrome_logs ? '' : "\033[1;93m"
+    colorcodes['biblue']     = monochrome_logs ? '' : "\033[1;94m"
+    colorcodes['bipurple']   = monochrome_logs ? '' : "\033[1;95m"
+    colorcodes['bicyan']     = monochrome_logs ? '' : "\033[1;96m"
+    colorcodes['biwhite']    = monochrome_logs ? '' : "\033[1;97m"
+
+    return colorcodes
+}
+
+//
+// Does what is says on the tin
+//
+def dashedLine(monochrome_logs) {
+    Map colors = logColours(monochrome_logs)
+    return "-${colors.dim}----------------------------------------------------${colors.reset}-"
+}
+
+//
+// nf-core logo
+//
+def logo(workflow, monochrome_logs) {
+    Map colors = logColours(monochrome_logs)
+    String.format(
+        """\n
+        ${dashedLine(monochrome_logs)}
+                                                ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
+        ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
+        ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
+        ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
+                                                ${colors.green}`._,._,\'${colors.reset}
+        ${dashedLine(monochrome_logs)}
+        """.stripIndent()
+    )
+}
diff --git a/subworkflows/nf-core/initialise/meta.yml b/subworkflows/nf-core/initialise/meta.yml
index 69596bb5..1d364847 100644
--- a/subworkflows/nf-core/initialise/meta.yml
+++ b/subworkflows/nf-core/initialise/meta.yml
@@ -6,28 +6,28 @@ keywords:
   - check
   - help
   - version
-modules:
+components: []
 input:
   - version:
-    type: boolean
-    description: |
-      Structure: val(version)
-      Boolean to show the pipeline version and exit.
+      type: boolean
+      description: |
+        Structure: val(version)
+        Boolean to show the pipeline version and exit.
   - help:
-    type: boolean
-    description: |
-      Structure: val(help)
-      Boolean to show the pipeline help message and exit.
+      type: boolean
+      description: |
+        Structure: val(help)
+        Boolean to show the pipeline help message and exit.
   - validate_params:
-    type: boolean
-    description: |
-      Structure: val(validate_params)
-      Whether to validate the parameters prior to starting the pipeline.
+      type: boolean
+      description: |
+        Structure: val(validate_params)
+        Whether to validate the parameters prior to starting the pipeline.
 output:
   - summary_params:
-    type: value
-    description: |
-      Structure: val(summary_params)
-      A map of the parameters used in the pipeline.
+      type: value
+      description: |
+        Structure: val(summary_params)
+        A map of the parameters used in the pipeline.
 authors:
   - "@adamrtalbot"

From e37fba215c02025b1a749fe1150edd27eb547c5b Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 9 Oct 2023 10:03:32 +0200
Subject: [PATCH 515/852] fix linting

---
 .nf-core.yml    |  3 ++-
 modules.json    | 26 +++++++++++++++++++-------
 nextflow.config |  1 +
 3 files changed, 22 insertions(+), 8 deletions(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index 78f1faff..8d668011 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -8,6 +8,7 @@ lint:
     - conf/modules.config
     - lib/WorkflowFetchngs.groovy
   files_unchanged:
+    - .gitattributes
+    - .prettierignore
     - assets/sendmail_template.txt
     - lib/NfcoreTemplate.groovy
-    - .gitattributes
diff --git a/modules.json b/modules.json
index aebf22de..9f6805c1 100644
--- a/modules.json
+++ b/modules.json
@@ -8,22 +8,30 @@
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
+                        "installed_by": [
+                            "fastq_download_prefetch_fasterqdump_sratools"
+                        ]
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
                         "git_sha": "4d9951c6c9c4c19ea944bb73149caf9d3cb1f2fc",
-                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
+                        "installed_by": [
+                            "fastq_download_prefetch_fasterqdump_sratools"
+                        ]
                     },
                     "sratools/prefetch": {
                         "branch": "master",
                         "git_sha": "4d9951c6c9c4c19ea944bb73149caf9d3cb1f2fc",
-                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
+                        "installed_by": [
+                            "fastq_download_prefetch_fasterqdump_sratools"
+                        ]
                     }
                 }
             },
@@ -32,15 +40,19 @@
                     "fastq_download_prefetch_fasterqdump_sratools": {
                         "branch": "master",
                         "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "initialise": {
                         "branch": "master",
                         "git_sha": "8340fb3779fe3233a455aeee1f60ceb203434ab6",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     }
                 }
             }
         }
     }
-}
+}
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 8f6f9721..5ad350c9 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -50,6 +50,7 @@ params {
     validationFailUnrecognisedParams = false
     validationLenientMode            = false
     validationShowHiddenParams       = false
+    validationSchemaIgnoreParams     = ''
     validate_params                  = true
 
 }

From e6b7c71767a7f06fa37c8a1ec28d346d15667af6 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 9 Oct 2023 10:08:31 +0200
Subject: [PATCH 516/852] prettier

---
 modules.json | 26 +++++++-------------------
 1 file changed, 7 insertions(+), 19 deletions(-)

diff --git a/modules.json b/modules.json
index 9f6805c1..aebf22de 100644
--- a/modules.json
+++ b/modules.json
@@ -8,30 +8,22 @@
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "fastq_download_prefetch_fasterqdump_sratools"
-                        ]
+                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
                         "git_sha": "4d9951c6c9c4c19ea944bb73149caf9d3cb1f2fc",
-                        "installed_by": [
-                            "fastq_download_prefetch_fasterqdump_sratools"
-                        ]
+                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/prefetch": {
                         "branch": "master",
                         "git_sha": "4d9951c6c9c4c19ea944bb73149caf9d3cb1f2fc",
-                        "installed_by": [
-                            "fastq_download_prefetch_fasterqdump_sratools"
-                        ]
+                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     }
                 }
             },
@@ -40,19 +32,15 @@
                     "fastq_download_prefetch_fasterqdump_sratools": {
                         "branch": "master",
                         "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     },
                     "initialise": {
                         "branch": "master",
                         "git_sha": "8340fb3779fe3233a455aeee1f60ceb203434ab6",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }
         }
     }
-}
\ No newline at end of file
+}

From b37087e7da4814eeca851826a62fe8d84724e81c Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 9 Oct 2023 11:40:58 +0200
Subject: [PATCH 517/852] use /tmp for nf-test tests

---
 .gitignore                            | 15 ++++++++-------
 nf-test.config                        |  2 +-
 workflows/sra/tests/main.nf.test.snap |  2 +-
 3 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/.gitignore b/.gitignore
index b1b5890a..267dd7d9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,11 +1,12 @@
+*.pyc
+.DS_Store
 .nextflow*
-work/
+.nf-test.log
+.nf-test/
 data/
+nf-test
 results/
-.DS_Store
-testing/
+test.xml
 testing*
-*.pyc
-.nf-test/
-nf-test
-.nf-test.log
+testing/
+work/
diff --git a/nf-test.config b/nf-test.config
index 0799cb40..cb656b94 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -3,7 +3,7 @@ config {
     testsDir "."
 
     // nf-test directory including temporary files for each test
-    workDir ".nf-test"
+    workDir "/tmp"
 
     // location of library folder that is added automatically to the classpath
     libDir "lib/"
diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
index 955dd72a..d53f3de2 100644
--- a/workflows/sra/tests/main.nf.test.snap
+++ b/workflows/sra/tests/main.nf.test.snap
@@ -50,6 +50,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-06T12:18:32.149462"
+        "timestamp": "2023-10-09T11:10:06.701286"
     }
 }
\ No newline at end of file

From cb6d4f34586d7ff0d54dfa3803cd2eebdb161175 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 9 Oct 2023 12:37:44 +0200
Subject: [PATCH 518/852] update snapshots

---
 .../sra/tests/sra_force_sratools_download.nf.test.snap      | 6 +++---
 .../sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap     | 2 +-
 .../sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap  | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
index 5cb1876c..a22fad41 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
@@ -6,7 +6,7 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192"
+                    "samplesheet.csv:md5,f582a7cf6b4a507e3ccbd2ebd134bd26"
                 ],
                 "2": [
                     "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
@@ -37,7 +37,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192"
+                    "samplesheet.csv:md5,f582a7cf6b4a507e3ccbd2ebd134bd26"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -48,6 +48,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-06T12:24:57.695874"
+        "timestamp": "2023-10-09T12:31:35.173406"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
index 60cd3444..3e26ff24 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
@@ -50,6 +50,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-06T12:03:19.401141"
+        "timestamp": "2023-10-09T11:48:46.177797"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
index c3e9ae8b..cacb42cc 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
@@ -50,6 +50,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-06T11:59:31.7356"
+        "timestamp": "2023-10-09T11:44:49.759545"
     }
 }
\ No newline at end of file

From 07b253567bb9701735fb12469f00fcf19c3d9818 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 10 Oct 2023 10:57:10 +0100
Subject: [PATCH 519/852] Remove nf-test files from .gitattributes

---
 .gitattributes | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.gitattributes b/.gitattributes
index c1c17000..7a2dabc2 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1,5 +1,4 @@
 *.config linguist-language=nextflow
 *.nf.test linguist-language=nextflow
-tests/**/*nf.test.snap linguist-generated
 modules/nf-core/** linguist-generated
 subworkflows/nf-core/** linguist-generated

From 7169d6bf31a6ca86cd0ccfb6093549867873ab42 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 10 Oct 2023 10:57:31 +0100
Subject: [PATCH 520/852] Remove unused multiqc_config.yml

---
 assets/multiqc_config.yml | 13 -------------
 1 file changed, 13 deletions(-)
 delete mode 100644 assets/multiqc_config.yml

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
deleted file mode 100644
index a8974f98..00000000
--- a/assets/multiqc_config.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/fetchngs/releases/tag/dev" target="_blank">nf-core/fetchngs</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/fetchngs/dev/docs/output" target="_blank">documentation</a>.
-report_section_order:
-  "nf-core-fetchngs-methods-description":
-    order: -1000
-  software_versions:
-    order: -1001
-  "nf-core-fetchngs-summary":
-    order: -1002
-
-export_plots: true

From 728360ce4c69f956ea11cc8cc6dd2b8456558d3e Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Tue, 10 Oct 2023 12:39:36 +0200
Subject: [PATCH 521/852] Update main.nf

---
 main.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/main.nf b/main.nf
index b7445e20..d6c239a0 100644
--- a/main.nf
+++ b/main.nf
@@ -17,6 +17,8 @@ nextflow.enable.dsl = 2
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
+include { paramsHelp; paramsSummaryLog; validateParameters } from 'plugin/nf-validation'
+
 // Check if --input file is empty
 ch_input = file(params.input, checkIfExists: true)
 if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") }

From 4d9a38dcdc42fbbe341ff6860ff57bbbff4ef564 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Tue, 10 Oct 2023 12:42:22 +0200
Subject: [PATCH 522/852] Apply suggestions from code review

---
 .gitignore      | 1 -
 .nf-core.yml    | 1 -
 .prettierignore | 1 -
 3 files changed, 3 deletions(-)

diff --git a/.gitignore b/.gitignore
index 267dd7d9..ff233cdb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,7 +2,6 @@
 .DS_Store
 .nextflow*
 .nf-test.log
-.nf-test/
 data/
 nf-test
 results/
diff --git a/.nf-core.yml b/.nf-core.yml
index 8d668011..143f4821 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -9,6 +9,5 @@ lint:
     - lib/WorkflowFetchngs.groovy
   files_unchanged:
     - .gitattributes
-    - .prettierignore
     - assets/sendmail_template.txt
     - lib/NfcoreTemplate.groovy
diff --git a/.prettierignore b/.prettierignore
index bd464e26..437d763d 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -5,7 +5,6 @@ slackreport.json
 work/
 data/
 results/
-.nf-test/
 .DS_Store
 testing/
 testing*

From 56abd32f7a81e812b449b79bd1abf960448387fa Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Tue, 10 Oct 2023 14:22:14 +0200
Subject: [PATCH 523/852] Apply suggestions from code review

---
 .nf-core.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.nf-core.yml b/.nf-core.yml
index 143f4821..bb27a4e9 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -9,5 +9,6 @@ lint:
     - lib/WorkflowFetchngs.groovy
   files_unchanged:
     - .gitattributes
+    - .gitignore
     - assets/sendmail_template.txt
     - lib/NfcoreTemplate.groovy

From 538cc2339fd7be0748cf93f2b5693054faf8c593 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 10 Oct 2023 14:47:47 +0100
Subject: [PATCH 524/852] Per module/subworkflow tags.yml file

Changes:
- Add separate tags.yml files for all modules and subworkflows that featured in the original tags.yml file.
- Removes old tags.yml file
- Adds github action to combine all tags.yml files for pattern matching using yq
---
 .github/workflows/ci.yml                          |  9 ++++++++-
 .../local/multiqc_mappings_config/tests/tags.yml  |  2 ++
 modules/local/sra_fastq_ftp/tests/tags.yml        |  2 ++
 modules/local/sra_ids_to_runinfo/tests/tags.yml   |  2 ++
 .../local/sra_merge_samplesheet/tests/tags.yml    |  2 ++
 modules/local/sra_runinfo_to_ftp/tests/tags.yml   |  2 ++
 modules/local/sra_to_samplesheet/tests/tags.yml   |  2 ++
 {.github => workflows/sra/tests}/tags.yml         | 15 ---------------
 8 files changed, 20 insertions(+), 16 deletions(-)
 create mode 100644 modules/local/multiqc_mappings_config/tests/tags.yml
 create mode 100644 modules/local/sra_fastq_ftp/tests/tags.yml
 create mode 100644 modules/local/sra_ids_to_runinfo/tests/tags.yml
 create mode 100644 modules/local/sra_merge_samplesheet/tests/tags.yml
 create mode 100644 modules/local/sra_runinfo_to_ftp/tests/tags.yml
 create mode 100644 modules/local/sra_to_samplesheet/tests/tags.yml
 rename {.github => workflows/sra/tests}/tags.yml (83%)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 68e2773c..9273f90e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -30,10 +30,17 @@ jobs:
       tags: ${{ steps.filter.outputs.changes }}
     steps:
       - uses: actions/checkout@v3
+      - name: Combine all tags.yml files
+        id: get_username
+        uses: mikefarah/yq@master
+        with:
+          cmd: find . -name "tags.yml" -type f -exec yq ea '. as $item ireduce ({}; . * $item )' {} + > tags.yml
+      - name: debug
+        run: cat tags.yml
       - uses: dorny/paths-filter@v2
         id: filter
         with:
-          filters: ".github/tags.yml"
+          filters: "tags.yml"
 
   define_nxf_versions:
     name: Choose nextflow versions to test against depending on target branch
diff --git a/modules/local/multiqc_mappings_config/tests/tags.yml b/modules/local/multiqc_mappings_config/tests/tags.yml
new file mode 100644
index 00000000..595e2e31
--- /dev/null
+++ b/modules/local/multiqc_mappings_config/tests/tags.yml
@@ -0,0 +1,2 @@
+multiqc_mappings_config:
+  - modules/local/multiqc_mappings_config/**
diff --git a/modules/local/sra_fastq_ftp/tests/tags.yml b/modules/local/sra_fastq_ftp/tests/tags.yml
new file mode 100644
index 00000000..e7474bef
--- /dev/null
+++ b/modules/local/sra_fastq_ftp/tests/tags.yml
@@ -0,0 +1,2 @@
+sra_fastq_ftp:
+  - modules/local/sra_fastq_ftp/**
diff --git a/modules/local/sra_ids_to_runinfo/tests/tags.yml b/modules/local/sra_ids_to_runinfo/tests/tags.yml
new file mode 100644
index 00000000..63ea7db3
--- /dev/null
+++ b/modules/local/sra_ids_to_runinfo/tests/tags.yml
@@ -0,0 +1,2 @@
+sra_ids_to_runinfo:
+  - modules/local/sra_ids_to_runinfo/**
diff --git a/modules/local/sra_merge_samplesheet/tests/tags.yml b/modules/local/sra_merge_samplesheet/tests/tags.yml
new file mode 100644
index 00000000..a4292b70
--- /dev/null
+++ b/modules/local/sra_merge_samplesheet/tests/tags.yml
@@ -0,0 +1,2 @@
+sra_merge_samplesheet:
+  - modules/local/sra_merge_samplesheet/**
diff --git a/modules/local/sra_runinfo_to_ftp/tests/tags.yml b/modules/local/sra_runinfo_to_ftp/tests/tags.yml
new file mode 100644
index 00000000..0987a1e6
--- /dev/null
+++ b/modules/local/sra_runinfo_to_ftp/tests/tags.yml
@@ -0,0 +1,2 @@
+sra_runinfo_to_ftp:
+  - modules/local/sra_runinfo_to_ftp/**
diff --git a/modules/local/sra_to_samplesheet/tests/tags.yml b/modules/local/sra_to_samplesheet/tests/tags.yml
new file mode 100644
index 00000000..2f2d527b
--- /dev/null
+++ b/modules/local/sra_to_samplesheet/tests/tags.yml
@@ -0,0 +1,2 @@
+sra_to_samplesheet:
+  - modules/local/sra_to_samplesheet/**
diff --git a/.github/tags.yml b/workflows/sra/tests/tags.yml
similarity index 83%
rename from .github/tags.yml
rename to workflows/sra/tests/tags.yml
index 03569f78..52c3e591 100644
--- a/.github/tags.yml
+++ b/workflows/sra/tests/tags.yml
@@ -1,18 +1,3 @@
-# local modules
-multiqc_mappings_config:
-  - modules/local/multiqc_mappings_config/**
-sra_fastq_ftp:
-  - modules/local/sra_fastq_ftp/**
-sra_ids_to_runinfo:
-  - modules/local/sra_ids_to_runinfo/**
-sra_merge_samplesheet:
-  - modules/local/sra_merge_samplesheet/**
-sra_runinfo_to_ftp:
-  - modules/local/sra_runinfo_to_ftp/**
-sra_to_samplesheet:
-  - modules/local/sra_to_samplesheet/**
-
-# workflow: sra
 sra_custom_ena_metadata_fields:
   - modules/local/sra_ids_to_runinfo/**
   - modules/local/sra_runinfo_to_ftp/**

From ff7fa147b662aed6949b278271784a8da8478a4b Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 10 Oct 2023 14:55:34 +0100
Subject: [PATCH 525/852] Escape single quotes

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 9273f90e..63dede75 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -34,7 +34,7 @@ jobs:
         id: get_username
         uses: mikefarah/yq@master
         with:
-          cmd: find . -name "tags.yml" -type f -exec yq ea '. as $item ireduce ({}; . * $item )' {} + > tags.yml
+          cmd: find . -name "tags.yml" -type f -exec yq ea \'. as $item ireduce ({}; . * $item )\' {} + > tags.yml
       - name: debug
         run: cat tags.yml
       - uses: dorny/paths-filter@v2

From d15e6bec17185b5d9591b8bcab4641fad50df5a7 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 10 Oct 2023 15:02:54 +0100
Subject: [PATCH 526/852] quote command line

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 63dede75..13b86c93 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -34,7 +34,7 @@ jobs:
         id: get_username
         uses: mikefarah/yq@master
         with:
-          cmd: find . -name "tags.yml" -type f -exec yq ea \'. as $item ireduce ({}; . * $item )\' {} + > tags.yml
+          cmd: "find . -name 'tags.yml' -type f -exec yq ea '. as $item ireduce ({}; . * $item )' {} + > tags.yml"
       - name: debug
         run: cat tags.yml
       - uses: dorny/paths-filter@v2

From 264be7a9abe09c6d4862dec05b3126941f2831a6 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 10 Oct 2023 15:06:33 +0100
Subject: [PATCH 527/852] escape AND quote

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 13b86c93..c1ba3574 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -34,7 +34,7 @@ jobs:
         id: get_username
         uses: mikefarah/yq@master
         with:
-          cmd: "find . -name 'tags.yml' -type f -exec yq ea '. as $item ireduce ({}; . * $item )' {} + > tags.yml"
+          cmd: "find . -name 'tags.yml' -type f -exec yq ea '. as $item ireduce (\\{\\}; . * $item )' {} + > tags.yml"
       - name: debug
         run: cat tags.yml
       - uses: dorny/paths-filter@v2

From 4f1e6388983c4674a7b3d28cf4b85fec35e4ac75 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 10 Oct 2023 15:20:37 +0100
Subject: [PATCH 528/852] Trying to use cat

---
 .github/workflows/ci.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c1ba3574..85e53716 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -32,15 +32,13 @@ jobs:
       - uses: actions/checkout@v3
       - name: Combine all tags.yml files
         id: get_username
-        uses: mikefarah/yq@master
-        with:
-          cmd: "find . -name 'tags.yml' -type f -exec yq ea '. as $item ireduce (\\{\\}; . * $item )' {} + > tags.yml"
+        run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml
       - name: debug
         run: cat tags.yml
       - uses: dorny/paths-filter@v2
         id: filter
         with:
-          filters: "tags.yml"
+          filters: ".github/tags.yml"
 
   define_nxf_versions:
     name: Choose nextflow versions to test against depending on target branch

From 051588c227232ae0a59872eece21b1e4b2e96d3a Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 10 Oct 2023 15:21:35 +0100
Subject: [PATCH 529/852] fixup

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 85e53716..436b61a5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -34,7 +34,7 @@ jobs:
         id: get_username
         run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml
       - name: debug
-        run: cat tags.yml
+        run: cat .github/tags.yml
       - uses: dorny/paths-filter@v2
         id: filter
         with:

From f81daf8e922b14ee500619d16da37ad98defe572 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 11 Oct 2023 12:02:14 +0100
Subject: [PATCH 530/852] Remove all files in lib directory

---
 lib/NfcoreTemplate.groovy         | 330 ------------------------------
 lib/Utils.groovy                  |  47 -----
 lib/WorkflowMain.groovy           | 216 -------------------
 lib/nfcore_external_java_deps.jar | Bin 2291171 -> 0 bytes
 4 files changed, 593 deletions(-)
 delete mode 100755 lib/NfcoreTemplate.groovy
 delete mode 100644 lib/Utils.groovy
 delete mode 100755 lib/WorkflowMain.groovy
 delete mode 100644 lib/nfcore_external_java_deps.jar

diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
deleted file mode 100755
index ed58a7ae..00000000
--- a/lib/NfcoreTemplate.groovy
+++ /dev/null
@@ -1,330 +0,0 @@
-//
-// This file holds several functions used within the nf-core pipeline template.
-//
-
-import org.yaml.snakeyaml.Yaml
-import groovy.json.JsonOutput
-
-class NfcoreTemplate {
-
-    //
-    // Check AWS Batch related parameters have been specified correctly
-    //
-    public static void awsBatch(workflow, params) {
-        if (workflow.profile.contains('awsbatch')) {
-            // Check params.awsqueue and params.awsregion have been set if running on AWSBatch
-            assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
-            // Check outdir paths to be S3 buckets if running on AWSBatch
-            assert params.outdir.startsWith('s3:')       : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!"
-        }
-    }
-
-    //
-    //  Warn if a -profile or Nextflow config has not been provided to run the pipeline
-    //
-    public static void checkConfigProvided(workflow, log) {
-        if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
-            log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
-                    "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
-                    "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
-                    "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
-                    "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
-                    "Please refer to the quick start section and usage docs for the pipeline.\n "
-        }
-    }
-
-    //
-    // Generate version string
-    //
-    public static String version(workflow) {
-        String version_string = ""
-
-        if (workflow.manifest.version) {
-            def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
-            version_string += "${prefix_v}${workflow.manifest.version}"
-        }
-
-        if (workflow.commitId) {
-            def git_shortsha = workflow.commitId.substring(0, 7)
-            version_string += "-g${git_shortsha}"
-        }
-
-        return version_string
-    }
-
-    //
-    // Construct and send completion email
-    //
-    public static void email(workflow, params, summary_params, projectDir, log) {
-
-        // Set up the e-mail variables
-        def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
-        if (!workflow.success) {
-            subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
-        }
-
-        def summary = [:]
-        for (group in summary_params.keySet()) {
-            summary << summary_params[group]
-        }
-
-        def misc_fields = [:]
-        misc_fields['Date Started']              = workflow.start
-        misc_fields['Date Completed']            = workflow.complete
-        misc_fields['Pipeline script file path'] = workflow.scriptFile
-        misc_fields['Pipeline script hash ID']   = workflow.scriptId
-        if (workflow.repository) misc_fields['Pipeline repository Git URL']    = workflow.repository
-        if (workflow.commitId)   misc_fields['Pipeline repository Git Commit'] = workflow.commitId
-        if (workflow.revision)   misc_fields['Pipeline Git branch/tag']        = workflow.revision
-        misc_fields['Nextflow Version']           = workflow.nextflow.version
-        misc_fields['Nextflow Build']             = workflow.nextflow.build
-        misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
-
-        def email_fields = [:]
-        email_fields['version']      = NfcoreTemplate.version(workflow)
-        email_fields['runName']      = workflow.runName
-        email_fields['success']      = workflow.success
-        email_fields['dateComplete'] = workflow.complete
-        email_fields['duration']     = workflow.duration
-        email_fields['exitStatus']   = workflow.exitStatus
-        email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
-        email_fields['errorReport']  = (workflow.errorReport ?: 'None')
-        email_fields['commandLine']  = workflow.commandLine
-        email_fields['projectDir']   = workflow.projectDir
-        email_fields['summary']      = summary << misc_fields
-
-        // Check if we are only sending emails on failure
-        def email_address = params.email
-        if (!params.email && params.email_on_fail && !workflow.success) {
-            email_address = params.email_on_fail
-        }
-
-        // Render the TXT template
-        def engine       = new groovy.text.GStringTemplateEngine()
-        def tf           = new File("$projectDir/assets/email_template.txt")
-        def txt_template = engine.createTemplate(tf).make(email_fields)
-        def email_txt    = txt_template.toString()
-
-        // Render the HTML template
-        def hf            = new File("$projectDir/assets/email_template.html")
-        def html_template = engine.createTemplate(hf).make(email_fields)
-        def email_html    = html_template.toString()
-
-        // Render the sendmail template
-        def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir" ]
-        def sf                     = new File("$projectDir/assets/sendmail_template.txt")
-        def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
-        def sendmail_html          = sendmail_template.toString()
-
-        // Send the HTML e-mail
-        Map colors = logColours(params.monochrome_logs)
-        if (email_address) {
-            try {
-                if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
-                // Try to send HTML e-mail using sendmail
-                [ 'sendmail', '-t' ].execute() << sendmail_html
-                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
-            } catch (all) {
-                // Catch failures and try with plaintext
-                def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
-                mail_cmd.execute() << email_html
-                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
-            }
-        }
-
-        // Write summary e-mail HTML to a file
-        def output_d = new File("${params.outdir}/pipeline_info/")
-        if (!output_d.exists()) {
-            output_d.mkdirs()
-        }
-        def output_hf = new File(output_d, "pipeline_report.html")
-        output_hf.withWriter { w -> w << email_html }
-        def output_tf = new File(output_d, "pipeline_report.txt")
-        output_tf.withWriter { w -> w << email_txt }
-    }
-
-    //
-    // Construct and send a notification to a web server as JSON
-    // e.g. Microsoft Teams and Slack
-    //
-    public static void IM_notification(workflow, params, summary_params, projectDir, log) {
-        def hook_url = params.hook_url
-
-        def summary = [:]
-        for (group in summary_params.keySet()) {
-            summary << summary_params[group]
-        }
-
-        def misc_fields = [:]
-        misc_fields['start']                                = workflow.start
-        misc_fields['complete']                             = workflow.complete
-        misc_fields['scriptfile']                           = workflow.scriptFile
-        misc_fields['scriptid']                             = workflow.scriptId
-        if (workflow.repository) misc_fields['repository']  = workflow.repository
-        if (workflow.commitId)   misc_fields['commitid']    = workflow.commitId
-        if (workflow.revision)   misc_fields['revision']    = workflow.revision
-        misc_fields['nxf_version']                          = workflow.nextflow.version
-        misc_fields['nxf_build']                            = workflow.nextflow.build
-        misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
-
-        def msg_fields = [:]
-        msg_fields['version']      = NfcoreTemplate.version(workflow)
-        msg_fields['runName']      = workflow.runName
-        msg_fields['success']      = workflow.success
-        msg_fields['dateComplete'] = workflow.complete
-        msg_fields['duration']     = workflow.duration
-        msg_fields['exitStatus']   = workflow.exitStatus
-        msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
-        msg_fields['errorReport']  = (workflow.errorReport ?: 'None')
-        msg_fields['commandLine']  = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "")
-        msg_fields['projectDir']   = workflow.projectDir
-        msg_fields['summary']      = summary << misc_fields
-
-        // Render the JSON template
-        def engine       = new groovy.text.GStringTemplateEngine()
-        // Different JSON depending on the service provider
-        // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format
-        def json_path     = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json"
-        def hf            = new File("$projectDir/assets/${json_path}")
-        def json_template = engine.createTemplate(hf).make(msg_fields)
-        def json_message  = json_template.toString()
-
-        // POST
-        def post = new URL(hook_url).openConnection();
-        post.setRequestMethod("POST")
-        post.setDoOutput(true)
-        post.setRequestProperty("Content-Type", "application/json")
-        post.getOutputStream().write(json_message.getBytes("UTF-8"));
-        def postRC = post.getResponseCode();
-        if (! postRC.equals(200)) {
-            log.warn(post.getErrorStream().getText());
-        }
-    }
-
-    //
-    // Dump pipeline parameters in a json file
-    //
-    public static void dump_parameters(workflow, params) {
-        def output_d = new File("${params.outdir}/pipeline_info/")
-        if (!output_d.exists()) {
-            output_d.mkdirs()
-        }
-
-        def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
-        def output_pf  = new File(output_d, "params_${timestamp}.json")
-        def jsonStr    = JsonOutput.toJson(params)
-        output_pf.text = JsonOutput.prettyPrint(jsonStr)
-    }
-
-    //
-    // Print pipeline summary on completion
-    //
-    public static void summary(workflow, params, log) {
-        Map colors = logColours(params.monochrome_logs)
-        if (workflow.success) {
-            if (workflow.stats.ignoredCount == 0) {
-                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
-            } else {
-                log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
-            }
-        } else {
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
-        }
-    }
-
-    //
-    // ANSII Colours used for terminal logging
-    //
-    public static Map logColours(Boolean monochrome_logs) {
-        Map colorcodes = [:]
-
-        // Reset / Meta
-        colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
-        colorcodes['bold']       = monochrome_logs ? '' : "\033[1m"
-        colorcodes['dim']        = monochrome_logs ? '' : "\033[2m"
-        colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m"
-        colorcodes['blink']      = monochrome_logs ? '' : "\033[5m"
-        colorcodes['reverse']    = monochrome_logs ? '' : "\033[7m"
-        colorcodes['hidden']     = monochrome_logs ? '' : "\033[8m"
-
-        // Regular Colors
-        colorcodes['black']      = monochrome_logs ? '' : "\033[0;30m"
-        colorcodes['red']        = monochrome_logs ? '' : "\033[0;31m"
-        colorcodes['green']      = monochrome_logs ? '' : "\033[0;32m"
-        colorcodes['yellow']     = monochrome_logs ? '' : "\033[0;33m"
-        colorcodes['blue']       = monochrome_logs ? '' : "\033[0;34m"
-        colorcodes['purple']     = monochrome_logs ? '' : "\033[0;35m"
-        colorcodes['cyan']       = monochrome_logs ? '' : "\033[0;36m"
-        colorcodes['white']      = monochrome_logs ? '' : "\033[0;37m"
-
-        // Bold
-        colorcodes['bblack']     = monochrome_logs ? '' : "\033[1;30m"
-        colorcodes['bred']       = monochrome_logs ? '' : "\033[1;31m"
-        colorcodes['bgreen']     = monochrome_logs ? '' : "\033[1;32m"
-        colorcodes['byellow']    = monochrome_logs ? '' : "\033[1;33m"
-        colorcodes['bblue']      = monochrome_logs ? '' : "\033[1;34m"
-        colorcodes['bpurple']    = monochrome_logs ? '' : "\033[1;35m"
-        colorcodes['bcyan']      = monochrome_logs ? '' : "\033[1;36m"
-        colorcodes['bwhite']     = monochrome_logs ? '' : "\033[1;37m"
-
-        // Underline
-        colorcodes['ublack']     = monochrome_logs ? '' : "\033[4;30m"
-        colorcodes['ured']       = monochrome_logs ? '' : "\033[4;31m"
-        colorcodes['ugreen']     = monochrome_logs ? '' : "\033[4;32m"
-        colorcodes['uyellow']    = monochrome_logs ? '' : "\033[4;33m"
-        colorcodes['ublue']      = monochrome_logs ? '' : "\033[4;34m"
-        colorcodes['upurple']    = monochrome_logs ? '' : "\033[4;35m"
-        colorcodes['ucyan']      = monochrome_logs ? '' : "\033[4;36m"
-        colorcodes['uwhite']     = monochrome_logs ? '' : "\033[4;37m"
-
-        // High Intensity
-        colorcodes['iblack']     = monochrome_logs ? '' : "\033[0;90m"
-        colorcodes['ired']       = monochrome_logs ? '' : "\033[0;91m"
-        colorcodes['igreen']     = monochrome_logs ? '' : "\033[0;92m"
-        colorcodes['iyellow']    = monochrome_logs ? '' : "\033[0;93m"
-        colorcodes['iblue']      = monochrome_logs ? '' : "\033[0;94m"
-        colorcodes['ipurple']    = monochrome_logs ? '' : "\033[0;95m"
-        colorcodes['icyan']      = monochrome_logs ? '' : "\033[0;96m"
-        colorcodes['iwhite']     = monochrome_logs ? '' : "\033[0;97m"
-
-        // Bold High Intensity
-        colorcodes['biblack']    = monochrome_logs ? '' : "\033[1;90m"
-        colorcodes['bired']      = monochrome_logs ? '' : "\033[1;91m"
-        colorcodes['bigreen']    = monochrome_logs ? '' : "\033[1;92m"
-        colorcodes['biyellow']   = monochrome_logs ? '' : "\033[1;93m"
-        colorcodes['biblue']     = monochrome_logs ? '' : "\033[1;94m"
-        colorcodes['bipurple']   = monochrome_logs ? '' : "\033[1;95m"
-        colorcodes['bicyan']     = monochrome_logs ? '' : "\033[1;96m"
-        colorcodes['biwhite']    = monochrome_logs ? '' : "\033[1;97m"
-
-        return colorcodes
-    }
-
-    //
-    // Does what is says on the tin
-    //
-    public static String dashedLine(monochrome_logs) {
-        Map colors = logColours(monochrome_logs)
-        return "-${colors.dim}----------------------------------------------------${colors.reset}-"
-    }
-
-    //
-    // nf-core logo
-    //
-    public static String logo(workflow, monochrome_logs) {
-        Map colors = logColours(monochrome_logs)
-        String workflow_version = NfcoreTemplate.version(workflow)
-        String.format(
-            """\n
-            ${dashedLine(monochrome_logs)}
-                                                    ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
-            ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
-            ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
-            ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
-                                                    ${colors.green}`._,._,\'${colors.reset}
-            ${colors.purple}  ${workflow.manifest.name} ${workflow_version}${colors.reset}
-            ${dashedLine(monochrome_logs)}
-            """.stripIndent()
-        )
-    }
-}
diff --git a/lib/Utils.groovy b/lib/Utils.groovy
deleted file mode 100644
index 8d030f4e..00000000
--- a/lib/Utils.groovy
+++ /dev/null
@@ -1,47 +0,0 @@
-//
-// This file holds several Groovy functions that could be useful for any Nextflow pipeline
-//
-
-import org.yaml.snakeyaml.Yaml
-
-class Utils {
-
-    //
-    // When running with -profile conda, warn if channels have not been set-up appropriately
-    //
-    public static void checkCondaChannels(log) {
-        Yaml parser = new Yaml()
-        def channels = []
-        try {
-            def config = parser.load("conda config --show channels".execute().text)
-            channels = config.channels
-        } catch(NullPointerException | IOException e) {
-            log.warn "Could not verify conda channel configuration."
-            return
-        }
-
-        // Check that all channels are present
-        // This channel list is ordered by required channel priority.
-        def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
-        def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
-
-        // Check that they are in the right order
-        def channel_priority_violation = false
-        def n = required_channels_in_order.size()
-        for (int i = 0; i < n - 1; i++) {
-            channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
-        }
-
-        if (channels_missing | channel_priority_violation) {
-            log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-                "  There is a problem with your Conda configuration!\n\n" +
-                "  You will need to set-up the conda-forge and bioconda channels correctly.\n" +
-                "  Please refer to https://bioconda.github.io/\n" +
-                "  The observed channel order is \n" +
-                "  ${channels}\n" +
-                "  but the following channel order is required:\n" +
-                "  ${required_channels_in_order}\n" +
-                "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-        }
-    }
-}
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
deleted file mode 100755
index 4ec4029a..00000000
--- a/lib/WorkflowMain.groovy
+++ /dev/null
@@ -1,216 +0,0 @@
-//
-// This file holds several functions specific to the main.nf workflow in the nf-core/fetchngs pipeline
-//
-
-import nextflow.Nextflow
-
-class WorkflowMain {
-
-    //
-    // Citation string for pipeline
-    //
-    public static String citation(workflow) {
-        return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-            "* The pipeline\n" +
-            "  https://doi.org/10.5281/zenodo.5070524\n\n" +
-            "* The nf-core framework\n" +
-            "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
-            "* Software dependencies\n" +
-            "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
-    }
-
-
-    //
-    // Validate parameters and print summary to screen
-    //
-    public static void initialise(workflow, params, log) {
-
-        // Print workflow version and exit on --version
-        if (params.version) {
-            String workflow_version = NfcoreTemplate.version(workflow)
-            log.info "${workflow.manifest.name} ${workflow_version}"
-            System.exit(0)
-        }
-
-        // Check that a -profile or Nextflow config has been provided to run the pipeline
-        NfcoreTemplate.checkConfigProvided(workflow, log)
-
-        // Check that conda channels are set-up correctly
-        if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-            Utils.checkCondaChannels(log)
-        }
-
-        // Check AWS batch settings
-        NfcoreTemplate.awsBatch(workflow, params)
-
-        // Check input has been provided
-        if (!params.input) {
-            Nextflow.error("Please provide an input file containing ids to the pipeline - one per line e.g. '--input ids.csv'")
-        }
-
-        // Check valid input_type has been provided
-        def input_types = ['sra', 'synapse']
-        if (!input_types.contains(params.input_type)) {
-            Nextflow.error("Invalid option: '${params.input_type}'. Valid options for '--input_type': ${input_types.join(', ')}.")
-        }
-    }
-
-    // Check if input ids are from the SRA
-    public static Boolean isSraId(input) {
-        def is_sra = false
-        def total_ids = 0
-        def no_match_ids = []
-        def pattern = /^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM]))(\d+)$/
-        input.eachLine { line ->
-            total_ids += 1
-            if (!(line =~ pattern)) {
-                no_match_ids << line
-            }
-        }
-
-        def num_match = total_ids - no_match_ids.size()
-        if (num_match > 0) {
-            if (num_match == total_ids) {
-                is_sra = true
-            } else {
-                Nextflow.error("Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / GEO / DDBJ or Synapse ids!")
-            }
-        }
-        return is_sra
-    }
-
-    // Check if input ids are from the Synapse platform
-    public static Boolean isSynapseId(input) {
-        def is_synapse = false
-        def total_ids = 0
-        def no_match_ids = []
-        def pattern = /^syn\d{8}$/
-        input.eachLine { line ->
-            total_ids += 1
-            if (!(line =~ pattern)) {
-                no_match_ids << line
-            }
-        }
-
-        def num_match = total_ids - no_match_ids.size()
-        if (num_match > 0) {
-            if (num_match == total_ids) {
-                is_synapse = true
-            } else {
-                Nextflow.error("Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / GEO / DDBJ or Synapse ids!")
-            }
-        }
-        return is_synapse
-    }
-
-    //
-    // Check and validate parameters
-    //
-    public static void sraInitialise(params, valid_params) {
-        // Check minimal ENA fields are provided to download FastQ files
-        def ena_metadata_fields = params.ena_metadata_fields ? params.ena_metadata_fields.split(',').collect{ it.trim().toLowerCase() } : valid_params['ena_metadata_fields']
-        if (!ena_metadata_fields.containsAll(valid_params['ena_metadata_fields'])) {
-            Nextflow.error("Invalid option: '${params.ena_metadata_fields}'. Minimally required fields for '--ena_metadata_fields': '${valid_params['ena_metadata_fields'].join(',')}'")
-        }
-    }
-
-    //
-    // Print a warning after pipeline has completed
-    //
-    public static void sraCurateSamplesheetWarn(log) {
-        log.warn "=============================================================================\n" +
-            "  Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" +
-            "  Public databases don't reliably hold information such as strandedness\n" +
-            "  information, controls etc\n\n" +
-            "  All of the sample metadata obtained from the ENA has been appended\n" +
-            "  as additional columns to help you manually curate the samplesheet before\n" +
-            "  running nf-core/other pipelines.\n" +
-            "==================================================================================="
-    }
-
-    //
-    // Convert metadata obtained from the 'synapse show' command to a Groovy map
-    //
-    public static Map synapseShowToMap(synapse_file) {
-        def meta = [:]
-        def category = ''
-        synapse_file.eachLine { line ->
-            def entries = [null, null]
-            if (!line.startsWith(' ') && !line.trim().isEmpty()) {
-                category = line.tokenize(':')[0]
-            } else {
-                entries = line.trim().tokenize('=')
-            }
-            meta["${category}|${entries[0]}"] = entries[1]
-        }
-        meta.id = meta['properties|id']
-        meta.name = meta['properties|name']
-        meta.md5 = meta['File|md5']
-        return meta.findAll{ it.value != null }
-    }
-
-    //
-    // Print a warning after pipeline has completed
-    //
-    public static void synapseCurateSamplesheetWarn(log) {
-        log.warn "=============================================================================\n" +
-            "  Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" +
-            "  Where applicable, default values will be used for sample-specific metadata\n" +
-            "  such as strandedness, controls etc as this information is not provided\n" +
-            "  in a standardised manner when uploading data to Synapse.\n" +
-            "==================================================================================="
-    }
-
-    //
-    // Obtain Sample ID from File Name
-    //
-    public static String synapseSampleNameFromFastQ(input_file, pattern) {
-
-        def sampleids = ""
-
-        def filePattern = pattern.toString()
-        int p = filePattern.lastIndexOf('/')
-            if( p != -1 )
-                filePattern = filePattern.substring(p+1)
-
-        input_file.each {
-            String fileName = input_file.getFileName().toString()
-
-            String indexOfWildcards = filePattern.findIndexOf { it=='*' || it=='?' }
-            String indexOfBrackets = filePattern.findIndexOf { it=='{' || it=='[' }
-            if( indexOfWildcards==-1 && indexOfBrackets==-1 ) {
-                if( fileName == filePattern )
-                    return actual.getSimpleName()
-                throw new IllegalArgumentException("Not a valid file pair globbing pattern: pattern=$filePattern file=$fileName")
-            }
-
-            int groupCount = 0
-            for( int i=0; i<filePattern.size(); i++ ) {
-                def ch = filePattern[i]
-                if( ch=='?' || ch=='*' )
-                    groupCount++
-                else if( ch=='{' || ch=='[' )
-                    break
-            }
-
-            def regex = filePattern
-                    .replace('.','\\.')
-                    .replace('*','(.*)')
-                    .replace('?','(.?)')
-                    .replace('{','(?:')
-                    .replace('}',')')
-                    .replace(',','|')
-
-            def matcher = (fileName =~ /$regex/)
-            if( matcher.matches() ) {
-                int c=Math.min(groupCount, matcher.groupCount())
-                int end = c ? matcher.end(c) : ( indexOfBrackets != -1 ? indexOfBrackets : fileName.size() )
-                def prefix = fileName.substring(0,end)
-                while(prefix.endsWith('-') || prefix.endsWith('_') || prefix.endsWith('.') )
-                    prefix=prefix[0..-2]
-                sampleids = prefix
-            }
-        }
-        return sampleids
-    }
-}
diff --git a/lib/nfcore_external_java_deps.jar b/lib/nfcore_external_java_deps.jar
deleted file mode 100644
index 805c8bb5e4fd43a12a5891eea5a68788309629b0..0000000000000000000000000000000000000000
GIT binary patch
literal 0
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From 7a46eb97226099e062c71e1daf74fbeb6270dc29 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 11 Oct 2023 12:02:39 +0100
Subject: [PATCH 531/852] Remove nf-core/initialise subworkflow

---
 modules.json                             |   5 -
 subworkflows/nf-core/initialise/main.nf  | 170 -----------------------
 subworkflows/nf-core/initialise/meta.yml |  33 -----
 3 files changed, 208 deletions(-)
 delete mode 100644 subworkflows/nf-core/initialise/main.nf
 delete mode 100644 subworkflows/nf-core/initialise/meta.yml

diff --git a/modules.json b/modules.json
index aebf22de..6dd402db 100644
--- a/modules.json
+++ b/modules.json
@@ -33,11 +33,6 @@
                         "branch": "master",
                         "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
                         "installed_by": ["subworkflows"]
-                    },
-                    "initialise": {
-                        "branch": "master",
-                        "git_sha": "8340fb3779fe3233a455aeee1f60ceb203434ab6",
-                        "installed_by": ["subworkflows"]
                     }
                 }
             }
diff --git a/subworkflows/nf-core/initialise/main.nf b/subworkflows/nf-core/initialise/main.nf
deleted file mode 100644
index 31fb1b4c..00000000
--- a/subworkflows/nf-core/initialise/main.nf
+++ /dev/null
@@ -1,170 +0,0 @@
-// This is a reimplementation of the basic initialise methods in the nf-core template
-// The role of this subworkflow is to check the input parameters and print help messages
-// Use this to start your nf-core pipeline
-
-include { paramsHelp; paramsSummaryLog; paramsSummaryMap; validateParameters } from 'plugin/nf-validation'
-
-workflow INITIALISE {
-
-    take:
-        version         // bool
-        help            // bool
-        validate_params // bool
-        logo            // bool
-
-    main:
-
-        // Get version string for use with --version or printing to log when creating
-        String version_string = ""
-
-        if (workflow.manifest.version) {
-            def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
-            version_string += "${prefix_v}${workflow.manifest.version}"
-        }
-
-        if (workflow.commitId) {
-            def git_shortsha = workflow.commitId.substring(0, 7)
-            version_string += "-g${git_shortsha}"
-        }
-
-        // Print workflow version and exit on --version
-        if (version) {
-            log.info "${workflow.manifest.name} ${version_string}"
-            System.exit(0)
-        }
-
-        if ( logo ) {
-            log.info logo(workflow, params.monochrome_logs)
-        }
-        log.info "${workflow.manifest.name} ${version_string}"
-
-        // Print citation for nf-core
-        def citation = "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-            "* The nf-core framework\n" +
-            "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
-            "* Software dependencies\n" +
-            "  ${workflow.manifest.homePage}/blob/master/CITATIONS.md"
-        log.info citation
-
-        // Print help message if needed
-        if (params.help) {
-            def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv -profile docker"
-            log.info paramsHelp(command)
-            System.exit(0)
-        }
-
-        if ( params.validate_params != false ){
-            validateParameters()
-        }
-
-        if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
-            log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
-                    "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
-                    "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
-                    "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
-                    "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
-                    "Please refer to the quick start section and usage docs for the pipeline.\n "
-        }
-
-        log.info paramsSummaryLog(workflow)
-
-        summary_params = paramsSummaryMap(workflow)
-
-    emit:
-        summary_params
-
-}
-
-//
-// ANSII Colours used for terminal logging
-//
-def logColours(Boolean monochrome_logs) {
-    Map colorcodes = [:]
-
-    // Reset / Meta
-    colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
-    colorcodes['bold']       = monochrome_logs ? '' : "\033[1m"
-    colorcodes['dim']        = monochrome_logs ? '' : "\033[2m"
-    colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m"
-    colorcodes['blink']      = monochrome_logs ? '' : "\033[5m"
-    colorcodes['reverse']    = monochrome_logs ? '' : "\033[7m"
-    colorcodes['hidden']     = monochrome_logs ? '' : "\033[8m"
-
-    // Regular Colors
-    colorcodes['black']      = monochrome_logs ? '' : "\033[0;30m"
-    colorcodes['red']        = monochrome_logs ? '' : "\033[0;31m"
-    colorcodes['green']      = monochrome_logs ? '' : "\033[0;32m"
-    colorcodes['yellow']     = monochrome_logs ? '' : "\033[0;33m"
-    colorcodes['blue']       = monochrome_logs ? '' : "\033[0;34m"
-    colorcodes['purple']     = monochrome_logs ? '' : "\033[0;35m"
-    colorcodes['cyan']       = monochrome_logs ? '' : "\033[0;36m"
-    colorcodes['white']      = monochrome_logs ? '' : "\033[0;37m"
-
-    // Bold
-    colorcodes['bblack']     = monochrome_logs ? '' : "\033[1;30m"
-    colorcodes['bred']       = monochrome_logs ? '' : "\033[1;31m"
-    colorcodes['bgreen']     = monochrome_logs ? '' : "\033[1;32m"
-    colorcodes['byellow']    = monochrome_logs ? '' : "\033[1;33m"
-    colorcodes['bblue']      = monochrome_logs ? '' : "\033[1;34m"
-    colorcodes['bpurple']    = monochrome_logs ? '' : "\033[1;35m"
-    colorcodes['bcyan']      = monochrome_logs ? '' : "\033[1;36m"
-    colorcodes['bwhite']     = monochrome_logs ? '' : "\033[1;37m"
-
-    // Underline
-    colorcodes['ublack']     = monochrome_logs ? '' : "\033[4;30m"
-    colorcodes['ured']       = monochrome_logs ? '' : "\033[4;31m"
-    colorcodes['ugreen']     = monochrome_logs ? '' : "\033[4;32m"
-    colorcodes['uyellow']    = monochrome_logs ? '' : "\033[4;33m"
-    colorcodes['ublue']      = monochrome_logs ? '' : "\033[4;34m"
-    colorcodes['upurple']    = monochrome_logs ? '' : "\033[4;35m"
-    colorcodes['ucyan']      = monochrome_logs ? '' : "\033[4;36m"
-    colorcodes['uwhite']     = monochrome_logs ? '' : "\033[4;37m"
-
-    // High Intensity
-    colorcodes['iblack']     = monochrome_logs ? '' : "\033[0;90m"
-    colorcodes['ired']       = monochrome_logs ? '' : "\033[0;91m"
-    colorcodes['igreen']     = monochrome_logs ? '' : "\033[0;92m"
-    colorcodes['iyellow']    = monochrome_logs ? '' : "\033[0;93m"
-    colorcodes['iblue']      = monochrome_logs ? '' : "\033[0;94m"
-    colorcodes['ipurple']    = monochrome_logs ? '' : "\033[0;95m"
-    colorcodes['icyan']      = monochrome_logs ? '' : "\033[0;96m"
-    colorcodes['iwhite']     = monochrome_logs ? '' : "\033[0;97m"
-
-    // Bold High Intensity
-    colorcodes['biblack']    = monochrome_logs ? '' : "\033[1;90m"
-    colorcodes['bired']      = monochrome_logs ? '' : "\033[1;91m"
-    colorcodes['bigreen']    = monochrome_logs ? '' : "\033[1;92m"
-    colorcodes['biyellow']   = monochrome_logs ? '' : "\033[1;93m"
-    colorcodes['biblue']     = monochrome_logs ? '' : "\033[1;94m"
-    colorcodes['bipurple']   = monochrome_logs ? '' : "\033[1;95m"
-    colorcodes['bicyan']     = monochrome_logs ? '' : "\033[1;96m"
-    colorcodes['biwhite']    = monochrome_logs ? '' : "\033[1;97m"
-
-    return colorcodes
-}
-
-//
-// Does what is says on the tin
-//
-def dashedLine(monochrome_logs) {
-    Map colors = logColours(monochrome_logs)
-    return "-${colors.dim}----------------------------------------------------${colors.reset}-"
-}
-
-//
-// nf-core logo
-//
-def logo(workflow, monochrome_logs) {
-    Map colors = logColours(monochrome_logs)
-    String.format(
-        """\n
-        ${dashedLine(monochrome_logs)}
-                                                ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
-        ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
-        ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
-        ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
-                                                ${colors.green}`._,._,\'${colors.reset}
-        ${dashedLine(monochrome_logs)}
-        """.stripIndent()
-    )
-}
diff --git a/subworkflows/nf-core/initialise/meta.yml b/subworkflows/nf-core/initialise/meta.yml
deleted file mode 100644
index 1d364847..00000000
--- a/subworkflows/nf-core/initialise/meta.yml
+++ /dev/null
@@ -1,33 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "initialise"
-description: Validate input parameters and print help messages
-keywords:
-  - admin
-  - check
-  - help
-  - version
-components: []
-input:
-  - version:
-      type: boolean
-      description: |
-        Structure: val(version)
-        Boolean to show the pipeline version and exit.
-  - help:
-      type: boolean
-      description: |
-        Structure: val(help)
-        Boolean to show the pipeline help message and exit.
-  - validate_params:
-      type: boolean
-      description: |
-        Structure: val(validate_params)
-        Whether to validate the parameters prior to starting the pipeline.
-output:
-  - summary_params:
-      type: value
-      description: |
-        Structure: val(summary_params)
-        A map of the parameters used in the pipeline.
-authors:
-  - "@adamrtalbot"

From d88b631acbb86271e66077517a639bea99b432da Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 11 Oct 2023 12:10:36 +0100
Subject: [PATCH 532/852] Update workflow main scripts

---
 main.nf                   | 111 ++++++++++++++------------------------
 workflows/sra/main.nf     |  24 ++++-----
 workflows/synapse/main.nf |   6 +--
 3 files changed, 53 insertions(+), 88 deletions(-)

diff --git a/main.nf b/main.nf
index b7445e20..7794d1b9 100644
--- a/main.nf
+++ b/main.nf
@@ -13,99 +13,42 @@ nextflow.enable.dsl = 2
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    VALIDATE & PRINT PARAMETER SUMMARY
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-// Check if --input file is empty
-ch_input = file(params.input, checkIfExists: true)
-if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") }
-
-// Read in ids from --input file
-Channel
-    .from(file(params.input, checkIfExists: true))
-    .splitCsv(header:false, sep:'', strip:true)
-    .map { it[0] }
-    .unique()
-    .set { ch_ids }
-
-// Auto-detect input id type
-def input_type = ''
-if (WorkflowMain.isSraId(ch_input)) {
-    input_type = 'sra'
-} else if (WorkflowMain.isSynapseId(ch_input)) {
-    input_type = 'synapse'
-} else {
-    error('Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!')
-}
-
-if (params.input_type != input_type) {
-    error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!")
-}
-
-if (params.input_type == 'sra') {
-    def valid_params = [
-        ena_metadata_fields : ['run_accession', 'experiment_accession', 'library_layout', 'fastq_ftp', 'fastq_md5']
-    ]
-
-    // Validate input parameters
-    WorkflowMain.sraInitialise(params, valid_params)
-} else if (params.input_type == 'synapse') {
-
-    // Create channel for synapse config
-    if (params.synapse_config) {
-        ch_synapse_config = file(params.synapse_config, checkIfExists: true)
-    } else {
-        error('Please provide a Synapse config file for download authentication!')
-    }
-}
-
-/*
-========================================================================================
-    IMPORT MODULES/SUBWORKFLOWS
-========================================================================================
-*/
-
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from './modules/nf-core/custom/dumpsoftwareversions'
-include { INITIALISE                  } from './subworkflows/nf-core/initialise/main'
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    IMPORT WORKFLOWS
+    NAMED WORKFLOWS FOR PIPELINE
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 if (params.input_type == 'sra')     include { SRA     } from './workflows/sra'
 if (params.input_type == 'synapse') include { SYNAPSE } from './workflows/synapse'
 
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    NAMED WORKFLOWS FOR PIPELINE
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
 //
 // WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided
 //
 workflow NFCORE_FETCHNGS {
-    INITIALISE ( params.version, params.help, params.validate_params, true )
 
+    take:
+    ids // channel: database ids read in from --input
+
+    main:
+    
     ch_versions = Channel.empty()
 
     //
     // WORKFLOW: Download FastQ files for SRA / ENA / GEO / DDBJ ids
     //
     if (params.input_type == 'sra') {
-        SRA ( ch_ids )
-        ch_versions = ch_versions.mix(SRA.out.versions)
+        SRA ( ids )
+        ch_versions = SRA.out.versions
 
     //
     // WORKFLOW: Download FastQ files for Synapse ids
     //
     } else if (params.input_type == 'synapse') {
-        SYNAPSE ( ch_ids, ch_synapse_config )
-        ch_versions = ch_versions.mix(SYNAPSE.out.versions)
+        SYNAPSE ( ids )
+        ch_versions = SYNAPSE.out.versions
     }
+
+    emit:
+    versions = ch_versions
 }
 
 /*
@@ -114,12 +57,36 @@ workflow NFCORE_FETCHNGS {
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
+include { PIPELINE_INITIALISATION } from './subworkflows/local/nf_core_fetchngs_utils'
+include { PIPELINE_COMPLETION     } from './subworkflows/local/nf_core_fetchngs_utils'
+
 //
 // WORKFLOW: Execute a single named workflow for the pipeline
-// See: https://github.com/nf-core/rnaseq/issues/619
 //
 workflow {
-    NFCORE_FETCHNGS ()
+
+    //
+    // SUBWORKFLOW: Run initialisation tasks
+    //
+    PIPELINE_INITIALISATION ()
+
+    //
+    // WORKFLOW: Run primary workflows for the pipeline
+    //
+    NFCORE_FETCHNGS (
+        PIPELINE_INITIALISATION.out.ids
+    )
+
+    //
+    // SUBWORKFLOW: Run completion tasks
+    //
+    PIPELINE_COMPLETION (
+        NFCORE_FETCHNGS.out.versions,
+        params.input_type,
+        params.email,
+        params.email_on_fail,
+        PIPELINE_INITIALISATION.out.summary_params
+    )
 }
 
 /*
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 3fd22f5d..a8f54646 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -62,10 +62,7 @@ workflow SRA {
         .unique()
         .set { ch_sra_metadata }
 
-    ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first())
-
     fastq_files = Channel.empty()
-
     if (!params.skip_fastq_download) {
 
         ch_sra_metadata
@@ -97,18 +94,19 @@ workflow SRA {
         ch_versions = ch_versions.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.versions.first())
 
         // Isolate FASTQ channel which will be added to emit block
-        fastq_files.mix(
-            SRA_FASTQ_FTP.out.fastq,
-            FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads
-        ).map { meta, fastq ->
-            def reads = fastq instanceof List ? fastq.flatten() : [ fastq ]
-            def meta_clone = meta.clone()
+        fastq_files
+            .mix(SRA_FASTQ_FTP.out.fastq, FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads)
+            .map { 
+                meta, fastq ->
+                    def reads = fastq instanceof List ? fastq.flatten() : [ fastq ]
+                    def meta_clone = meta.clone()
 
-            meta_clone.fastq_1 = reads[0] ? "${params.outdir}/fastq/${reads[0].getName()}" : ''
-            meta_clone.fastq_2 = reads[1] && !meta.single_end ? "${params.outdir}/fastq/${reads[1].getName()}" : ''
+                    meta_clone.fastq_1 = reads[0] ? "${params.outdir}/fastq/${reads[0].getName()}" : ''
+                    meta_clone.fastq_2 = reads[1] && !meta.single_end ? "${params.outdir}/fastq/${reads[1].getName()}" : ''
 
-            return meta_clone
-        }.set { ch_sra_metadata }
+                    return meta_clone
+            }
+            .set { ch_sra_metadata }
     }
 
     //
diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf
index d2681866..6b5ea02c 100644
--- a/workflows/synapse/main.nf
+++ b/workflows/synapse/main.nf
@@ -106,9 +106,9 @@ workflow SYNAPSE {
     ch_versions = ch_versions.mix(SYNAPSE_MERGE_SAMPLESHEET.out.versions)
 
     emit:
-        fastq       = ch_fastq
-        samplesheet = SYNAPSE_MERGE_SAMPLESHEET.out.samplesheet
-        versions    = ch_versions.unique()
+    fastq       = ch_fastq
+    samplesheet = SYNAPSE_MERGE_SAMPLESHEET.out.samplesheet
+    versions    = ch_versions.unique()
 }
 
 /*

From 4328622547fb3a1119f412ded0dd8b752981ec35 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 11 Oct 2023 12:10:57 +0100
Subject: [PATCH 533/852] Add subworkflows to replace files in lib directory

---
 .../local/nextflow_pipeline_utils/main.nf     | 123 +++++++
 .../local/nf_core_fetchngs_utils/main.nf      | 296 +++++++++++++++++
 .../local/nf_core_pipeline_utils/main.nf      | 308 ++++++++++++++++++
 .../local/nf_validation_plugin_utils/main.nf  |  52 +++
 4 files changed, 779 insertions(+)
 create mode 100644 subworkflows/local/nextflow_pipeline_utils/main.nf
 create mode 100644 subworkflows/local/nf_core_fetchngs_utils/main.nf
 create mode 100644 subworkflows/local/nf_core_pipeline_utils/main.nf
 create mode 100644 subworkflows/local/nf_validation_plugin_utils/main.nf

diff --git a/subworkflows/local/nextflow_pipeline_utils/main.nf b/subworkflows/local/nextflow_pipeline_utils/main.nf
new file mode 100644
index 00000000..e56394ed
--- /dev/null
+++ b/subworkflows/local/nextflow_pipeline_utils/main.nf
@@ -0,0 +1,123 @@
+//
+// Subworkflow with functionality that may be useful for any Nextflow pipeline
+//
+
+import org.yaml.snakeyaml.Yaml
+import groovy.json.JsonOutput
+
+/*
+========================================================================================
+    SUBWORKFLOW DEFINITION
+========================================================================================
+*/
+
+workflow NEXTFLOW_PIPELINE_UTILS {
+
+    take:
+    print_version        // bool
+    dump_parameters      // bool
+    output_directory     // path: base directory used to publish pipeline results
+    check_conda_channels // bool
+
+    main:
+
+    //
+    // Print workflow version and exit on --version
+    //
+    if (print_version) {
+        log.info "${workflow.manifest.name} ${getWorkflowVersion()}"
+        System.exit(0)
+    }
+
+    //
+    // Dump pipeline parameters to a JSON file
+    //
+    if (dump_parameters && output_directory) {
+        dumpParametersToJSON(output_directory)
+    }
+
+    //
+    // When running with Conda, warn if channels have not been set-up appropriately
+    //
+    if (check_conda_channels) {
+        checkCondaChannels()
+    }
+}
+
+/*
+========================================================================================
+    FUNCTIONS
+========================================================================================
+*/
+
+//
+// Generate version string
+//
+def getWorkflowVersion() {
+    String version_string = ""
+    if (workflow.manifest.version) {
+        def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
+        version_string += "${prefix_v}${workflow.manifest.version}"
+    }
+
+    if (workflow.commitId) {
+        def git_shortsha = workflow.commitId.substring(0, 7)
+        version_string += "-g${git_shortsha}"
+    }
+
+    return version_string
+}
+
+//
+// Dump pipeline parameters to a JSON file
+//
+def dumpParametersToJSON(output_directory) {
+    def output_d = new File("${output_directory}/pipeline_info/")
+    if (!output_d.exists()) {
+        output_d.mkdirs()
+    }
+
+    def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+    def output_pf  = new File(output_d, "params_${timestamp}.json")
+    def jsonStr    = JsonOutput.toJson(params)
+    output_pf.text = JsonOutput.prettyPrint(jsonStr)
+}
+
+//
+// When running with -profile conda, warn if channels have not been set-up appropriately
+//
+def checkCondaChannels() {
+    Yaml parser = new Yaml()
+    def channels = []
+    try {
+        def config = parser.load("conda config --show channels".execute().text)
+        channels = config.channels
+    } catch(NullPointerException | IOException e) {
+        log.warn "Could not verify conda channel configuration."
+        return
+    }
+
+    // Check that all channels are present
+    // This channel list is ordered by required channel priority.
+    def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
+    def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
+
+    // Check that they are in the right order
+    def channel_priority_violation = false
+    def n = required_channels_in_order.size()
+    for (int i = 0; i < n - 1; i++) {
+        channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
+    }
+
+    if (channels_missing | channel_priority_violation) {
+        log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+            "  There is a problem with your Conda configuration!\n\n" +
+            "  You will need to set-up the conda-forge and bioconda channels correctly.\n" +
+            "  Please refer to https://bioconda.github.io/\n" +
+            "  The observed channel order is \n" +
+            "  ${channels}\n" +
+            "  but the following channel order is required:\n" +
+            "  ${required_channels_in_order}\n" +
+            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+    }
+}
diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf
new file mode 100644
index 00000000..129b2e3f
--- /dev/null
+++ b/subworkflows/local/nf_core_fetchngs_utils/main.nf
@@ -0,0 +1,296 @@
+//
+// Subworkflow with functionality specific to the nf-core/fetchngs pipeline
+//
+
+/*
+========================================================================================
+    IMPORT MODULES/SUBWORKFLOWS
+========================================================================================
+*/
+
+include { CUSTOM_DUMPSOFTWAREVERSIONS                 } from '../../../modules/nf-core/custom/dumpsoftwareversions'
+include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion } from '../nextflow_pipeline_utils'
+include { NF_VALIDATION_PLUGIN_UTILS                  } from '../nf_validation_plugin_utils'
+include { NF_CORE_PIPELINE_UTILS; workflowCitation; nfCoreLogo; dashedLine; completionEmail; completionSummary } from '../nf_core_pipeline_utils'
+
+/*
+========================================================================================
+    SUBWORKFLOW TO INITIALISE PIPELINE
+========================================================================================
+*/
+
+workflow PIPELINE_INITIALISATION {
+
+    main:
+
+    //
+    // Print version and exit if required and dump pipeline parameters to JSON file
+    //
+    NEXTFLOW_PIPELINE_UTILS (
+        params.version,
+        true,
+        params.outdir,
+        workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
+    )
+
+    //
+    // Validate parameters and generate parameter summary to stdout
+    //
+    def pre_help_text = nfCoreLogo(getWorkflowVersion())
+    def post_help_text = '\n' + workflowCitation() + '\n' + dashedLine()
+    def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input ids.csv --outdir <OUTDIR>"
+    NF_VALIDATION_PLUGIN_UTILS (
+        params.help,
+        workflow_command,
+        pre_help_text,
+        post_help_text,
+        params.validate_params
+    )
+
+    //
+    // Check config provided to the pipeline
+    // 
+    NF_CORE_PIPELINE_UTILS ()
+
+    //
+    // Auto-detect input id type
+    //
+    ch_input = file(params.input)
+    def input_type = ''
+    if (isSraId(ch_input)) {
+        input_type = 'sra'
+        sraCheckENAMetadataFields()
+    } else if (isSynapseId(ch_input)) {
+        input_type = 'synapse'
+    } else {
+        error('Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!')
+    }
+
+    if (params.input_type != input_type) {
+        error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!")
+    }
+
+    // Read in ids from --input file
+    Channel
+        .from(ch_input)
+        .splitCsv(header:false, sep:'', strip:true)
+        .map { it[0] }
+        .unique()
+        .set { ch_ids }
+
+    emit:
+    ids            = ch_ids
+    summary_params = NF_VALIDATION_PLUGIN_UTILS.out.summary_params
+}
+
+/*
+========================================================================================
+    SUBWORKFLOW FOR PIPELINE COMPLETION
+========================================================================================
+*/
+
+workflow PIPELINE_COMPLETION {
+
+    take:
+    versions       // channel: software tools versions
+    input_type     //  string: 'sra' or 'synapse'
+    email          //  string: email address
+    email_on_fail  //  string: email address sent on pipeline failure
+    summary_params //     map: Groovy map of the parameters used in the pipeline
+
+    main:
+
+    //
+    // MODULE: Dump software versions for all tools used in the workflow
+    //
+    CUSTOM_DUMPSOFTWAREVERSIONS (
+        versions.collectFile(name: 'collated_versions.yml')
+    )
+
+    //
+    // Completion email and summary
+    //
+    workflow.onComplete {
+        if (email || email_on_fail) {
+            completionEmail(summary_params)
+        }
+
+        completionSummary()
+
+        if (input_type == 'sra') {
+            sraCurateSamplesheetWarn()
+        } else if (input_type == 'synapse') {
+            synapseCurateSamplesheetWarn()
+        }
+    }
+}
+
+/*
+========================================================================================
+    FUNCTIONS
+========================================================================================
+*/
+
+//
+// Check if input ids are from the SRA
+//
+def isSraId(input) {
+    def is_sra = false
+    def total_ids = 0
+    def no_match_ids = []
+    def pattern = /^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM]))(\d+)$/
+    input.eachLine { line ->
+        total_ids += 1
+        if (!(line =~ pattern)) {
+            no_match_ids << line
+        }
+    }
+
+    def num_match = total_ids - no_match_ids.size()
+    if (num_match > 0) {
+        if (num_match == total_ids) {
+            is_sra = true
+        } else {
+            error("Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / GEO / DDBJ or Synapse ids!")
+        }
+    }
+    return is_sra
+}
+
+//
+// Check if input ids are from the Synapse platform
+//
+def isSynapseId(input) {
+    def is_synapse = false
+    def total_ids = 0
+    def no_match_ids = []
+    def pattern = /^syn\d{8}$/
+    input.eachLine { line ->
+        total_ids += 1
+        if (!(line =~ pattern)) {
+            no_match_ids << line
+        }
+    }
+
+    def num_match = total_ids - no_match_ids.size()
+    if (num_match > 0) {
+        if (num_match == total_ids) {
+            is_synapse = true
+        } else {
+            error("Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / GEO / DDBJ or Synapse ids!")
+        }
+    }
+    return is_synapse
+}
+
+//
+// Check and validate parameters
+//
+def sraCheckENAMetadataFields() {
+    // Check minimal ENA fields are provided to download FastQ files
+    def valid_ena_metadata_fields = ['run_accession', 'experiment_accession', 'library_layout', 'fastq_ftp', 'fastq_md5']
+    def ena_metadata_fields = params.ena_metadata_fields ? params.ena_metadata_fields.split(',').collect{ it.trim().toLowerCase() } : valid_ena_metadata_fields
+    if (!ena_metadata_fields.containsAll(valid_ena_metadata_fields)) {
+        error("Invalid option: '${params.ena_metadata_fields}'. Minimally required fields for '--ena_metadata_fields': '${valid_ena_metadata_fields.join(',')}'")
+    }
+}
+
+//
+// Print a warning after pipeline has completed
+//
+def sraCurateSamplesheetWarn() {
+    log.warn "=============================================================================\n" +
+        "  Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" +
+        "  Public databases don't reliably hold information such as strandedness\n" +
+        "  information, controls etc\n\n" +
+        "  All of the sample metadata obtained from the ENA has been appended\n" +
+        "  as additional columns to help you manually curate the samplesheet before\n" +
+        "  running nf-core/other pipelines.\n" +
+        "==================================================================================="
+}
+
+//
+// Convert metadata obtained from the 'synapse show' command to a Groovy map
+//
+def synapseShowToMap(synapse_file) {
+    def meta = [:]
+    def category = ''
+    synapse_file.eachLine { line ->
+        def entries = [null, null]
+        if (!line.startsWith(' ') && !line.trim().isEmpty()) {
+            category = line.tokenize(':')[0]
+        } else {
+            entries = line.trim().tokenize('=')
+        }
+        meta["${category}|${entries[0]}"] = entries[1]
+    }
+    meta.id = meta['properties|id']
+    meta.name = meta['properties|name']
+    meta.md5 = meta['File|md5']
+    return meta.findAll{ it.value != null }
+}
+
+//
+// Print a warning after pipeline has completed
+//
+def synapseCurateSamplesheetWarn() {
+    log.warn "=============================================================================\n" +
+        "  Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" +
+        "  Where applicable, default values will be used for sample-specific metadata\n" +
+        "  such as strandedness, controls etc as this information is not provided\n" +
+        "  in a standardised manner when uploading data to Synapse.\n" +
+        "==================================================================================="
+}
+
+//
+// Obtain Sample ID from File Name
+//
+def synapseSampleNameFromFastQ(input_file, pattern) {
+
+    def sampleids = ""
+
+    def filePattern = pattern.toString()
+    int p = filePattern.lastIndexOf('/')
+        if( p != -1 )
+            filePattern = filePattern.substring(p+1)
+
+    input_file.each {
+        String fileName = input_file.getFileName().toString()
+
+        String indexOfWildcards = filePattern.findIndexOf { it=='*' || it=='?' }
+        String indexOfBrackets = filePattern.findIndexOf { it=='{' || it=='[' }
+        if( indexOfWildcards==-1 && indexOfBrackets==-1 ) {
+            if( fileName == filePattern )
+                return actual.getSimpleName()
+            throw new IllegalArgumentException("Not a valid file pair globbing pattern: pattern=$filePattern file=$fileName")
+        }
+
+        int groupCount = 0
+        for( int i=0; i<filePattern.size(); i++ ) {
+            def ch = filePattern[i]
+            if( ch=='?' || ch=='*' )
+                groupCount++
+            else if( ch=='{' || ch=='[' )
+                break
+        }
+
+        def regex = filePattern
+                .replace('.','\\.')
+                .replace('*','(.*)')
+                .replace('?','(.?)')
+                .replace('{','(?:')
+                .replace('}',')')
+                .replace(',','|')
+
+        def matcher = (fileName =~ /$regex/)
+        if( matcher.matches() ) {
+            int c=Math.min(groupCount, matcher.groupCount())
+            int end = c ? matcher.end(c) : ( indexOfBrackets != -1 ? indexOfBrackets : fileName.size() )
+            def prefix = fileName.substring(0,end)
+            while(prefix.endsWith('-') || prefix.endsWith('_') || prefix.endsWith('.') )
+                prefix=prefix[0..-2]
+            sampleids = prefix
+        }
+    }
+    return sampleids
+}
diff --git a/subworkflows/local/nf_core_pipeline_utils/main.nf b/subworkflows/local/nf_core_pipeline_utils/main.nf
new file mode 100644
index 00000000..18bf238b
--- /dev/null
+++ b/subworkflows/local/nf_core_pipeline_utils/main.nf
@@ -0,0 +1,308 @@
+//
+// Subworkflow with utility functions specific to the nf-core pipeline template
+//
+
+/*
+========================================================================================
+    SUBWORKFLOW DEFINITION
+========================================================================================
+*/
+
+workflow NF_CORE_PIPELINE_UTILS {
+
+    main:
+    checkConfigProvided()
+
+}
+
+/*
+========================================================================================
+    FUNCTIONS
+========================================================================================
+*/
+
+//
+//  Warn if a -profile or Nextflow config has not been provided to run the pipeline
+//
+def checkConfigProvided() {
+    if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
+        log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
+            "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
+            "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
+            "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
+            "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
+            "Please refer to the quick start section and usage docs for the pipeline.\n "
+    }
+}
+
+//
+// Citation string for pipeline
+//
+def workflowCitation() {
+    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
+        "* The pipeline\n" +
+        "  ${workflow.manifest.doi}\n\n" +
+        "* The nf-core framework\n" +
+        "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
+        "* Software dependencies\n" +
+        "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
+}
+
+//
+// nf-core logo
+//
+def nfCoreLogo(workflow_version) {
+    Map colors = logColours()
+    String.format(
+        """\n
+        ${dashedLine()}
+                                                ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
+        ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
+        ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
+        ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
+                                                ${colors.green}`._,._,\'${colors.reset}
+        ${colors.purple}  ${workflow.manifest.name} ${workflow_version}${colors.reset}
+        ${dashedLine()}
+        """.stripIndent()
+    )
+}
+
+//
+// Return dashed line
+//
+def dashedLine() {
+    Map colors = logColours()
+    return "-${colors.dim}----------------------------------------------------${colors.reset}-"
+}
+
+//
+// ANSII colours used for terminal logging
+//
+def logColours() {
+    Map colorcodes = [:]
+
+    // Reset / Meta
+    colorcodes['reset']      = params.monochrome_logs ? '' : "\033[0m"
+    colorcodes['bold']       = params.monochrome_logs ? '' : "\033[1m"
+    colorcodes['dim']        = params.monochrome_logs ? '' : "\033[2m"
+    colorcodes['underlined'] = params.monochrome_logs ? '' : "\033[4m"
+    colorcodes['blink']      = params.monochrome_logs ? '' : "\033[5m"
+    colorcodes['reverse']    = params.monochrome_logs ? '' : "\033[7m"
+    colorcodes['hidden']     = params.monochrome_logs ? '' : "\033[8m"
+
+    // Regular Colors
+    colorcodes['black']      = params.monochrome_logs ? '' : "\033[0;30m"
+    colorcodes['red']        = params.monochrome_logs ? '' : "\033[0;31m"
+    colorcodes['green']      = params.monochrome_logs ? '' : "\033[0;32m"
+    colorcodes['yellow']     = params.monochrome_logs ? '' : "\033[0;33m"
+    colorcodes['blue']       = params.monochrome_logs ? '' : "\033[0;34m"
+    colorcodes['purple']     = params.monochrome_logs ? '' : "\033[0;35m"
+    colorcodes['cyan']       = params.monochrome_logs ? '' : "\033[0;36m"
+    colorcodes['white']      = params.monochrome_logs ? '' : "\033[0;37m"
+
+    // Bold
+    colorcodes['bblack']     = params.monochrome_logs ? '' : "\033[1;30m"
+    colorcodes['bred']       = params.monochrome_logs ? '' : "\033[1;31m"
+    colorcodes['bgreen']     = params.monochrome_logs ? '' : "\033[1;32m"
+    colorcodes['byellow']    = params.monochrome_logs ? '' : "\033[1;33m"
+    colorcodes['bblue']      = params.monochrome_logs ? '' : "\033[1;34m"
+    colorcodes['bpurple']    = params.monochrome_logs ? '' : "\033[1;35m"
+    colorcodes['bcyan']      = params.monochrome_logs ? '' : "\033[1;36m"
+    colorcodes['bwhite']     = params.monochrome_logs ? '' : "\033[1;37m"
+
+    // Underline
+    colorcodes['ublack']     = params.monochrome_logs ? '' : "\033[4;30m"
+    colorcodes['ured']       = params.monochrome_logs ? '' : "\033[4;31m"
+    colorcodes['ugreen']     = params.monochrome_logs ? '' : "\033[4;32m"
+    colorcodes['uyellow']    = params.monochrome_logs ? '' : "\033[4;33m"
+    colorcodes['ublue']      = params.monochrome_logs ? '' : "\033[4;34m"
+    colorcodes['upurple']    = params.monochrome_logs ? '' : "\033[4;35m"
+    colorcodes['ucyan']      = params.monochrome_logs ? '' : "\033[4;36m"
+    colorcodes['uwhite']     = params.monochrome_logs ? '' : "\033[4;37m"
+
+    // High Intensity
+    colorcodes['iblack']     = params.monochrome_logs ? '' : "\033[0;90m"
+    colorcodes['ired']       = params.monochrome_logs ? '' : "\033[0;91m"
+    colorcodes['igreen']     = params.monochrome_logs ? '' : "\033[0;92m"
+    colorcodes['iyellow']    = params.monochrome_logs ? '' : "\033[0;93m"
+    colorcodes['iblue']      = params.monochrome_logs ? '' : "\033[0;94m"
+    colorcodes['ipurple']    = params.monochrome_logs ? '' : "\033[0;95m"
+    colorcodes['icyan']      = params.monochrome_logs ? '' : "\033[0;96m"
+    colorcodes['iwhite']     = params.monochrome_logs ? '' : "\033[0;97m"
+
+    // Bold High Intensity
+    colorcodes['biblack']    = params.monochrome_logs ? '' : "\033[1;90m"
+    colorcodes['bired']      = params.monochrome_logs ? '' : "\033[1;91m"
+    colorcodes['bigreen']    = params.monochrome_logs ? '' : "\033[1;92m"
+    colorcodes['biyellow']   = params.monochrome_logs ? '' : "\033[1;93m"
+    colorcodes['biblue']     = params.monochrome_logs ? '' : "\033[1;94m"
+    colorcodes['bipurple']   = params.monochrome_logs ? '' : "\033[1;95m"
+    colorcodes['bicyan']     = params.monochrome_logs ? '' : "\033[1;96m"
+    colorcodes['biwhite']    = params.monochrome_logs ? '' : "\033[1;97m"
+
+    return colorcodes
+}
+
+//
+// Construct and send completion email
+//
+def completionEmail(summary_params) {
+
+    // Set up the e-mail variables
+    def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
+    if (!workflow.success) {
+        subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
+    }
+
+    def summary = [:]
+    for (group in summary_params.keySet()) {
+        summary << summary_params[group]
+    }
+
+    def misc_fields = [:]
+    misc_fields['Date Started']              = workflow.start
+    misc_fields['Date Completed']            = workflow.complete
+    misc_fields['Pipeline script file path'] = workflow.scriptFile
+    misc_fields['Pipeline script hash ID']   = workflow.scriptId
+    if (workflow.repository) misc_fields['Pipeline repository Git URL']    = workflow.repository
+    if (workflow.commitId)   misc_fields['Pipeline repository Git Commit'] = workflow.commitId
+    if (workflow.revision)   misc_fields['Pipeline Git branch/tag']        = workflow.revision
+    misc_fields['Nextflow Version']           = workflow.nextflow.version
+    misc_fields['Nextflow Build']             = workflow.nextflow.build
+    misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
+
+    def email_fields = [:]
+    email_fields['version']      = NfcoreTemplate.version(workflow)
+    email_fields['runName']      = workflow.runName
+    email_fields['success']      = workflow.success
+    email_fields['dateComplete'] = workflow.complete
+    email_fields['duration']     = workflow.duration
+    email_fields['exitStatus']   = workflow.exitStatus
+    email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+    email_fields['errorReport']  = (workflow.errorReport ?: 'None')
+    email_fields['commandLine']  = workflow.commandLine
+    email_fields['projectDir']   = workflow.projectDir
+    email_fields['summary']      = summary << misc_fields
+
+    // Check if we are only sending emails on failure
+    def email_address = params.email
+    if (!params.email && params.email_on_fail && !workflow.success) {
+        email_address = params.email_on_fail
+    }
+
+    // Render the TXT template
+    def engine       = new groovy.text.GStringTemplateEngine()
+    def tf           = new File("${workflow.projectDir}/assets/email_template.txt")
+    def txt_template = engine.createTemplate(tf).make(email_fields)
+    def email_txt    = txt_template.toString()
+
+    // Render the HTML template
+    def hf            = new File("${workflow.projectDir}/assets/email_template.html")
+    def html_template = engine.createTemplate(hf).make(email_fields)
+    def email_html    = html_template.toString()
+
+    // Render the sendmail template
+    def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}" ]
+    def sf                     = new File("${workflow.projectDir}/assets/sendmail_template.txt")
+    def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
+    def sendmail_html          = sendmail_template.toString()
+
+    // Send the HTML e-mail
+    Map colors = logColours()
+    if (email_address) {
+        try {
+            if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+            // Try to send HTML e-mail using sendmail
+            [ 'sendmail', '-t' ].execute() << sendmail_html
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
+        } catch (all) {
+            // Catch failures and try with plaintext
+            def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
+            mail_cmd.execute() << email_html
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
+        }
+    }
+
+    // Write summary e-mail HTML to a file
+    def output_d = new File("${params.outdir}/pipeline_info/")
+    if (!output_d.exists()) {
+        output_d.mkdirs()
+    }
+    def output_hf = new File(output_d, "pipeline_report.html")
+    output_hf.withWriter { w -> w << email_html }
+    def output_tf = new File(output_d, "pipeline_report.txt")
+    output_tf.withWriter { w -> w << email_txt }
+}
+
+//
+// Print pipeline summary on completion
+//
+def completionSummary() {
+    Map colors = logColours()
+    if (workflow.success) {
+        if (workflow.stats.ignoredCount == 0) {
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
+        } else {
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
+        }
+    } else {
+        log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
+    }
+}
+
+//
+// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack
+//
+def imNotification(summary_params) {
+    def hook_url = params.hook_url
+
+    def summary = [:]
+    for (group in summary_params.keySet()) {
+        summary << summary_params[group]
+    }
+
+    def misc_fields = [:]
+    misc_fields['start']                                = workflow.start
+    misc_fields['complete']                             = workflow.complete
+    misc_fields['scriptfile']                           = workflow.scriptFile
+    misc_fields['scriptid']                             = workflow.scriptId
+    if (workflow.repository) misc_fields['repository']  = workflow.repository
+    if (workflow.commitId)   misc_fields['commitid']    = workflow.commitId
+    if (workflow.revision)   misc_fields['revision']    = workflow.revision
+    misc_fields['nxf_version']                          = workflow.nextflow.version
+    misc_fields['nxf_build']                            = workflow.nextflow.build
+    misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
+
+    def msg_fields = [:]
+    msg_fields['version']      = NfcoreTemplate.version(workflow)
+    msg_fields['runName']      = workflow.runName
+    msg_fields['success']      = workflow.success
+    msg_fields['dateComplete'] = workflow.complete
+    msg_fields['duration']     = workflow.duration
+    msg_fields['exitStatus']   = workflow.exitStatus
+    msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+    msg_fields['errorReport']  = (workflow.errorReport ?: 'None')
+    msg_fields['commandLine']  = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "")
+    msg_fields['projectDir']   = workflow.projectDir
+    msg_fields['summary']      = summary << misc_fields
+
+    // Render the JSON template
+    def engine       = new groovy.text.GStringTemplateEngine()
+    // Different JSON depending on the service provider
+    // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format
+    def json_path     = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json"
+    def hf            = new File("${workflow.projectDir}/assets/${json_path}")
+    def json_template = engine.createTemplate(hf).make(msg_fields)
+    def json_message  = json_template.toString()
+
+    // POST
+    def post = new URL(hook_url).openConnection();
+    post.setRequestMethod("POST")
+    post.setDoOutput(true)
+    post.setRequestProperty("Content-Type", "application/json")
+    post.getOutputStream().write(json_message.getBytes("UTF-8"));
+    def postRC = post.getResponseCode();
+    if (! postRC.equals(200)) {
+        log.warn(post.getErrorStream().getText());
+    }
+}
diff --git a/subworkflows/local/nf_validation_plugin_utils/main.nf b/subworkflows/local/nf_validation_plugin_utils/main.nf
new file mode 100644
index 00000000..be815a7f
--- /dev/null
+++ b/subworkflows/local/nf_validation_plugin_utils/main.nf
@@ -0,0 +1,52 @@
+//
+// Subworkflow that uses the nf-validation plugin to render help text and parameter summary
+//
+
+/*
+========================================================================================
+    IMPORT NF-VALIDATION PLUGIN
+========================================================================================
+*/
+
+include { paramsHelp; paramsSummaryLog; paramsSummaryMap; validateParameters } from 'plugin/nf-validation'
+
+/*
+========================================================================================
+    SUBWORKFLOW DEFINITION
+========================================================================================
+*/
+
+workflow NF_VALIDATION_PLUGIN_UTILS {
+
+    take:
+    print_help       // bool
+    workflow_command // string: default commmand used to run pipeline
+    pre_help_text    // string: string to be printed before help text and summary log
+    post_help_text   // string: string to be printed after help text and summary log
+    validate_params  // bool
+
+    main:
+
+    //
+    // Print help message if needed
+    //
+    if (print_help && workflow_command) {
+        log.info pre_help_text + paramsHelp(workflow_command) + post_help_text
+        System.exit(0)
+    }
+
+    //
+    // Print parameter summary to stdout
+    //
+    log.info pre_help_text + paramsSummaryLog(workflow) + post_help_text
+
+    //
+    // Validate parameters relative to the parameter JSON schema
+    //
+    if (validate_params){
+        validateParameters()
+    }
+
+    emit:
+    summary_params = paramsSummaryMap(workflow)
+}

From 2f68d1efa8bfb77b3d2a3088526e4971fb96a346 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 11 Oct 2023 12:26:26 +0100
Subject: [PATCH 534/852] Invoke imNotification in completion subworkflow

---
 main.nf                                           | 1 +
 subworkflows/local/nf_core_fetchngs_utils/main.nf | 7 ++++++-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 7794d1b9..6d3ea228 100644
--- a/main.nf
+++ b/main.nf
@@ -85,6 +85,7 @@ workflow {
         params.input_type,
         params.email,
         params.email_on_fail,
+        params.hook_url,
         PIPELINE_INITIALISATION.out.summary_params
     )
 }
diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf
index 129b2e3f..5cc2162b 100644
--- a/subworkflows/local/nf_core_fetchngs_utils/main.nf
+++ b/subworkflows/local/nf_core_fetchngs_utils/main.nf
@@ -11,7 +11,7 @@
 include { CUSTOM_DUMPSOFTWAREVERSIONS                 } from '../../../modules/nf-core/custom/dumpsoftwareversions'
 include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion } from '../nextflow_pipeline_utils'
 include { NF_VALIDATION_PLUGIN_UTILS                  } from '../nf_validation_plugin_utils'
-include { NF_CORE_PIPELINE_UTILS; workflowCitation; nfCoreLogo; dashedLine; completionEmail; completionSummary } from '../nf_core_pipeline_utils'
+include { NF_CORE_PIPELINE_UTILS; workflowCitation; nfCoreLogo; dashedLine; completionEmail; completionSummary; imNotification } from '../nf_core_pipeline_utils'
 
 /*
 ========================================================================================
@@ -96,6 +96,7 @@ workflow PIPELINE_COMPLETION {
     input_type     //  string: 'sra' or 'synapse'
     email          //  string: email address
     email_on_fail  //  string: email address sent on pipeline failure
+    hook_url       //  string: hook URL for notifications
     summary_params //     map: Groovy map of the parameters used in the pipeline
 
     main:
@@ -117,6 +118,10 @@ workflow PIPELINE_COMPLETION {
 
         completionSummary()
 
+        if (hook_url) {
+            imNotification(summary_params)
+        }
+
         if (input_type == 'sra') {
             sraCurateSamplesheetWarn()
         } else if (input_type == 'synapse') {

From d1e1bc67a12562bb86f01801cf15e06d61f64282 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 11 Oct 2023 16:16:36 +0200
Subject: [PATCH 535/852] EC lint

---
 main.nf               | 2 +-
 workflows/sra/main.nf | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/main.nf b/main.nf
index 6d3ea228..bf39d7ea 100644
--- a/main.nf
+++ b/main.nf
@@ -29,7 +29,7 @@ workflow NFCORE_FETCHNGS {
     ids // channel: database ids read in from --input
 
     main:
-    
+
     ch_versions = Channel.empty()
 
     //
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index a8f54646..ddac096d 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -96,7 +96,7 @@ workflow SRA {
         // Isolate FASTQ channel which will be added to emit block
         fastq_files
             .mix(SRA_FASTQ_FTP.out.fastq, FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads)
-            .map { 
+            .map {
                 meta, fastq ->
                     def reads = fastq instanceof List ? fastq.flatten() : [ fastq ]
                     def meta_clone = meta.clone()

From 770de1b7404b40a4f86f3198cbad0f9eff9ca6d8 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 11 Oct 2023 16:17:06 +0200
Subject: [PATCH 536/852] update nf-core modules

---
 .nf-core.yml                                  |   5 +
 modules.json                                  |   6 +-
 .../dumpsoftwareversions/tests/main.nf.test   |  38 ++++++
 .../tests/main.nf.test.snap                   |  27 +++++
 .../dumpsoftwareversions/tests/tags.yml       |   2 +
 .../sratools/fasterqdump/tests/main.nf.test   |  69 +++++++++++
 .../fasterqdump/tests/main.nf.test.snap       |  70 +++++++++++
 .../sratools/fasterqdump/tests/tags.yml       |   2 +
 .../sratools/prefetch/tests/main.nf.test      |  53 +++++++++
 .../sratools/prefetch/tests/main.nf.test.snap | 110 ++++++++++++++++++
 .../nf-core/sratools/prefetch/tests/tags.yml  |   2 +
 workflows/sra/tests/main.nf.test              |   6 +
 .../sra_custom_ena_metadata_fields.nf.test    |   6 +
 .../tests/sra_force_sratools_download.nf.test |   6 +
 .../sra_nf_core_pipeline_atacseq.nf.test      |   6 +
 .../tests/sra_nf_core_pipeline_rnaseq.nf.test |   6 +
 .../sra_nf_core_pipeline_taxprofiler.nf.test  |   6 +
 .../sra_nf_core_pipeline_viralrecon.nf.test   |   6 +
 .../sra/tests/sra_skip_fastq_download.nf.test |   6 +
 workflows/sra/tests/tags.yml                  |  40 -------
 20 files changed, 429 insertions(+), 43 deletions(-)
 create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
 create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml
 create mode 100644 modules/nf-core/sratools/fasterqdump/tests/main.nf.test
 create mode 100644 modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/sratools/fasterqdump/tests/tags.yml
 create mode 100644 modules/nf-core/sratools/prefetch/tests/main.nf.test
 create mode 100644 modules/nf-core/sratools/prefetch/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/sratools/prefetch/tests/tags.yml

diff --git a/.nf-core.yml b/.nf-core.yml
index bb27a4e9..0e89cae9 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -4,9 +4,14 @@ lint:
   files_exist:
     - .github/workflows/awsfulltest.yml
     - .github/workflows/awstest.yml
+    - assets/multiqc_config.yml
     - conf/igenomes.config
     - conf/modules.config
+    - lib/NfcoreTemplate.groovy
+    - lib/Utils.groovy
     - lib/WorkflowFetchngs.groovy
+    - lib/WorkflowMain.groovy
+    - lib/nfcore_external_java_deps.jar
   files_unchanged:
     - .gitattributes
     - .gitignore
diff --git a/modules.json b/modules.json
index 6dd402db..d629089b 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
+                        "git_sha": "1526dc37227a1101bdca25339337362e187a6b3b",
                         "installed_by": ["modules"]
                     },
                     "custom/sratoolsncbisettings": {
@@ -17,12 +17,12 @@
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "4d9951c6c9c4c19ea944bb73149caf9d3cb1f2fc",
+                        "git_sha": "b4d743f1bb8d92eb129a5925a9211beb689be625",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/prefetch": {
                         "branch": "master",
-                        "git_sha": "4d9951c6c9c4c19ea944bb73149caf9d3cb1f2fc",
+                        "git_sha": "096ea8a4db569cc680ada4105e1d313cc56329c8",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     }
                 }
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
new file mode 100644
index 00000000..73027efc
--- /dev/null
+++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
@@ -0,0 +1,38 @@
+nextflow_process {
+
+    name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS"
+    script "modules/nf-core/custom/dumpsoftwareversions/main.nf"
+    process "CUSTOM_DUMPSOFTWAREVERSIONS"
+    tag "custom"
+    tag "dumpsoftwareversions"
+    tag "custom/dumpsoftwareversions"
+    tag "modules_nfcore"
+
+    test("Should run without failures") {
+        setup {
+            run("FASTQC") {
+                script "modules/nf-core/fastqc/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([ [], file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = FASTQC.out.versions
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
new file mode 100644
index 00000000..7398cf5c
--- /dev/null
+++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
@@ -0,0 +1,27 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    "software_versions.yml:md5,252b721b2ad1475301c9d778c7ce8db2"
+                ],
+                "1": [
+                    "software_versions_mqc.yml:md5,70324befa5d37dd5317190017d53e6dd"
+                ],
+                "2": [
+                    "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3"
+                ],
+                "mqc_yml": [
+                    "software_versions_mqc.yml:md5,70324befa5d37dd5317190017d53e6dd"
+                ],
+                "versions": [
+                    "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3"
+                ],
+                "yml": [
+                    "software_versions.yml:md5,252b721b2ad1475301c9d778c7ce8db2"
+                ]
+            }
+        ],
+        "timestamp": "2023-10-11T15:13:35.246649"
+    }
+}
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml
new file mode 100644
index 00000000..405aa24a
--- /dev/null
+++ b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml
@@ -0,0 +1,2 @@
+custom/dumpsoftwareversions:
+  - modules/nf-core/custom/dumpsoftwareversions/**
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
new file mode 100644
index 00000000..7da3af20
--- /dev/null
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
@@ -0,0 +1,69 @@
+nextflow_process {
+    name "Test Process SRATOOLS_FASTERQDUMP"
+    script "modules/nf-core/sratools/fasterqdump/main.nf"
+    process "SRATOOLS_FASTERQDUMP"
+    tag "sratools/fasterqdump"
+    tag "modules_nfcore"
+
+    test("Single-end") {
+
+        setup {
+            run("UNTAR") {
+                script "modules/nf-core/untar/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([ [], file(params.test_data['sarscov2']['illumina']['SRR13255544_tar_gz'], checkIfExists: true) ])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = UNTAR.out.untar.collect{ meta, files -> files }.map{ files -> [ [ id:'test_single_end', single_end:true ], files]}
+                input[1] = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true)
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("Paired-end") {
+
+        setup {
+            run("UNTAR") {
+                script "modules/nf-core/untar/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([ [], file(params.test_data['sarscov2']['illumina']['SRR11140744_tar_gz'], checkIfExists: true) ])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = UNTAR.out.untar.collect{ meta, files -> files }.map{ files -> [ [ id:'test_paired_end', single_end:false ], files]}
+                input[1] = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true)
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
new file mode 100644
index 00000000..d3bf90f7
--- /dev/null
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
@@ -0,0 +1,70 @@
+{
+    "Single-end": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_single_end",
+                            "single_end": true
+                        },
+                        "test_single_end.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test_single_end",
+                            "single_end": true
+                        },
+                        "test_single_end.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
+                ]
+            }
+        ],
+        "timestamp": "2023-10-10T18:11:12.87053"
+    },
+    "Paired-end": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_paired_end",
+                            "single_end": false
+                        },
+                        [
+                            "test_paired_end_1.fastq.gz:md5,193809c784a4ea132ab2a253fa4f55b6",
+                            "test_paired_end_2.fastq.gz:md5,3e3b3af3413f50a1685fd7b3f1456d4e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test_paired_end",
+                            "single_end": false
+                        },
+                        [
+                            "test_paired_end_1.fastq.gz:md5,193809c784a4ea132ab2a253fa4f55b6",
+                            "test_paired_end_2.fastq.gz:md5,3e3b3af3413f50a1685fd7b3f1456d4e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
+                ]
+            }
+        ],
+        "timestamp": "2023-10-10T18:11:50.928006"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/sratools/fasterqdump/tests/tags.yml b/modules/nf-core/sratools/fasterqdump/tests/tags.yml
new file mode 100644
index 00000000..5d1ddcb3
--- /dev/null
+++ b/modules/nf-core/sratools/fasterqdump/tests/tags.yml
@@ -0,0 +1,2 @@
+sratools/fasterqdump:
+  - modules/nf-core/sratools/fasterqdump/**
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test
new file mode 100644
index 00000000..1234a82b
--- /dev/null
+++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test
@@ -0,0 +1,53 @@
+nextflow_process {
+    name "Test Process SRATOOLS_PREFETCH"
+    script "modules/nf-core/sratools/prefetch/main.nf"
+    process "SRATOOLS_PREFETCH"
+    tag "sratools/prefetch"
+    tag "modules_nfcore"
+
+    test("sratools/prefetch") {
+
+        when {
+            params {
+                outdir = "output"
+            }
+            process {
+                """
+                input[0] = Channel.of([ [ id:'test', single_end:false ], 'DRR000774' ])
+                input[1] = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true)
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+            { assert snapshot(process).match() }
+            )
+        }
+    }
+
+    test("sratools/prefetch with sralite") {
+
+        when {
+            params {
+                outdir = "output"
+            }
+            process {
+                """
+                input[0] = Channel.of([ [ id:'test', single_end:false ], 'SRR1170046' ])
+                input[1] = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true)
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+            { assert snapshot(process).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap
new file mode 100644
index 00000000..95ea067f
--- /dev/null
+++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap
@@ -0,0 +1,110 @@
+{
+    "sratools/prefetch with sralite": {
+        "content": [
+            {
+                "stderr": [
+                    
+                ],
+                "errorReport": null,
+                "exitStatus": 0,
+                "out": {
+                    "0": [
+                        [
+                            {
+                                "id": "test",
+                                "single_end": false
+                            },
+                            [
+                                "SRR1170046.sralite:md5,7acfce556ca0951aff49d780899c105b"
+                            ]
+                        ]
+                    ],
+                    "1": [
+                        "versions.yml:md5,c967dea4135cb75490e1e801c4639efc"
+                    ],
+                    "sra": [
+                        [
+                            {
+                                "id": "test",
+                                "single_end": false
+                            },
+                            [
+                                "SRR1170046.sralite:md5,7acfce556ca0951aff49d780899c105b"
+                            ]
+                        ]
+                    ],
+                    "versions": [
+                        "versions.yml:md5,c967dea4135cb75490e1e801c4639efc"
+                    ]
+                },
+                "failed": false,
+                "stdout": [
+                    
+                ],
+                "errorMessage": null,
+                "trace": {
+                    "tasksFailed": 0,
+                    "tasksCount": 1,
+                    "tasksSucceeded": 1
+                },
+                "name": "SRATOOLS_PREFETCH",
+                "success": true
+            }
+        ],
+        "timestamp": "2023-10-10T15:26:45.715617"
+    },
+    "sratools/prefetch": {
+        "content": [
+            {
+                "stderr": [
+                    
+                ],
+                "errorReport": null,
+                "exitStatus": 0,
+                "out": {
+                    "0": [
+                        [
+                            {
+                                "id": "test",
+                                "single_end": false
+                            },
+                            [
+                                "DRR000774.sra:md5,7647dba20c89c0e3d7ad13842f060eb0"
+                            ]
+                        ]
+                    ],
+                    "1": [
+                        "versions.yml:md5,c967dea4135cb75490e1e801c4639efc"
+                    ],
+                    "sra": [
+                        [
+                            {
+                                "id": "test",
+                                "single_end": false
+                            },
+                            [
+                                "DRR000774.sra:md5,7647dba20c89c0e3d7ad13842f060eb0"
+                            ]
+                        ]
+                    ],
+                    "versions": [
+                        "versions.yml:md5,c967dea4135cb75490e1e801c4639efc"
+                    ]
+                },
+                "failed": false,
+                "stdout": [
+                    
+                ],
+                "errorMessage": null,
+                "trace": {
+                    "tasksFailed": 0,
+                    "tasksCount": 1,
+                    "tasksSucceeded": 1
+                },
+                "name": "SRATOOLS_PREFETCH",
+                "success": true
+            }
+        ],
+        "timestamp": "2023-10-10T09:58:01.781848"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/sratools/prefetch/tests/tags.yml b/modules/nf-core/sratools/prefetch/tests/tags.yml
new file mode 100644
index 00000000..52110bfd
--- /dev/null
+++ b/modules/nf-core/sratools/prefetch/tests/tags.yml
@@ -0,0 +1,2 @@
+sratools/prefetch:
+  - modules/nf-core/sratools/prefetch/**
diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index b525bec5..dcf67105 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -3,6 +3,12 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "workflows/sra/main.nf"
     workflow "SRA"
+    tag "multiqc_mappings_config"
+    tag "sra_fastq_ftp"
+    tag "sra_ids_to_runinfo"
+    tag "sra_merge_samplesheet"
+    tag "sra_runinfo_to_ftp"
+    tag "sra_to_samplesheet"
     tag "workflows"
     tag "workflows_sra"
     tag "sra_default_parameters"
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index 7c9df9d9..04a60471 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -3,6 +3,12 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "workflows/sra/main.nf"
     workflow "SRA"
+    tag "multiqc_mappings_config"
+    tag "sra_fastq_ftp"
+    tag "sra_ids_to_runinfo"
+    tag "sra_merge_samplesheet"
+    tag "sra_runinfo_to_ftp"
+    tag "sra_to_samplesheet"
     tag "workflows"
     tag "workflows_sra"
     tag "sra_custom_ena_metadata_fields"
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index 2548689d..c669af8d 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -3,6 +3,12 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "workflows/sra/main.nf"
     workflow "SRA"
+    tag "multiqc_mappings_config"
+    tag "sra_fastq_ftp"
+    tag "sra_ids_to_runinfo"
+    tag "sra_merge_samplesheet"
+    tag "sra_runinfo_to_ftp"
+    tag "sra_to_samplesheet"
     tag "workflows"
     tag "workflows_sra"
     tag "sra_force_sratools_download"
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index ad60725c..e88e5f63 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -3,6 +3,12 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "workflows/sra/main.nf"
     workflow "SRA"
+    tag "multiqc_mappings_config"
+    tag "sra_fastq_ftp"
+    tag "sra_ids_to_runinfo"
+    tag "sra_merge_samplesheet"
+    tag "sra_runinfo_to_ftp"
+    tag "sra_to_samplesheet"
     tag "workflows"
     tag "workflows_sra"
     tag "sra_nf_core_pipeline_atacseq"
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index 993590ff..63c871ca 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -3,6 +3,12 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "workflows/sra/main.nf"
     workflow "SRA"
+    tag "multiqc_mappings_config"
+    tag "sra_fastq_ftp"
+    tag "sra_ids_to_runinfo"
+    tag "sra_merge_samplesheet"
+    tag "sra_runinfo_to_ftp"
+    tag "sra_to_samplesheet"
     tag "workflows"
     tag "workflows_sra"
     tag "sra_nf_core_pipeline_rnaseq"
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index a5e69da1..15a31848 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -3,6 +3,12 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "workflows/sra/main.nf"
     workflow "SRA"
+    tag "multiqc_mappings_config"
+    tag "sra_fastq_ftp"
+    tag "sra_ids_to_runinfo"
+    tag "sra_merge_samplesheet"
+    tag "sra_runinfo_to_ftp"
+    tag "sra_to_samplesheet"
     tag "workflows"
     tag "workflows_sra"
     tag "sra_nf_core_pipeline_taxprofiler"
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index f64cf92e..4c11d571 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -3,6 +3,12 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "workflows/sra/main.nf"
     workflow "SRA"
+    tag "multiqc_mappings_config"
+    tag "sra_fastq_ftp"
+    tag "sra_ids_to_runinfo"
+    tag "sra_merge_samplesheet"
+    tag "sra_runinfo_to_ftp"
+    tag "sra_to_samplesheet"
     tag "workflows"
     tag "workflows_sra"
     tag "sra_nf_core_pipeline_viralrecon"
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index aa290c68..8cb68641 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -3,6 +3,12 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "workflows/sra/main.nf"
     workflow "SRA"
+    tag "multiqc_mappings_config"
+    tag "sra_fastq_ftp"
+    tag "sra_ids_to_runinfo"
+    tag "sra_merge_samplesheet"
+    tag "sra_runinfo_to_ftp"
+    tag "sra_to_samplesheet"
     tag "workflows"
     tag "workflows_sra"
     tag "sra_skip_fastq_download"
diff --git a/workflows/sra/tests/tags.yml b/workflows/sra/tests/tags.yml
index 52c3e591..ae41e37d 100644
--- a/workflows/sra/tests/tags.yml
+++ b/workflows/sra/tests/tags.yml
@@ -1,56 +1,16 @@
 sra_custom_ena_metadata_fields:
-  - modules/local/sra_ids_to_runinfo/**
-  - modules/local/sra_runinfo_to_ftp/**
-  - modules/local/sra_fastq_ftp/**
-  - modules/local/sra_to_samplesheet/**
-  - modules/local/sra_merge_samplesheet/**
   - workflows/sra/**
 sra_default_parameters:
-  - modules/local/sra_ids_to_runinfo/**
-  - modules/local/sra_runinfo_to_ftp/**
-  - modules/local/sra_fastq_ftp/**
-  - modules/local/sra_to_samplesheet/**
-  - modules/local/sra_merge_samplesheet/**
   - workflows/sra/**
 sra_force_sratools_download:
-  - modules/local/sra_ids_to_runinfo/**
-  - modules/local/sra_runinfo_to_ftp/**
-  - modules/local/sra_fastq_ftp/**
-  - modules/local/sra_to_samplesheet/**
-  - modules/local/sra_merge_samplesheet/**
   - workflows/sra/**
 sra_nf_core_pipeline_atacseq:
-  - modules/local/sra_ids_to_runinfo/**
-  - modules/local/sra_runinfo_to_ftp/**
-  - modules/local/sra_fastq_ftp/**
-  - modules/local/sra_to_samplesheet/**
-  - modules/local/sra_merge_samplesheet/**
   - workflows/sra/**
 sra_nf_core_pipeline_rnaseq:
-  - modules/local/sra_ids_to_runinfo/**
-  - modules/local/sra_runinfo_to_ftp/**
-  - modules/local/sra_fastq_ftp/**
-  - modules/local/sra_to_samplesheet/**
-  - modules/local/sra_merge_samplesheet/**
   - workflows/sra/**
 sra_nf_core_pipeline_taxprofiler:
-  - modules/local/sra_ids_to_runinfo/**
-  - modules/local/sra_runinfo_to_ftp/**
-  - modules/local/sra_fastq_ftp/**
-  - modules/local/sra_to_samplesheet/**
-  - modules/local/sra_merge_samplesheet/**
   - workflows/sra/**
 sra_nf_core_pipeline_viralrecon:
-  - modules/local/sra_ids_to_runinfo/**
-  - modules/local/sra_runinfo_to_ftp/**
-  - modules/local/sra_fastq_ftp/**
-  - modules/local/sra_to_samplesheet/**
-  - modules/local/sra_merge_samplesheet/**
   - workflows/sra/**
 sra_skip_fastq_download:
-  - modules/local/sra_ids_to_runinfo/**
-  - modules/local/sra_runinfo_to_ftp/**
-  - modules/local/sra_fastq_ftp/**
-  - modules/local/sra_to_samplesheet/**
-  - modules/local/sra_merge_samplesheet/**
   - workflows/sra/**

From 6002c61f880b28bfcb817d9833854a141713d595 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 11 Oct 2023 16:20:27 +0200
Subject: [PATCH 537/852] update nf-test version

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 436b61a5..70f7f815 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -15,7 +15,7 @@ on:
 
 env:
   NXF_ANSI_LOG: false
-  NFTEST_VER: "0.8.0"
+  NFTEST_VER: "0.8.1"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"

From f85e0321d27fa8e759a19ed39d9347883bd2feab Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 12 Oct 2023 11:04:40 +0100
Subject: [PATCH 538/852] Use relative paths for main script location for
 nf-test

---
 modules/local/multiqc_mappings_config/tests/main.nf.test     | 2 +-
 modules/local/sra_fastq_ftp/tests/main.nf.test               | 2 +-
 modules/local/sra_ids_to_runinfo/tests/main.nf.test          | 2 +-
 modules/local/sra_merge_samplesheet/tests/main.nf.test       | 2 +-
 modules/local/sra_runinfo_to_ftp/tests/main.nf.test          | 2 +-
 modules/local/sra_to_samplesheet/tests/main.nf.test          | 2 +-
 workflows/sra/tests/main.nf.test                             | 2 +-
 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test   | 2 +-
 workflows/sra/tests/sra_force_sratools_download.nf.test      | 2 +-
 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test     | 2 +-
 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test      | 2 +-
 workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test | 2 +-
 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test  | 2 +-
 workflows/sra/tests/sra_skip_fastq_download.nf.test          | 2 +-
 14 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test
index 3bf79537..75356197 100644
--- a/modules/local/multiqc_mappings_config/tests/main.nf.test
+++ b/modules/local/multiqc_mappings_config/tests/main.nf.test
@@ -1,7 +1,7 @@
 nextflow_process {
 
     name "Test process: MULTIQC_MAPPINGS_CONFIG"
-    script "modules/local/multiqc_mappings_config/main.nf"
+    script "../main.nf"
     process "MULTIQC_MAPPINGS_CONFIG"
     tag "modules"
     tag "modules_local"
diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test
index 7892d156..ab846e5d 100644
--- a/modules/local/sra_fastq_ftp/tests/main.nf.test
+++ b/modules/local/sra_fastq_ftp/tests/main.nf.test
@@ -1,7 +1,7 @@
 nextflow_process {
 
     name "Test process: SRA_FASTQ_FTP"
-    script "modules/local/sra_fastq_ftp/main.nf"
+    script "../main.nf"
     process "SRA_FASTQ_FTP"
     tag "modules"
     tag "modules_local"
diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test
index f8a44086..087f9069 100644
--- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test
+++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test
@@ -1,7 +1,7 @@
 nextflow_process {
 
     name "Test process: SRA_IDS_TO_RUNINFO"
-    script "modules/local/sra_ids_to_runinfo/main.nf"
+    script "../main.nf"
     process "SRA_IDS_TO_RUNINFO"
     tag "modules"
     tag "modules_local"
diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test b/modules/local/sra_merge_samplesheet/tests/main.nf.test
index e37039bd..b7c98622 100644
--- a/modules/local/sra_merge_samplesheet/tests/main.nf.test
+++ b/modules/local/sra_merge_samplesheet/tests/main.nf.test
@@ -1,7 +1,7 @@
 nextflow_process {
 
     name "Test process: SRA_MERGE_SAMPLESHEET"
-    script "modules/local/sra_merge_samplesheet/main.nf"
+    script "../main.nf"
     process "SRA_MERGE_SAMPLESHEET"
     tag "modules"
     tag "modules_local"
diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
index 1558ff39..3b1405f9 100644
--- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
+++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
@@ -1,7 +1,7 @@
 nextflow_process {
 
     name "Test process: SRA_RUNINFO_TO_FTP"
-    script "modules/local/sra_runinfo_to_ftp/main.nf"
+    script "../main.nf"
     process "SRA_RUNINFO_TO_FTP"
     tag "modules"
     tag "modules_local"
diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test
index b2ec5b11..6094717b 100644
--- a/modules/local/sra_to_samplesheet/tests/main.nf.test
+++ b/modules/local/sra_to_samplesheet/tests/main.nf.test
@@ -1,7 +1,7 @@
 nextflow_process {
 
     name "Test process: SRA_TO_SAMPLESHEET"
-    script "modules/local/sra_to_samplesheet/main.nf"
+    script "../main.nf"
     process "SRA_TO_SAMPLESHEET"
     tag "modules"
     tag "modules_local"
diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index dcf67105..6b459773 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -1,7 +1,7 @@
 nextflow_workflow {
 
     name "Test workflow: sra/main.nf"
-    script "workflows/sra/main.nf"
+    script "../main.nf"
     workflow "SRA"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index 04a60471..0d0b85df 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -1,7 +1,7 @@
 nextflow_workflow {
 
     name "Test workflow: sra/main.nf"
-    script "workflows/sra/main.nf"
+    script "../main.nf"
     workflow "SRA"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index c669af8d..5cd54142 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -1,7 +1,7 @@
 nextflow_workflow {
 
     name "Test workflow: sra/main.nf"
-    script "workflows/sra/main.nf"
+    script "../main.nf"
     workflow "SRA"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index e88e5f63..ef069674 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -1,7 +1,7 @@
 nextflow_workflow {
 
     name "Test workflow: sra/main.nf"
-    script "workflows/sra/main.nf"
+    script "../main.nf"
     workflow "SRA"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index 63c871ca..4eb57027 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -1,7 +1,7 @@
 nextflow_workflow {
 
     name "Test workflow: sra/main.nf"
-    script "workflows/sra/main.nf"
+    script "../main.nf"
     workflow "SRA"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index 15a31848..019c9af8 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -1,7 +1,7 @@
 nextflow_workflow {
 
     name "Test workflow: sra/main.nf"
-    script "workflows/sra/main.nf"
+    script "../main.nf"
     workflow "SRA"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index 4c11d571..dce26b16 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -1,7 +1,7 @@
 nextflow_workflow {
 
     name "Test workflow: sra/main.nf"
-    script "workflows/sra/main.nf"
+    script "../main.nf"
     workflow "SRA"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index 8cb68641..142e8aff 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -1,7 +1,7 @@
 nextflow_workflow {
 
     name "Test workflow: sra/main.nf"
-    script "workflows/sra/main.nf"
+    script "../main.nf"
     workflow "SRA"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"

From 3776119a8717fc723bd60188124f9a92943713fa Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 12 Oct 2023 11:05:06 +0100
Subject: [PATCH 539/852] Remove nf-test branch from ci.yml

---
 .github/workflows/ci.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 70f7f815..ef127625 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -11,7 +11,6 @@ on:
       - master
       - dev
       - refactor
-      - nf-test
 
 env:
   NXF_ANSI_LOG: false

From c44000154a7232911c081fa1511639c1ce635dc0 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 12 Oct 2023 11:14:23 +0100
Subject: [PATCH 540/852] Update CHANGELOG and author contributions

---
 CHANGELOG.md | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c500efcc..9264eb59 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,25 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unpublished Version / DEV]
 
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Adam Talbot](https://github.com/adamrtalbot)
+- [Edmund Miller](https://github.com/Emiller88)
+- [Esha Joshi](https://github.com/ejseqera)
+- [Harshil Patel](https://github.com/drpatelh)
+- [James Fellows Yates](https://github.com/jfy133)
+- [Maxime Garcia](https://github.com/maxulysse)
+- [Rob Syme](https://github.com/robsyme)
+- [Sateesh Peri](https://github.com/sateeshperi)
+
+Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
+
+### Enhancements & fixes
+
+- [PR #XXX](https://github.com/nf-core/fetchngs/pull/XXX) - Use nf-test for all pipeline testing
+
 ### Enhancements & fixes
 
 ## [[1.10.1](https://github.com/nf-core/fetchngs/releases/tag/1.10.1)] - 2023-10-08
@@ -14,8 +33,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 Special thanks to the following for their contributions to the release:
 
 - [Adam Talbot](https://github.com/adamrtalbot)
+- [Davide Carlson](https://github.com/davidecarlson)
 - [Harshil Patel](https://github.com/drpatelh)
 - [Maxime Garcia](https://github.com/maxulysse)
+- [MCMandR](https://github.com/MCMandR)
 - [Rob Syme](https://github.com/robsyme)
 
 Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.

From 46f258fd879870aae381e9db9e6a14e443ad3ef7 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 12 Oct 2023 11:17:42 +0100
Subject: [PATCH 541/852] Add nf-test citation

---
 CITATIONS.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/CITATIONS.md b/CITATIONS.md
index 570e7e5b..482d5600 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -37,7 +37,7 @@
 - [Synapse](https://pubmed.ncbi.nlm.nih.gov/24071850/)
   > Omberg L, Ellrott K, Yuan Y, Kandoth C, Wong C, Kellen MR, Friend SH, Stuart J, Liang H, Margolin AA. Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas. Nat Genet. 2013 Oct;45(10):1121-6. doi: 10.1038/ng.2761. PMID: 24071850; PMCID: PMC3950337.
 
-## Software packaging/containerisation tools
+## Software packaging/containerisation/testing tools
 
 - [Anaconda](https://anaconda.com)
 
@@ -55,6 +55,8 @@
 
   > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
 
+- [nf-test](https://code.askimed.com/nf-test)
+
 - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
 
   > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

From 025f0ae6bb4807a6c5a688e211845fe6149ee76f Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 12 Oct 2023 12:26:38 +0200
Subject: [PATCH 542/852] update custom/dumpsoftwareversions

---
 modules.json                                  |  2 +-
 .../dumpsoftwareversions/tests/main.nf.test   | 23 +++++++++----------
 .../tests/main.nf.test.snap                   | 10 ++++----
 3 files changed, 17 insertions(+), 18 deletions(-)

diff --git a/modules.json b/modules.json
index d629089b..87e40abf 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "1526dc37227a1101bdca25339337362e187a6b3b",
+                        "git_sha": "1b372269755a5c4a13c23bc130ebada8cb9d4cd0",
                         "installed_by": ["modules"]
                     },
                     "custom/sratoolsncbisettings": {
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
index 73027efc..d528d3cb 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
+++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
@@ -9,21 +9,20 @@ nextflow_process {
     tag "modules_nfcore"
 
     test("Should run without failures") {
-        setup {
-            run("FASTQC") {
-                script "modules/nf-core/fastqc/main.nf"
-                process {
-                    """
-                    input[0] = Channel.of([ [], file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ])
-                    """
-                }
-            }
-        }
-
         when {
             process {
                 """
-                input[0] = FASTQC.out.versions
+                def tool1_version = '''
+                TOOL1:
+                    tool1: 0.11.9
+                '''.stripIndent()
+
+                def tool2_version = '''
+                TOOL2:
+                    tool2: 1.9
+                '''.stripIndent()
+
+                input[0] = Channel.of(tool1_version, tool2_version).collectFile()
                 """
             }
         }
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
index 7398cf5c..8713b921 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
+++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
@@ -3,25 +3,25 @@
         "content": [
             {
                 "0": [
-                    "software_versions.yml:md5,252b721b2ad1475301c9d778c7ce8db2"
+                    "software_versions.yml:md5,a027f820f30b8191a20ca16465daaf37"
                 ],
                 "1": [
-                    "software_versions_mqc.yml:md5,70324befa5d37dd5317190017d53e6dd"
+                    "software_versions_mqc.yml:md5,ee4a1d028ad29987f9ac511f4668f17c"
                 ],
                 "2": [
                     "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3"
                 ],
                 "mqc_yml": [
-                    "software_versions_mqc.yml:md5,70324befa5d37dd5317190017d53e6dd"
+                    "software_versions_mqc.yml:md5,ee4a1d028ad29987f9ac511f4668f17c"
                 ],
                 "versions": [
                     "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3"
                 ],
                 "yml": [
-                    "software_versions.yml:md5,252b721b2ad1475301c9d778c7ce8db2"
+                    "software_versions.yml:md5,a027f820f30b8191a20ca16465daaf37"
                 ]
             }
         ],
-        "timestamp": "2023-10-11T15:13:35.246649"
+        "timestamp": "2023-10-11T17:10:02.930699"
     }
 }

From f65a861e36aa2238295219572480f64bc1249554 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 12 Oct 2023 11:38:23 +0100
Subject: [PATCH 543/852] Remove workflows/nextflow.config

---
 nextflow.config           | 17 ++++++++++-------
 workflows/nextflow.config | 12 ------------
 2 files changed, 10 insertions(+), 19 deletions(-)
 delete mode 100644 workflows/nextflow.config

diff --git a/nextflow.config b/nextflow.config
index 5ad350c9..3589e118 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -65,6 +65,16 @@ try {
     System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
 }
 
+// Module specific configs
+includeConfig './modules/nf-core/custom/dumpsoftwareversions/nextflow.config'
+
+// Workflow specific configs
+if (params.input_type == 'sra') {
+    includeConfig './workflows/sra/nextflow.config'
+} else if (params.input_type == 'synapse') {
+    includeConfig './workflows/synapse/nextflow.config'
+}
+
 // Load nf-core/fetchngs custom profiles from different institutions.
 // Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
 // try {
@@ -227,13 +237,6 @@ manifest {
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
 
-// Module specific configs
-// Currently just dumpsoftwareversions
-includeConfig 'modules/nf-core/custom/dumpsoftwareversions/nextflow.config'
-
-// Workflow specific configs
-includeConfig 'workflows/nextflow.config'
-
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit
 def check_max(obj, type) {
diff --git a/workflows/nextflow.config b/workflows/nextflow.config
deleted file mode 100644
index d27deb3a..00000000
--- a/workflows/nextflow.config
+++ /dev/null
@@ -1,12 +0,0 @@
-// Read in specific config relating to workflow.
-
-switch ( params.input_type ) {
-    case "sra":
-        includeConfig './sra/nextflow.config'
-        break
-    case "synapse":
-        includeConfig './synapse/nextflow.config'
-        break
-    default:
-        break
-}
\ No newline at end of file

From 67f05771f286f141e15d628d39aede3c08087a59 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 12 Oct 2023 15:45:39 +0200
Subject: [PATCH 544/852] same install

---
 .github/workflows/ci.yml | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 70f7f815..16f6e1c8 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -76,9 +76,19 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      - name: Cache nf-test installation
+        id: cache-software
+        uses: actions/cache@v3
+        with:
+          path: |
+            /usr/local/bin/nf-test
+            /home/runner/.nf-test/nf-test.jar
+          key: ${{ runner.os }}-${{ env.NF_TEST_VER }}-nftest
+
       - name: Install nf-test
+        if: steps.cache-software.outputs.cache-hit != 'true'
         run: |
-          wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
+          wget -qO- https://code.askimed.com/install/nf-test | bash
           sudo mv nf-test /usr/local/bin/
 
       - name: Run nf-test

From 92e75880697e99fed3df6e1290380c268683e409 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 12 Oct 2023 15:47:54 +0200
Subject: [PATCH 545/852] fix env

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 16f6e1c8..2dd4d4e7 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -83,7 +83,7 @@ jobs:
           path: |
             /usr/local/bin/nf-test
             /home/runner/.nf-test/nf-test.jar
-          key: ${{ runner.os }}-${{ env.NF_TEST_VER }}-nftest
+          key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest
 
       - name: Install nf-test
         if: steps.cache-software.outputs.cache-hit != 'true'

From 803c473e82be0b7f9d46749aee603f2347c528e8 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 12 Oct 2023 18:43:49 +0100
Subject: [PATCH 546/852] Add nf-test authors to credits for release

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9264eb59..9fbb2013 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,10 +13,12 @@ Special thanks to the following for their contributions to the release:
 - [Edmund Miller](https://github.com/Emiller88)
 - [Esha Joshi](https://github.com/ejseqera)
 - [Harshil Patel](https://github.com/drpatelh)
+- [Lukas Forer](https://github.com/lukfor)
 - [James Fellows Yates](https://github.com/jfy133)
 - [Maxime Garcia](https://github.com/maxulysse)
 - [Rob Syme](https://github.com/robsyme)
 - [Sateesh Peri](https://github.com/sateeshperi)
+- [Sebastian Schönherr](https://github.com/seppinho)
 
 Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
 

From 9eebe984d5cf799a5c9361a84f1cad71fc7f4354 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 13 Oct 2023 09:43:49 +0100
Subject: [PATCH 547/852] Re-order tags in workflow nf-test files

---
 workflows/sra/tests/main.nf.test                             | 4 ++--
 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test   | 4 ++--
 workflows/sra/tests/sra_force_sratools_download.nf.test      | 4 ++--
 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test     | 4 ++--
 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test      | 4 ++--
 workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test | 4 ++--
 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test  | 4 ++--
 workflows/sra/tests/sra_skip_fastq_download.nf.test          | 4 ++--
 8 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 6b459773..1595f94d 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -3,14 +3,14 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
     tag "sra_ids_to_runinfo"
     tag "sra_merge_samplesheet"
     tag "sra_runinfo_to_ftp"
     tag "sra_to_samplesheet"
-    tag "workflows"
-    tag "workflows_sra"
     tag "sra_default_parameters"
 
     test("Parameters: default") {
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index 0d0b85df..ca3d5bd0 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -3,14 +3,14 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
     tag "sra_ids_to_runinfo"
     tag "sra_merge_samplesheet"
     tag "sra_runinfo_to_ftp"
     tag "sra_to_samplesheet"
-    tag "workflows"
-    tag "workflows_sra"
     tag "sra_custom_ena_metadata_fields"
 
     test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") {
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index 5cd54142..f8f6ff5c 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -3,14 +3,14 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
     tag "sra_ids_to_runinfo"
     tag "sra_merge_samplesheet"
     tag "sra_runinfo_to_ftp"
     tag "sra_to_samplesheet"
-    tag "workflows"
-    tag "workflows_sra"
     tag "sra_force_sratools_download"
 
     test("Parameters: --force_sratools_download") {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index ef069674..5a854533 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -3,14 +3,14 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
     tag "sra_ids_to_runinfo"
     tag "sra_merge_samplesheet"
     tag "sra_runinfo_to_ftp"
     tag "sra_to_samplesheet"
-    tag "workflows"
-    tag "workflows_sra"
     tag "sra_nf_core_pipeline_atacseq"
 
     test("Parameters: --nf_core_pipeline atacseq") {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index 4eb57027..aeb06857 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -3,14 +3,14 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
     tag "sra_ids_to_runinfo"
     tag "sra_merge_samplesheet"
     tag "sra_runinfo_to_ftp"
     tag "sra_to_samplesheet"
-    tag "workflows"
-    tag "workflows_sra"
     tag "sra_nf_core_pipeline_rnaseq"
 
     test("Parameters: --nf_core_pipeline rnaseq") {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index 019c9af8..c460ffbd 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -3,14 +3,14 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
     tag "sra_ids_to_runinfo"
     tag "sra_merge_samplesheet"
     tag "sra_runinfo_to_ftp"
     tag "sra_to_samplesheet"
-    tag "workflows"
-    tag "workflows_sra"
     tag "sra_nf_core_pipeline_taxprofiler"
 
     test("Parameters: --nf_core_pipeline taxprofiler") {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index dce26b16..f90d8958 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -3,14 +3,14 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
     tag "sra_ids_to_runinfo"
     tag "sra_merge_samplesheet"
     tag "sra_runinfo_to_ftp"
     tag "sra_to_samplesheet"
-    tag "workflows"
-    tag "workflows_sra"
     tag "sra_nf_core_pipeline_viralrecon"
 
     test("Parameters: --nf_core_pipeline viralrecon") {
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index 142e8aff..8d21a3d9 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -3,14 +3,14 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
     tag "sra_ids_to_runinfo"
     tag "sra_merge_samplesheet"
     tag "sra_runinfo_to_ftp"
     tag "sra_to_samplesheet"
-    tag "workflows"
-    tag "workflows_sra"
     tag "sra_skip_fastq_download"
 
     test("Parameters: --skip_fastq_download") {

From f06790c3dec3eb4a8aea62b3290361ffae33375b Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 13 Oct 2023 10:45:36 +0200
Subject: [PATCH 548/852] add pipeline level tests

---
 conf/test.config       |  2 +-
 tests/main.nf.test     | 27 +++++++++++++++++++++++++++
 tests/sra_ids_test.csv |  7 +++++++
 3 files changed, 35 insertions(+), 1 deletion(-)
 create mode 100644 tests/main.nf.test
 create mode 100644 tests/sra_ids_test.csv

diff --git a/conf/test.config b/conf/test.config
index cb77f578..67291b47 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -20,7 +20,7 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv'
+    input  = 'tests/sra_ids_test.csv'
 
     validationSchemaIgnoreParams = 'test_data_base,merge_samplesheet_ids,fastq_ftp_ids,test_data'
 }
diff --git a/tests/main.nf.test b/tests/main.nf.test
new file mode 100644
index 00000000..7bf19f34
--- /dev/null
+++ b/tests/main.nf.test
@@ -0,0 +1,27 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    tag "pipeline"
+
+    test("Run with profile test") {
+
+        when {
+            params {
+                outdir     = "results"
+                max_cpus   = 2
+                max_memory = '6.GB'
+                max_time   = '6.h'
+                input      = "$projectDir/tests/sra_ids_test.csv"
+                validationSchemaIgnoreParams = 'test_data_base,merge_samplesheet_ids,fastq_ftp_ids,test_data'
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+}
diff --git a/tests/sra_ids_test.csv b/tests/sra_ids_test.csv
new file mode 100644
index 00000000..ec8b5cc9
--- /dev/null
+++ b/tests/sra_ids_test.csv
@@ -0,0 +1,7 @@
+SRR9984183
+SRR13191702
+ERR1160846
+SRR12848126
+SRR14593545
+SRR14709033
+GSE214215

From 6f94f654f3568a93a4dc319bb8e620cca1c50a9e Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 13 Oct 2023 11:07:14 +0200
Subject: [PATCH 549/852] add tags

---
 tests/tags.yml | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 tests/tags.yml

diff --git a/tests/tags.yml b/tests/tags.yml
new file mode 100644
index 00000000..3a1868da
--- /dev/null
+++ b/tests/tags.yml
@@ -0,0 +1,4 @@
+pipeline_fetchngs:
+  - **.nf
+  - **.config
+  - **.nf.test

From e9917d81b017d73d7c929ff6fcbadeff3aec018b Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 13 Oct 2023 11:17:19 +0200
Subject: [PATCH 550/852] update tags

---
 tests/tags.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/tags.yml b/tests/tags.yml
index 3a1868da..5b091f8e 100644
--- a/tests/tags.yml
+++ b/tests/tags.yml
@@ -1,4 +1,4 @@
 pipeline_fetchngs:
-  - **.nf
-  - **.config
-  - **.nf.test
+  - "**.nf"
+  - "**.config"
+  - "**.nf.test"

From 91d59aa6251cb68a695d48901ee5e6fb4e72acad Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 13 Oct 2023 11:37:48 +0200
Subject: [PATCH 551/852] use proper tag

---
 tests/main.nf.test | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/main.nf.test b/tests/main.nf.test
index 7bf19f34..ac05aea9 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -3,6 +3,7 @@ nextflow_pipeline {
     name "Test pipeline"
     script "../main.nf"
     tag "pipeline"
+    tag "pipeline_fetchngs"
 
     test("Run with profile test") {
 

From 796728a52184426ba3c8a5761d16a8b7b321b5ae Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 13 Oct 2023 11:38:44 +0200
Subject: [PATCH 552/852] extends files to trigger test

---
 tests/tags.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/tags.yml b/tests/tags.yml
index 5b091f8e..80e5fd75 100644
--- a/tests/tags.yml
+++ b/tests/tags.yml
@@ -2,3 +2,4 @@ pipeline_fetchngs:
   - "**.nf"
   - "**.config"
   - "**.nf.test"
+  - "**.json"

From 8b6570b3a1cf7575721f51dead316b591c66d7e5 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Fri, 13 Oct 2023 12:23:23 +0200
Subject: [PATCH 553/852] Update conf/test.config

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
---
 conf/test.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/test.config b/conf/test.config
index 67291b47..c09a571c 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -20,7 +20,7 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input  = 'tests/sra_ids_test.csv'
+    input  = '${projectDir}/tests/sra_ids_test.csv'
 
     validationSchemaIgnoreParams = 'test_data_base,merge_samplesheet_ids,fastq_ftp_ids,test_data'
 }

From 4ec46062e22c5b1acdeea67258ad64d3548f60fc Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 13 Oct 2023 13:36:45 +0200
Subject: [PATCH 554/852] use same IDs as profile test

---
 workflows/sra/tests/main.nf.test                             | 2 +-
 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test   | 2 +-
 workflows/sra/tests/sra_force_sratools_download.nf.test      | 2 +-
 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test     | 2 +-
 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test      | 2 +-
 workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test | 2 +-
 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test  | 2 +-
 workflows/sra/tests/sra_skip_fastq_download.nf.test          | 2 +-
 8 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index dcf67105..af916f4c 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -18,7 +18,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
+                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
                 """
             }
             params {
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index 04a60471..0fdb67f3 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -18,7 +18,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
+                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
                 """
             }
             params {
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index c669af8d..7958a1ed 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -18,7 +18,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
+                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
                 """
             }
             params {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index e88e5f63..dfccf891 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -18,7 +18,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
+                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
                 """
             }
             params {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index 63c871ca..fd092bcd 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -18,7 +18,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
+                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
                 """
             }
             params {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index 15a31848..a41d2b7a 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -18,7 +18,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
+                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
                 """
             }
             params {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index 4c11d571..c052d915 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -18,7 +18,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
+                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
                 """
             }
             params {
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index 8cb68641..04eb3dd7 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -18,7 +18,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
+                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
                 """
             }
             params {

From c75c1d05dff6a6455de4a1a192bbe2c88825db43 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 13 Oct 2023 13:56:15 +0200
Subject: [PATCH 555/852] update snap

---
 workflows/sra/tests/main.nf.test.snap              | 14 +++++++-------
 .../sra_custom_ena_metadata_fields.nf.test.snap    | 14 +++++++-------
 .../tests/sra_force_sratools_download.nf.test.snap | 14 +++++++-------
 .../sra_nf_core_pipeline_atacseq.nf.test.snap      | 14 +++++++-------
 .../tests/sra_nf_core_pipeline_rnaseq.nf.test.snap | 14 +++++++-------
 .../sra_nf_core_pipeline_taxprofiler.nf.test.snap  | 14 +++++++-------
 .../sra_nf_core_pipeline_viralrecon.nf.test.snap   | 14 +++++++-------
 .../sra/tests/sra_skip_fastq_download.nf.test.snap | 14 +++++++-------
 8 files changed, 56 insertions(+), 56 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
index d53f3de2..4ba15917 100644
--- a/workflows/sra/tests/main.nf.test.snap
+++ b/workflows/sra/tests/main.nf.test.snap
@@ -6,14 +6,14 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192"
+                    "samplesheet.csv:md5,5926f40ded37e0e6ce0b290c445772ac"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
+                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
                 ],
                 "3": [
                     [
-                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
@@ -29,16 +29,16 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
+                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
                 ],
                 "sample_mappings": [
                     [
-                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192"
+                    "samplesheet.csv:md5,5926f40ded37e0e6ce0b290c445772ac"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -50,6 +50,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-09T11:10:06.701286"
+        "timestamp": "2023-10-13T13:45:55.621951"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
index 143375ac..5e98f3b1 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
@@ -6,14 +6,14 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,d161b1a26b415a61064d8c558c9695c5"
+                    "samplesheet.csv:md5,4ea86d2a38bf25d025331afd1925a138"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,e8a7d8effe4af1d999dc26cf92cf6621"
+                    "id_mappings.csv:md5,e581a9117ed2cc8e98e65c25fe7f34aa"
                 ],
                 "3": [
                     [
-                        "multiqc_config.yml:md5,b1c25951b237552448e878f7c9dc4235",
+                        "multiqc_config.yml:md5,0f18d574c7ddfa08cf444a593cb91cde",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
@@ -29,16 +29,16 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,e8a7d8effe4af1d999dc26cf92cf6621"
+                    "id_mappings.csv:md5,e581a9117ed2cc8e98e65c25fe7f34aa"
                 ],
                 "sample_mappings": [
                     [
-                        "multiqc_config.yml:md5,b1c25951b237552448e878f7c9dc4235",
+                        "multiqc_config.yml:md5,0f18d574c7ddfa08cf444a593cb91cde",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,d161b1a26b415a61064d8c558c9695c5"
+                    "samplesheet.csv:md5,4ea86d2a38bf25d025331afd1925a138"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -50,6 +50,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-06T12:10:32.762201"
+        "timestamp": "2023-10-13T13:41:56.570144"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
index a22fad41..1c92c75d 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
@@ -6,14 +6,14 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,f582a7cf6b4a507e3ccbd2ebd134bd26"
+                    "samplesheet.csv:md5,461dfaa7b95f84210840347ef8cc93c2"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
+                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
                 ],
                 "3": [
                     [
-                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
@@ -28,16 +28,16 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
+                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
                 ],
                 "sample_mappings": [
                     [
-                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,f582a7cf6b4a507e3ccbd2ebd134bd26"
+                    "samplesheet.csv:md5,461dfaa7b95f84210840347ef8cc93c2"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -48,6 +48,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-09T12:31:35.173406"
+        "timestamp": "2023-10-13T13:51:26.617172"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
index 3e26ff24..cabe296e 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
@@ -6,14 +6,14 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,46752dd6abac80b59573910f7ce4babe"
+                    "samplesheet.csv:md5,0deebc93328dcbb63762aa91d4fc9f35"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
+                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
                 ],
                 "3": [
                     [
-                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
@@ -29,16 +29,16 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
+                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
                 ],
                 "sample_mappings": [
                     [
-                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,46752dd6abac80b59573910f7ce4babe"
+                    "samplesheet.csv:md5,0deebc93328dcbb63762aa91d4fc9f35"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -50,6 +50,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-09T11:48:46.177797"
+        "timestamp": "2023-10-13T13:37:42.486986"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
index a0c20a40..111fe537 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
@@ -6,14 +6,14 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,69117245b73776d6e4daecdbfdff9767"
+                    "samplesheet.csv:md5,e20d0858b2ff04a62d50274a2527b913"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
+                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
                 ],
                 "3": [
                     [
-                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
@@ -29,16 +29,16 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
+                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
                 ],
                 "sample_mappings": [
                     [
-                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,69117245b73776d6e4daecdbfdff9767"
+                    "samplesheet.csv:md5,e20d0858b2ff04a62d50274a2527b913"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -50,6 +50,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-06T12:14:02.500312"
+        "timestamp": "2023-10-13T13:43:56.980991"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
index d9d6ddee..14c38837 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
@@ -6,14 +6,14 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,0705e78609390cc464c2fb10051178bc"
+                    "samplesheet.csv:md5,c781b226b9aac812c1d38881145a74d6"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
+                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
                 ],
                 "3": [
                     [
-                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
@@ -29,16 +29,16 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
+                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
                 ],
                 "sample_mappings": [
                     [
-                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,0705e78609390cc464c2fb10051178bc"
+                    "samplesheet.csv:md5,c781b226b9aac812c1d38881145a74d6"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -50,6 +50,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-06T12:07:01.184728"
+        "timestamp": "2023-10-13T13:39:55.31037"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
index cacb42cc..d26dd1cc 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
@@ -6,14 +6,14 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192"
+                    "samplesheet.csv:md5,5926f40ded37e0e6ce0b290c445772ac"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
+                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
                 ],
                 "3": [
                     [
-                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
@@ -29,16 +29,16 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
+                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
                 ],
                 "sample_mappings": [
                     [
-                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192"
+                    "samplesheet.csv:md5,5926f40ded37e0e6ce0b290c445772ac"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -50,6 +50,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-09T11:44:49.759545"
+        "timestamp": "2023-10-13T13:35:41.371352"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
index c137d853..f0bac51f 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
@@ -6,14 +6,14 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,b1636e896008b96044d352a0757a390b"
+                    "samplesheet.csv:md5,23d39235ed39f69cb8333322de77ed26"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
+                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
                 ],
                 "3": [
                     [
-                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
@@ -27,16 +27,16 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342"
+                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
                 ],
                 "sample_mappings": [
                     [
-                        "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a",
+                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,b1636e896008b96044d352a0757a390b"
+                    "samplesheet.csv:md5,23d39235ed39f69cb8333322de77ed26"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -46,6 +46,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-06T12:18:48.477246"
+        "timestamp": "2023-10-13T13:46:11.136377"
     }
 }
\ No newline at end of file

From 0f6cbd4721c854283562c7f894ea3afe877e2798 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 13 Oct 2023 14:36:20 +0200
Subject: [PATCH 556/852] add file for sratools/prefetch

---
 conf/test_data.config | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/conf/test_data.config b/conf/test_data.config
index 42d3d818..68e84262 100644
--- a/conf/test_data.config
+++ b/conf/test_data.config
@@ -24,6 +24,11 @@ params {
     }
 
     test_data {
+        'generic' {
+            'config' {
+                ncbi_user_settings                  = "${params.test_data_base}/data/generic/config/ncbi_user_settings.mkfg"
+            }
+        }
         'modules_local' {
                 multiqc_mappings_config             = "${params.test_data_base}/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv"
                 sra_merge_samplesheet_samplesheets  = merge_samplesheet_urls

From 1520425356b02d673680a181f64907114c33f333 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 13 Oct 2023 15:00:35 +0200
Subject: [PATCH 557/852] update modules

---
 modules.json                                  |  10 +-
 .../dumpsoftwareversions/tests/main.nf.test   |   5 +-
 .../sratoolsncbisettings/tests/main.nf.test   | 114 +++++++++++++++
 .../tests/main.nf.test.snap                   |  18 +++
 .../tests/nextflow.config                     |  16 +++
 .../sratools/fasterqdump/tests/main.nf.test   |   5 +-
 .../sratools/prefetch/tests/main.nf.test      |   9 +-
 .../sratools/prefetch/tests/main.nf.test.snap | 130 +++++++-----------
 .../tests/main.nf.test                        |  37 +++++
 .../tests/main.nf.test.snap                   |  57 ++++++++
 10 files changed, 304 insertions(+), 97 deletions(-)
 create mode 100644 modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
 create mode 100644 modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config
 create mode 100644 subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
 create mode 100644 subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap

diff --git a/modules.json b/modules.json
index 87e40abf..b826fae6 100644
--- a/modules.json
+++ b/modules.json
@@ -7,22 +7,22 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "1b372269755a5c4a13c23bc130ebada8cb9d4cd0",
+                        "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0",
                         "installed_by": ["modules"]
                     },
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "b4d743f1bb8d92eb129a5925a9211beb689be625",
+                        "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/prefetch": {
                         "branch": "master",
-                        "git_sha": "096ea8a4db569cc680ada4105e1d313cc56329c8",
+                        "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     }
                 }
@@ -31,7 +31,7 @@
                 "nf-core": {
                     "fastq_download_prefetch_fasterqdump_sratools": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
index d528d3cb..eec1db10 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
+++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
@@ -1,12 +1,13 @@
 nextflow_process {
 
     name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS"
-    script "modules/nf-core/custom/dumpsoftwareversions/main.nf"
+    script "../main.nf"
     process "CUSTOM_DUMPSOFTWAREVERSIONS"
+    tag "modules"
+    tag "modules_nfcore"
     tag "custom"
     tag "dumpsoftwareversions"
     tag "custom/dumpsoftwareversions"
-    tag "modules_nfcore"
 
     test("Should run without failures") {
         when {
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
new file mode 100644
index 00000000..ec4a7797
--- /dev/null
+++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
@@ -0,0 +1,114 @@
+nextflow_process {
+
+    name "Test Process CUSTOM_SRATOOLSNCBISETTINGS"
+    script "../main.nf"
+    process "CUSTOM_SRATOOLSNCBISETTINGS"
+    config "modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "custom"
+    tag "custom/sratoolsncbisettings"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                settings_path = '/tmp/.ncbi'
+                settings_file = "${params.settings_path}/user-settings.mkfg"
+            }
+
+            process {
+                """
+                file(params.settings_path).mkdirs()
+                def settings = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true)
+                settings.copyTo(params.settings_file)
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(
+                process.out.versions
+            ).match()
+
+            with(process.out.ncbi_settings) {
+                assert path(get(0)).readLines().any { it.contains('/LIBS/GUID') }
+                assert path(get(0)).readLines().any { it.contains('/libs/cloud/report_instance_identity') }
+            }
+        }
+
+    }
+
+    test("Should fail") {
+
+        when {
+            params {
+                settings_path = '/tmp/.ncbi'
+                settings_file = "${params.settings_path}/user-settings.mkfg"
+            }
+
+            process {
+                """
+                file(params.settings_path).mkdirs()
+                def settings = file(params.settings_file)
+                settings.text = '''
+                ## auto-generated configuration file - DO NOT EDIT ##
+                config/default = "false"
+                /repository/remote/main/CGI/resolver-cgi = "https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi"
+                /repository/remote/protected/CGI/resolver-cgi = "https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi"
+                /repository/user/ad/public/apps/file/volumes/flatAd = "."
+                /repository/user/ad/public/apps/refseq/volumes/refseqAd = "."
+                /repository/user/ad/public/apps/sra/volumes/sraAd = "."
+                /repository/user/ad/public/apps/sraPileup/volumes/ad = "."
+                /repository/user/ad/public/apps/sraRealign/volumes/ad = "."
+                /repository/user/ad/public/apps/wgs/volumes/wgsAd = "."
+                /repository/user/ad/public/root = "."
+                /repository/user/default-path = "/root/ncbi"
+                '''.stripIndent()
+                """
+            }
+        }
+
+        then {
+            assert process.failed
+            assert snapshot(
+                process.out.versions
+            ).match()
+            assert process.stdout.any { it.contains('Command error:') }
+            assert process.stdout.any { it.contains('missing the required entries') }
+            assert process.stdout.any { it.contains('/LIBS/GUID') }
+            assert process.stdout.any { it.contains('/libs/cloud/report_instance_identity') }
+        }
+
+    }
+
+    test("Should run with nonexisting") {
+
+        when {
+            params {
+                settings_path = '/tmp/.ncbi'
+                settings_file = "${params.settings_path}/user-settings.mkfg"
+            }
+
+            process {
+                """
+                def settings = file(params.settings_file)
+                settings.delete()
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out.versions).match()
+
+            with(process.out.ncbi_settings) {
+                { assert path(get(0)).readLines().any { it.contains('/LIBS/GUID') } }
+                { assert path(get(0)).readLines().any { it.contains('/libs/cloud/report_instance_identity') } }
+            }
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap
new file mode 100644
index 00000000..edb3b351
--- /dev/null
+++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap
@@ -0,0 +1,18 @@
+{
+    "Should run with nonexisting": {
+        "content": [
+            [
+                "versions.yml:md5,fec13b593c3b42ddd38f2fc77df25b70"
+            ]
+        ],
+        "timestamp": "2023-10-12T12:24:24.023849"
+    },
+    "Should run without failures": {
+        "content": [
+            [
+                "versions.yml:md5,fec13b593c3b42ddd38f2fc77df25b70"
+            ]
+        ],
+        "timestamp": "2023-10-12T10:40:51.717351"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config b/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config
new file mode 100644
index 00000000..c4a96e94
--- /dev/null
+++ b/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config
@@ -0,0 +1,16 @@
+params.settings_path = '/tmp/.ncbi'
+params.settings_file = "${params.settings_path}/user-settings.mkfg"
+
+env.NCBI_SETTINGS = params.settings_file
+
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    withName: CUSTOM_SRATOOLSNCBISETTINGS {
+        containerOptions = {
+            (workflow.containerEngine == 'singularity') ?
+            "-B ${params.settings_path}:${params.settings_path}" :
+            "-v ${params.settings_path}:${params.settings_path}"
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
index 7da3af20..ee4c5844 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
@@ -1,9 +1,10 @@
 nextflow_process {
     name "Test Process SRATOOLS_FASTERQDUMP"
-    script "modules/nf-core/sratools/fasterqdump/main.nf"
+    script "../main.nf"
     process "SRATOOLS_FASTERQDUMP"
-    tag "sratools/fasterqdump"
+    tag "modules"
     tag "modules_nfcore"
+    tag "sratools/fasterqdump"
 
     test("Single-end") {
 
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test
index 1234a82b..fcf4036d 100644
--- a/modules/nf-core/sratools/prefetch/tests/main.nf.test
+++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test
@@ -1,9 +1,10 @@
 nextflow_process {
     name "Test Process SRATOOLS_PREFETCH"
-    script "modules/nf-core/sratools/prefetch/main.nf"
+    script "../main.nf"
     process "SRATOOLS_PREFETCH"
-    tag "sratools/prefetch"
+    tag "modules"
     tag "modules_nfcore"
+    tag "sratools/prefetch"
 
     test("sratools/prefetch") {
 
@@ -23,7 +24,7 @@ nextflow_process {
         then {
             assertAll (
             { assert process.success },
-            { assert snapshot(process).match() }
+            { assert snapshot(process.out).match() }
             )
         }
     }
@@ -46,7 +47,7 @@ nextflow_process {
         then {
             assertAll (
             { assert process.success },
-            { assert snapshot(process).match() }
+            { assert snapshot(process.out).match() }
             )
         }
     }
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap
index 95ea067f..ab1d2088 100644
--- a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap
+++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap
@@ -2,109 +2,71 @@
     "sratools/prefetch with sralite": {
         "content": [
             {
-                "stderr": [
-                    
-                ],
-                "errorReport": null,
-                "exitStatus": 0,
-                "out": {
-                    "0": [
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
                         [
-                            {
-                                "id": "test",
-                                "single_end": false
-                            },
-                            [
-                                "SRR1170046.sralite:md5,7acfce556ca0951aff49d780899c105b"
-                            ]
+                            "SRR1170046.sralite:md5,7acfce556ca0951aff49d780899c105b"
                         ]
-                    ],
-                    "1": [
-                        "versions.yml:md5,c967dea4135cb75490e1e801c4639efc"
-                    ],
-                    "sra": [
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,c967dea4135cb75490e1e801c4639efc"
+                ],
+                "sra": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
                         [
-                            {
-                                "id": "test",
-                                "single_end": false
-                            },
-                            [
-                                "SRR1170046.sralite:md5,7acfce556ca0951aff49d780899c105b"
-                            ]
+                            "SRR1170046.sralite:md5,7acfce556ca0951aff49d780899c105b"
                         ]
-                    ],
-                    "versions": [
-                        "versions.yml:md5,c967dea4135cb75490e1e801c4639efc"
                     ]
-                },
-                "failed": false,
-                "stdout": [
-                    
                 ],
-                "errorMessage": null,
-                "trace": {
-                    "tasksFailed": 0,
-                    "tasksCount": 1,
-                    "tasksSucceeded": 1
-                },
-                "name": "SRATOOLS_PREFETCH",
-                "success": true
+                "versions": [
+                    "versions.yml:md5,c967dea4135cb75490e1e801c4639efc"
+                ]
             }
         ],
-        "timestamp": "2023-10-10T15:26:45.715617"
+        "timestamp": "2023-10-13T12:11:24.563510389"
     },
     "sratools/prefetch": {
         "content": [
             {
-                "stderr": [
-                    
-                ],
-                "errorReport": null,
-                "exitStatus": 0,
-                "out": {
-                    "0": [
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
                         [
-                            {
-                                "id": "test",
-                                "single_end": false
-                            },
-                            [
-                                "DRR000774.sra:md5,7647dba20c89c0e3d7ad13842f060eb0"
-                            ]
+                            "DRR000774.sra:md5,7647dba20c89c0e3d7ad13842f060eb0"
                         ]
-                    ],
-                    "1": [
-                        "versions.yml:md5,c967dea4135cb75490e1e801c4639efc"
-                    ],
-                    "sra": [
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,c967dea4135cb75490e1e801c4639efc"
+                ],
+                "sra": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
                         [
-                            {
-                                "id": "test",
-                                "single_end": false
-                            },
-                            [
-                                "DRR000774.sra:md5,7647dba20c89c0e3d7ad13842f060eb0"
-                            ]
+                            "DRR000774.sra:md5,7647dba20c89c0e3d7ad13842f060eb0"
                         ]
-                    ],
-                    "versions": [
-                        "versions.yml:md5,c967dea4135cb75490e1e801c4639efc"
                     ]
-                },
-                "failed": false,
-                "stdout": [
-                    
                 ],
-                "errorMessage": null,
-                "trace": {
-                    "tasksFailed": 0,
-                    "tasksCount": 1,
-                    "tasksSucceeded": 1
-                },
-                "name": "SRATOOLS_PREFETCH",
-                "success": true
+                "versions": [
+                    "versions.yml:md5,c967dea4135cb75490e1e801c4639efc"
+                ]
             }
         ],
-        "timestamp": "2023-10-10T09:58:01.781848"
+        "timestamp": "2023-10-13T12:11:02.75256571"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
new file mode 100644
index 00000000..be18fc3b
--- /dev/null
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
@@ -0,0 +1,37 @@
+nextflow_workflow {
+
+    name "Test workflow: fastq_download_prefetch_fasterqdump_sratools/main.nf"
+    script "../main.nf"
+    workflow "FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS"
+    tag "subworkflow"
+    tag "subworkflow_nfcore"
+    tag "custom/sratoolsncbisettings"
+    tag "sratools/prefetch"
+    tag "sratools/fasterqdump"
+    tag "fastq_download_prefetch_fasterqdump_sratools"
+
+    test("Parameters: default") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of(
+                    [[ id:'test_single_end', single_end:true  ], 'DRR000774'],
+                    [[ id:'test_paired_end', single_end:false ], 'SRR11140744']
+                )
+                input[1] = []
+                """
+            }
+            params {
+                outdir = "output"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
new file mode 100644
index 00000000..a73679e0
--- /dev/null
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
@@ -0,0 +1,57 @@
+{
+    "Parameters: default": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_paired_end",
+                            "single_end": false
+                        },
+                        [
+                            "test_paired_end_1.fastq.gz:md5,193809c784a4ea132ab2a253fa4f55b6",
+                            "test_paired_end_2.fastq.gz:md5,3e3b3af3413f50a1685fd7b3f1456d4e"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "test_single_end",
+                            "single_end": true
+                        },
+                        "test_single_end.fastq.gz:md5,19029a1132115b55277a0d79ee089b49"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,98d78bba9f3da39a0b7db6e9c7dcc224",
+                    "versions.yml:md5,9c558ff624585a6eee82a19c8c0136db",
+                    "versions.yml:md5,db0e1352064b53c651661f43f2620765"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test_paired_end",
+                            "single_end": false
+                        },
+                        [
+                            "test_paired_end_1.fastq.gz:md5,193809c784a4ea132ab2a253fa4f55b6",
+                            "test_paired_end_2.fastq.gz:md5,3e3b3af3413f50a1685fd7b3f1456d4e"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "test_single_end",
+                            "single_end": true
+                        },
+                        "test_single_end.fastq.gz:md5,19029a1132115b55277a0d79ee089b49"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,98d78bba9f3da39a0b7db6e9c7dcc224",
+                    "versions.yml:md5,9c558ff624585a6eee82a19c8c0136db",
+                    "versions.yml:md5,db0e1352064b53c651661f43f2620765"
+                ]
+            }
+        ],
+        "timestamp": "2023-10-12T20:09:55.255971"
+    }
+}
\ No newline at end of file

From a38f6410090a56ee395902bb8c0444f9e156ad05 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 13 Oct 2023 15:18:41 +0200
Subject: [PATCH 558/852] use nextflowpipelineutils from nf-core/modules

---
 modules.json                                  |   5 +
 .../local/nf_core_fetchngs_utils/main.nf      |   4 +-
 .../nextflowpipelineutils}/main.nf            |   3 +
 .../nf-core/nextflowpipelineutils/meta.yml    |  34 ++++++
 .../tests/main.functions.nf.test              |  70 ++++++++++++
 .../tests/main.functions.nf.test.snap         |  12 ++
 .../tests/main.workflow.nf.test               | 104 ++++++++++++++++++
 .../tests/main.workflow.nf.test.snap          |  44 ++++++++
 .../tests/nextflow.config                     |   9 ++
 9 files changed, 283 insertions(+), 2 deletions(-)
 rename subworkflows/{local/nextflow_pipeline_utils => nf-core/nextflowpipelineutils}/main.nf (99%)
 create mode 100644 subworkflows/nf-core/nextflowpipelineutils/meta.yml
 create mode 100644 subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test
 create mode 100644 subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test.snap
 create mode 100644 subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test
 create mode 100644 subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test.snap
 create mode 100644 subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config

diff --git a/modules.json b/modules.json
index b826fae6..3cc9d6dd 100644
--- a/modules.json
+++ b/modules.json
@@ -33,6 +33,11 @@
                         "branch": "master",
                         "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0",
                         "installed_by": ["subworkflows"]
+                    },
+                    "nextflowpipelineutils": {
+                        "branch": "master",
+                        "git_sha": "76cbb00305f6b045c15c1e202a5bdd516d6f64a3",
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }
diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf
index 5cc2162b..fd0e9855 100644
--- a/subworkflows/local/nf_core_fetchngs_utils/main.nf
+++ b/subworkflows/local/nf_core_fetchngs_utils/main.nf
@@ -9,7 +9,7 @@
 */
 
 include { CUSTOM_DUMPSOFTWAREVERSIONS                 } from '../../../modules/nf-core/custom/dumpsoftwareversions'
-include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion } from '../nextflow_pipeline_utils'
+include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion } from '../../nf-core/nextflowpipelineutils/main'
 include { NF_VALIDATION_PLUGIN_UTILS                  } from '../nf_validation_plugin_utils'
 include { NF_CORE_PIPELINE_UTILS; workflowCitation; nfCoreLogo; dashedLine; completionEmail; completionSummary; imNotification } from '../nf_core_pipeline_utils'
 
@@ -49,7 +49,7 @@ workflow PIPELINE_INITIALISATION {
 
     //
     // Check config provided to the pipeline
-    // 
+    //
     NF_CORE_PIPELINE_UTILS ()
 
     //
diff --git a/subworkflows/local/nextflow_pipeline_utils/main.nf b/subworkflows/nf-core/nextflowpipelineutils/main.nf
similarity index 99%
rename from subworkflows/local/nextflow_pipeline_utils/main.nf
rename to subworkflows/nf-core/nextflowpipelineutils/main.nf
index e56394ed..5cb9af8c 100644
--- a/subworkflows/local/nextflow_pipeline_utils/main.nf
+++ b/subworkflows/nf-core/nextflowpipelineutils/main.nf
@@ -42,6 +42,9 @@ workflow NEXTFLOW_PIPELINE_UTILS {
     if (check_conda_channels) {
         checkCondaChannels()
     }
+
+    emit:
+        out = true
 }
 
 /*
diff --git a/subworkflows/nf-core/nextflowpipelineutils/meta.yml b/subworkflows/nf-core/nextflowpipelineutils/meta.yml
new file mode 100644
index 00000000..f56b827b
--- /dev/null
+++ b/subworkflows/nf-core/nextflowpipelineutils/meta.yml
@@ -0,0 +1,34 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "nextflow_pipeline_utils"
+description: Subworkflow with functionality that may be useful for any Nextflow pipeline
+keywords:
+  - utility
+  - pipeline
+  - initialise
+  - version
+components: []
+input:
+  - print_version:
+      type: boolean
+      description: |
+        Print the version of the pipeline and exit
+  - dump_parameters:
+      type: boolean
+      description: |
+        Dump the parameters of the pipeline to a JSON file
+  - output_directory:
+      type: directory
+      description: Path to output dir to write JSON file to.
+      pattern: "results/"
+  - check_conda_channel:
+      type: boolean
+      description: |
+        Check if the conda channel priority is correct.
+output:
+  - out:
+      type: boolean
+      description: |
+        Dummy output for making using in process chaining.
+authors:
+  - "@adamrtalbot"
+  - "@drpatelh"
diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test b/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test
new file mode 100644
index 00000000..db757ed1
--- /dev/null
+++ b/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test
@@ -0,0 +1,70 @@
+
+nextflow_function {
+
+    name "Test Functions"
+    script "subworkflows/nf-core/nextflowpipelineutils/main.nf"
+    tag 'subworkflows'
+    tag 'nextflowpipelineutils'
+    tag 'subworkflows/nextflowpipelineutils'
+
+    test("Test Function getWorkflowVersion") {
+
+        function "getWorkflowVersion"
+
+        when {
+            function {
+                """
+                // no inputs
+                """
+            }
+        }
+
+        then {
+            assert function.success
+            assert snapshot(function.result).match()
+        }
+
+    }
+
+
+    test("Test Function dumpParametersToJSON") {
+
+        function "dumpParametersToJSON"
+
+        when {
+            function {
+                """
+                // define inputs of the function here. Example:
+                input[0] = "$outputDir"
+                """.stripIndent()
+            }
+        }
+
+        then {
+            assert function.success
+            assert function.result =~ /publish_dir_mode/
+            assert function.result =~ /copy/
+        }
+
+    }
+	
+    test("Test Function checkCondaChannels") {
+
+        function "checkCondaChannels"
+
+        when {
+            function {
+                """
+                // no inputs
+                """
+            }
+        }
+
+        then {
+            assert function.success
+            assert snapshot(function.result).match()
+        }
+
+    }
+
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test.snap b/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test.snap
new file mode 100644
index 00000000..956bfac7
--- /dev/null
+++ b/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test.snap
@@ -0,0 +1,12 @@
+{
+    "Test Function getWorkflowVersion": {
+        "content": [
+            ""
+        ],
+        "timestamp": "2023-10-12T17:09:20.935733"
+    },
+    "Test Function checkCondaChannels": {
+        "content": null,
+        "timestamp": "2023-10-12T17:09:24.933468"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test b/subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test
new file mode 100644
index 00000000..3cf7f034
--- /dev/null
+++ b/subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test
@@ -0,0 +1,104 @@
+nextflow_workflow {
+
+    name "Test Workflow NEXTFLOW_PIPELINE_UTILS"
+    script "../main.nf"
+    config "subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config"
+    workflow "NEXTFLOW_PIPELINE_UTILS"
+    tag 'subworkflows'
+    tag 'nextflowpipelineutils'
+    tag 'subworkflows/nextflowpipelineutils'
+
+    test("Should run no inputs") {
+
+        when {
+            params {
+                outdir = "tests/results"
+            }
+            workflow {
+                """
+                input[0] = false
+                input[1] = false
+                input[2] = null
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(workflow.out).match()
+        }
+
+    }
+
+    test("Should print version") {
+
+        when {
+            params {
+                outdir = "tests/results"
+            }
+            workflow {
+                """
+                input[0] = true
+                input[1] = false
+                input[2] = null
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.stdout.contains("nextflow_workflow v9.9.9")
+        }
+
+    }
+
+
+    test("Should dump params") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            workflow {
+                """
+                input[0] = false
+                input[1] = true
+                input[2] = params.outdir
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(workflow.out).match()
+        }
+
+    }
+
+    test("Should not create params JSON if no output directory") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            workflow {
+                """
+                input[0] = false
+                input[1] = true
+                input[2] = null
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(workflow.out, path(params.outdir).list()).match()
+        }
+
+    }
+
+}
diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test.snap
new file mode 100644
index 00000000..08040fd4
--- /dev/null
+++ b/subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test.snap
@@ -0,0 +1,44 @@
+{
+    "Should not create params JSON if no output directory": {
+        "content": [
+            {
+                "0": [
+                    true
+                ],
+                "out": [
+                    true
+                ]
+            },
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-10-13T11:55:54.576748"
+    },
+    "Should dump params": {
+        "content": [
+            {
+                "0": [
+                    true
+                ],
+                "out": [
+                    true
+                ]
+            }
+        ],
+        "timestamp": "2023-10-13T11:55:52.711329"
+    },
+    "Should run no inputs": {
+        "content": [
+            {
+                "0": [
+                    true
+                ],
+                "out": [
+                    true
+                ]
+            }
+        ],
+        "timestamp": "2023-10-13T11:55:49.048315"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config b/subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config
new file mode 100644
index 00000000..035c0f5d
--- /dev/null
+++ b/subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config
@@ -0,0 +1,9 @@
+manifest {
+    name            = 'nextflow_workflow'
+    author          = """nf-core"""
+    homePage        = 'https://127.0.0.1'
+    description     = """Dummy pipeline"""
+    nextflowVersion  = '!>=23.04.4'
+    version         = '9.9.9'
+    doi             = 'https://doi.org/10.5281/zenodo.5070524'
+}
\ No newline at end of file

From 135c6447e3b1ada4e84aa03e25beaa8e0b0276fd Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 13 Oct 2023 15:22:32 +0200
Subject: [PATCH 559/852] tags

---
 .../fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml | 2 ++
 subworkflows/nf-core/nextflowpipelineutils/tests/tags.yml       | 2 ++
 2 files changed, 4 insertions(+)
 create mode 100644 subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml
 create mode 100644 subworkflows/nf-core/nextflowpipelineutils/tests/tags.yml

diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml
new file mode 100644
index 00000000..ab064503
--- /dev/null
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml
@@ -0,0 +1,2 @@
+fastq_download_prefetch_fasterqdump_sratools:
+  - subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/**
diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/tags.yml b/subworkflows/nf-core/nextflowpipelineutils/tests/tags.yml
new file mode 100644
index 00000000..57127a2a
--- /dev/null
+++ b/subworkflows/nf-core/nextflowpipelineutils/tests/tags.yml
@@ -0,0 +1,2 @@
+nextflowpipelineutils:
+  - subworkflows/nf-core/nextflowpipelineutils/**

From a12c5a3b2452de4b16fb1d03b91f85ea81eacd0c Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 16 Oct 2023 15:51:54 +0200
Subject: [PATCH 560/852] Use nf-core nfvalidation subworkflow

---
 modules.json                                  |   5 +
 .../local/nf_core_fetchngs_utils/main.nf      |   4 +-
 .../local/nf_validation_plugin_utils/main.nf  |  52 -----
 .../nf-core/nfvalidation_plugin_utils/main.nf |  62 ++++++
 .../nfvalidation_plugin_utils/meta.yml        |  49 +++++
 .../tests/main.nf.test                        | 199 ++++++++++++++++++
 .../tests/main.nf.test.snap                   |  26 +++
 .../tests/nextflow_schema.json                |  96 +++++++++
 8 files changed, 439 insertions(+), 54 deletions(-)
 delete mode 100644 subworkflows/local/nf_validation_plugin_utils/main.nf
 create mode 100644 subworkflows/nf-core/nfvalidation_plugin_utils/main.nf
 create mode 100644 subworkflows/nf-core/nfvalidation_plugin_utils/meta.yml
 create mode 100644 subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test
 create mode 100644 subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test.snap
 create mode 100644 subworkflows/nf-core/nfvalidation_plugin_utils/tests/nextflow_schema.json

diff --git a/modules.json b/modules.json
index 3cc9d6dd..b8801dc6 100644
--- a/modules.json
+++ b/modules.json
@@ -38,6 +38,11 @@
                         "branch": "master",
                         "git_sha": "76cbb00305f6b045c15c1e202a5bdd516d6f64a3",
                         "installed_by": ["subworkflows"]
+                    },
+                    "nfvalidation_plugin_utils": {
+                        "branch": "master",
+                        "git_sha": "a8223a72def6cc46f4652a348feba21845ce68c6",
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }
diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf
index fd0e9855..05f9a2ba 100644
--- a/subworkflows/local/nf_core_fetchngs_utils/main.nf
+++ b/subworkflows/local/nf_core_fetchngs_utils/main.nf
@@ -9,8 +9,8 @@
 */
 
 include { CUSTOM_DUMPSOFTWAREVERSIONS                 } from '../../../modules/nf-core/custom/dumpsoftwareversions'
-include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion } from '../../nf-core/nextflowpipelineutils/main'
-include { NF_VALIDATION_PLUGIN_UTILS                  } from '../nf_validation_plugin_utils'
+include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion  } from '../../nf-core/nextflowpipelineutils/main'
+include { NF_VALIDATION_PLUGIN_UTILS                  } from '../../nf-core/nfvalidation_plugin_utils/main.nf'
 include { NF_CORE_PIPELINE_UTILS; workflowCitation; nfCoreLogo; dashedLine; completionEmail; completionSummary; imNotification } from '../nf_core_pipeline_utils'
 
 /*
diff --git a/subworkflows/local/nf_validation_plugin_utils/main.nf b/subworkflows/local/nf_validation_plugin_utils/main.nf
deleted file mode 100644
index be815a7f..00000000
--- a/subworkflows/local/nf_validation_plugin_utils/main.nf
+++ /dev/null
@@ -1,52 +0,0 @@
-//
-// Subworkflow that uses the nf-validation plugin to render help text and parameter summary
-//
-
-/*
-========================================================================================
-    IMPORT NF-VALIDATION PLUGIN
-========================================================================================
-*/
-
-include { paramsHelp; paramsSummaryLog; paramsSummaryMap; validateParameters } from 'plugin/nf-validation'
-
-/*
-========================================================================================
-    SUBWORKFLOW DEFINITION
-========================================================================================
-*/
-
-workflow NF_VALIDATION_PLUGIN_UTILS {
-
-    take:
-    print_help       // bool
-    workflow_command // string: default commmand used to run pipeline
-    pre_help_text    // string: string to be printed before help text and summary log
-    post_help_text   // string: string to be printed after help text and summary log
-    validate_params  // bool
-
-    main:
-
-    //
-    // Print help message if needed
-    //
-    if (print_help && workflow_command) {
-        log.info pre_help_text + paramsHelp(workflow_command) + post_help_text
-        System.exit(0)
-    }
-
-    //
-    // Print parameter summary to stdout
-    //
-    log.info pre_help_text + paramsSummaryLog(workflow) + post_help_text
-
-    //
-    // Validate parameters relative to the parameter JSON schema
-    //
-    if (validate_params){
-        validateParameters()
-    }
-
-    emit:
-    summary_params = paramsSummaryMap(workflow)
-}
diff --git a/subworkflows/nf-core/nfvalidation_plugin_utils/main.nf b/subworkflows/nf-core/nfvalidation_plugin_utils/main.nf
new file mode 100644
index 00000000..22531719
--- /dev/null
+++ b/subworkflows/nf-core/nfvalidation_plugin_utils/main.nf
@@ -0,0 +1,62 @@
+//
+// Subworkflow that uses the nf-validation plugin to render help text and parameter summary
+//
+
+/*
+========================================================================================
+    IMPORT NF-VALIDATION PLUGIN
+========================================================================================
+*/
+
+include { paramsHelp; paramsSummaryLog; paramsSummaryMap; validateParameters } from 'plugin/nf-validation'
+
+/*
+========================================================================================
+    SUBWORKFLOW DEFINITION
+========================================================================================
+*/
+
+workflow NF_VALIDATION_PLUGIN_UTILS {
+
+    take:
+        print_help        // bool
+        workflow_command   // string: default commmand used to run pipeline
+        pre_help_text     // string: string to be printed before help text and summary log
+        post_help_text    // string: string to be printed after help text and summary log
+        validate_params   // bool: Validate parameters
+        schema_filename    // path: JSON schema file, null to use default value
+
+    main:
+
+        log.debug "Using schema file: ${schema_filename}"
+
+        // Default values for strings
+        pre_help_text   = pre_help_text    ?: ''
+        post_help_text  = post_help_text   ?: ''
+        workflow_command = workflow_command  ?: ''
+
+        //
+        // Print help message if needed
+        //
+        if (print_help) {
+            log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text
+            System.exit(0)
+        }
+
+        //
+        // Print parameter summary to stdout
+        //
+        log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text
+
+        //
+        // Validate parameters relative to the parameter JSON schema
+        //
+        if (validate_params){
+            validateParameters(parameters_schema: schema_filename)
+        }
+
+        summary_params = paramsSummaryMap(workflow, parameters_schema: schema_filename)
+
+    emit:
+        summary_params = summary_params
+}
diff --git a/subworkflows/nf-core/nfvalidation_plugin_utils/meta.yml b/subworkflows/nf-core/nfvalidation_plugin_utils/meta.yml
new file mode 100644
index 00000000..6117b455
--- /dev/null
+++ b/subworkflows/nf-core/nfvalidation_plugin_utils/meta.yml
@@ -0,0 +1,49 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "nfvalidationpluginutils"
+## TODO nf-core: Add a description of the subworkflow and list keywords
+description: Sort SAM/BAM/CRAM file
+keywords:
+  - sort
+  - bam
+  - sam
+  - cram
+## TODO nf-core: Add a list of the modules and/or subworkflows used in the subworkflow
+components:
+  - samtools/sort
+  - samtools/index
+## TODO nf-core: List all of the channels used as input with a description and their structure
+input:
+  - ch_bam:
+      type: file
+      description: |
+        The input channel containing the BAM/CRAM/SAM files
+        Structure: [ val(meta), path(bam) ]
+      pattern: "*.{bam/cram/sam}"
+## TODO nf-core: List all of the channels used as output with a descriptions and their structure
+output:
+  - bam:
+      type: file
+      description: |
+        Channel containing BAM files
+        Structure: [ val(meta), path(bam) ]
+      pattern: "*.bam"
+  - bai:
+      type: file
+      description: |
+        Channel containing indexed BAM (BAI) files
+        Structure: [ val(meta), path(bai) ]
+      pattern: "*.bai"
+  - csi:
+      type: file
+      description: |
+        Channel containing CSI files
+        Structure: [ val(meta), path(csi) ]
+      pattern: "*.csi"
+  - versions:
+      type: file
+      description: |
+        File containing software versions
+        Structure: [ path(versions.yml) ]
+      pattern: "versions.yml"
+authors:
+  - "@adamrtalbot"
diff --git a/subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test b/subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test
new file mode 100644
index 00000000..6a0efd1e
--- /dev/null
+++ b/subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test
@@ -0,0 +1,199 @@
+nextflow_workflow {
+
+    name "Test Workflow NF_VALIDATION_PLUGIN_UTILS"
+    script "../main.nf"
+    workflow "NF_VALIDATION_PLUGIN_UTILS"
+    tag "subworkflow"
+    tag "subworkflow_nfcore"
+    tag "nfvalidationpluginutils"
+    tag "subworkflows/nfvalidationpluginutils"
+
+    test("Should run nothing") {
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+            }
+
+            workflow {
+                """
+                help            = false
+                workflow_command = null
+                pre_help_text   = null
+                post_help_text  = null
+                validate_params = false
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
+    test("Should run help") {
+
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+            }
+            workflow {
+                """
+                help             = true
+                workflow_command = null
+                pre_help_text    = null
+                post_help_text   = null
+                validate_params  = false
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.exitStatus == 0
+            assert workflow.stdout.any { it.contains('Input/output options') }
+            assert workflow.stdout.any { it.contains('--outdir') }
+            assert workflow.stdout.any { it.contains('--outdir') }
+        }
+
+    }
+
+    test("Should run help with command") {
+
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+            }
+            workflow {
+                """
+                help             = true
+                workflow_command  = "nextflow run noorg/doesntexist"
+                pre_help_text    = null
+                post_help_text   = null
+                validate_params  = false
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.exitStatus == 0
+            assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') }
+            assert workflow.stdout.any { it.contains('Input/output options') }
+            assert workflow.stdout.any { it.contains('--outdir') }
+            assert workflow.stdout.any { it.contains('--outdir') }
+        }
+
+    }
+
+    test("Should run help with extra text") {
+
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+            }
+            workflow {
+                """
+                help             = true
+                workflow_command  = "nextflow run noorg/doesntexist"
+                pre_help_text    = "pre-help-text"
+                post_help_text   = "post-help-text"
+                validate_params  = false
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.exitStatus == 0
+            assert workflow.stdout.any { it.contains('pre-help-text') }
+            assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') }
+            assert workflow.stdout.any { it.contains('Input/output options') }
+            assert workflow.stdout.any { it.contains('--outdir') }
+            assert workflow.stdout.any { it.contains('--outdir') }
+            assert workflow.stdout.any { it.contains('post-help-text') }
+        }
+
+    }
+
+    test("Should validate params") {
+
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+            }
+            workflow {
+                """
+                help             = false
+                workflow_command  = null
+                pre_help_text    = null
+                post_help_text   = null
+                validate_params  = true
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assert workflow.failed
+            assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') }
+            assert workflow.stdout.any { it.contains('The following invalid input values have been detected:') }
+        }
+
+    }
+
+}
diff --git a/subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test.snap b/subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test.snap
new file mode 100644
index 00000000..ae33a930
--- /dev/null
+++ b/subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test.snap
@@ -0,0 +1,26 @@
+{
+    "Should run help": {
+        "content": [
+            {
+                "stderr": [
+
+                ],
+                "errorReport": "",
+                "exitStatus": 0,
+                "failed": false,
+                "stdout": [
+
+                ],
+                "errorMessage": "",
+                "trace": {
+                    "tasksFailed": 0,
+                    "tasksCount": 0,
+                    "tasksSucceeded": 0
+                },
+                "name": "workflow",
+                "success": true
+            }
+        ],
+        "timestamp": "2023-10-13T13:18:16.933251413"
+    }
+}
diff --git a/subworkflows/nf-core/nfvalidation_plugin_utils/tests/nextflow_schema.json b/subworkflows/nf-core/nfvalidation_plugin_utils/tests/nextflow_schema.json
new file mode 100644
index 00000000..7626c1c9
--- /dev/null
+++ b/subworkflows/nf-core/nfvalidation_plugin_utils/tests/nextflow_schema.json
@@ -0,0 +1,96 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
+    "title": ". pipeline parameters",
+    "description": "",
+    "type": "object",
+    "definitions": {
+        "input_output_options": {
+            "title": "Input/output options",
+            "type": "object",
+            "fa_icon": "fas fa-terminal",
+            "description": "Define where the pipeline should find input data and save output data.",
+            "required": ["outdir"],
+            "properties": {
+                "validate_params": {
+                    "type": "boolean",
+                    "description": "Validate parameters?",
+                    "default": true,
+                    "hidden": true
+                },
+                "outdir": {
+                    "type": "string",
+                    "format": "directory-path",
+                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
+                    "fa_icon": "fas fa-folder-open"
+                },
+                "test_data_base": {
+                    "type": "string",
+                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules",
+                    "description": "Base for test data directory",
+                    "hidden": true
+                },
+                "test_data": {
+                    "type": "string",
+                    "description": "Fake test data param",
+                    "hidden": true
+                }
+            }
+        },
+        "generic_options": {
+            "title": "Generic options",
+            "type": "object",
+            "fa_icon": "fas fa-file-import",
+            "description": "Less common options for the pipeline, typically set in a config file.",
+            "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
+            "properties": {
+                "help": {
+                    "type": "boolean",
+                    "description": "Display help text.",
+                    "fa_icon": "fas fa-question-circle",
+                    "hidden": true
+                },
+                "version": {
+                    "type": "boolean",
+                    "description": "Display version and exit.",
+                    "fa_icon": "fas fa-question-circle",
+                    "hidden": true
+                },
+                "logo": {
+                    "type": "boolean",
+                    "default": true,
+                    "description": "Display nf-core logo in console output.",
+                    "fa_icon": "fas fa-image",
+                    "hidden": true
+                },
+                "singularity_pull_docker_container": {
+                    "type": "boolean",
+                    "description": "Pull Singularity container from Docker?",
+                    "hidden": true
+                },
+                "publish_dir_mode": {
+                    "type": "string",
+                    "default": "copy",
+                    "description": "Method used to save pipeline results to output directory.",
+                    "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
+                    "fa_icon": "fas fa-copy",
+                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
+                    "hidden": true
+                },
+                "monochrome_logs": {
+                    "type": "boolean",
+                    "description": "Use monochrome_logs",
+                    "hidden": true
+                }
+            }
+        }
+    },
+    "allOf": [
+        {
+            "$ref": "#/definitions/input_output_options"
+        },
+        {
+            "$ref": "#/definitions/generic_options"
+        }
+    ]
+}

From 94d75cb01b0545a4cc2edf992e073a83707990fb Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 16 Oct 2023 16:00:54 +0200
Subject: [PATCH 561/852] fix

---
 subworkflows/local/nf_core_fetchngs_utils/main.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf
index 05f9a2ba..f20bdbe7 100644
--- a/subworkflows/local/nf_core_fetchngs_utils/main.nf
+++ b/subworkflows/local/nf_core_fetchngs_utils/main.nf
@@ -44,7 +44,8 @@ workflow PIPELINE_INITIALISATION {
         workflow_command,
         pre_help_text,
         post_help_text,
-        params.validate_params
+        params.validate_params,
+        "nextflow_schema.json"
     )
 
     //

From f372eeb771adfb48cda42d42704e92b7876dc1b7 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 16 Oct 2023 16:06:50 +0200
Subject: [PATCH 562/852] Use nf-core subworkflow: NFCORE_PIPELINE_UTILS

---
 modules.json                                  |   5 +
 .../local/nf_core_fetchngs_utils/main.nf      |  14 +-
 .../nfcore_pipeline_utils}/main.nf            |   5 +-
 .../nf-core/nfcore_pipeline_utils/meta.yml    |  17 +++
 .../tests/main.function.nf.test               | 120 ++++++++++++++++++
 .../tests/main.function.nf.test.snap          |  78 ++++++++++++
 .../tests/main.workflow.nf.test               |  33 +++++
 .../tests/nextflow.config                     |   9 ++
 8 files changed, 277 insertions(+), 4 deletions(-)
 rename subworkflows/{local/nf_core_pipeline_utils => nf-core/nfcore_pipeline_utils}/main.nf (99%)
 create mode 100644 subworkflows/nf-core/nfcore_pipeline_utils/meta.yml
 create mode 100644 subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test
 create mode 100644 subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test.snap
 create mode 100644 subworkflows/nf-core/nfcore_pipeline_utils/tests/main.workflow.nf.test
 create mode 100644 subworkflows/nf-core/nfcore_pipeline_utils/tests/nextflow.config

diff --git a/modules.json b/modules.json
index 3cc9d6dd..d6f5a884 100644
--- a/modules.json
+++ b/modules.json
@@ -38,6 +38,11 @@
                         "branch": "master",
                         "git_sha": "76cbb00305f6b045c15c1e202a5bdd516d6f64a3",
                         "installed_by": ["subworkflows"]
+                    },
+                    "nfcore_pipeline_utils": {
+                        "branch": "master",
+                        "git_sha": "b1f3d31bbf14fe83959cc03f98db96c6b4f73b37",
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }
diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf
index fd0e9855..f3035b58 100644
--- a/subworkflows/local/nf_core_fetchngs_utils/main.nf
+++ b/subworkflows/local/nf_core_fetchngs_utils/main.nf
@@ -9,9 +9,17 @@
 */
 
 include { CUSTOM_DUMPSOFTWAREVERSIONS                 } from '../../../modules/nf-core/custom/dumpsoftwareversions'
-include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion } from '../../nf-core/nextflowpipelineutils/main'
+include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion  } from '../../nf-core/nextflowpipelineutils/main'
 include { NF_VALIDATION_PLUGIN_UTILS                  } from '../nf_validation_plugin_utils'
-include { NF_CORE_PIPELINE_UTILS; workflowCitation; nfCoreLogo; dashedLine; completionEmail; completionSummary; imNotification } from '../nf_core_pipeline_utils'
+include { 
+    NFCORE_PIPELINE_UTILS; 
+    workflowCitation; 
+    nfCoreLogo; 
+    dashedLine; 
+    completionEmail; 
+    completionSummary; 
+    imNotification 
+} from '../../nf-core/nf_core_pipeline_utils'
 
 /*
 ========================================================================================
@@ -50,7 +58,7 @@ workflow PIPELINE_INITIALISATION {
     //
     // Check config provided to the pipeline
     //
-    NF_CORE_PIPELINE_UTILS ()
+    NFCORE_PIPELINE_UTILS ()
 
     //
     // Auto-detect input id type
diff --git a/subworkflows/local/nf_core_pipeline_utils/main.nf b/subworkflows/nf-core/nfcore_pipeline_utils/main.nf
similarity index 99%
rename from subworkflows/local/nf_core_pipeline_utils/main.nf
rename to subworkflows/nf-core/nfcore_pipeline_utils/main.nf
index 18bf238b..b3b136dc 100644
--- a/subworkflows/local/nf_core_pipeline_utils/main.nf
+++ b/subworkflows/nf-core/nfcore_pipeline_utils/main.nf
@@ -8,11 +8,14 @@
 ========================================================================================
 */
 
-workflow NF_CORE_PIPELINE_UTILS {
+workflow NFCORE_PIPELINE_UTILS {
 
     main:
     checkConfigProvided()
 
+    emit:
+    success = true
+
 }
 
 /*
diff --git a/subworkflows/nf-core/nfcore_pipeline_utils/meta.yml b/subworkflows/nf-core/nfcore_pipeline_utils/meta.yml
new file mode 100644
index 00000000..5721b7e3
--- /dev/null
+++ b/subworkflows/nf-core/nfcore_pipeline_utils/meta.yml
@@ -0,0 +1,17 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "NFCORE_PIPELINE_UTILS"
+description: Subworkflow with utility functions specific to the nf-core pipeline template
+keywords:
+  - utility
+  - pipeline
+  - initialise
+  - version
+components: []
+input: []
+output:
+  - success:
+      type: boolean
+      description: |
+        Dummy output to indicate success
+authors:
+  - "@adamrtalbot"
diff --git a/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test b/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test
new file mode 100644
index 00000000..265ece39
--- /dev/null
+++ b/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test
@@ -0,0 +1,120 @@
+
+nextflow_function {
+
+    name "Test Functions"
+    script "../main.nf"
+    config "subworkflows/nf-core/nfcore_pipeline_utils/tests/nextflow.config"
+	
+    test("Test Function checkConfigProvided") {
+
+        function "checkConfigProvided"
+
+        when {
+            function {
+                """
+                // define inputs of the function here. Example:
+                // input[0] = 1
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert function.success                  },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+    test("Test Function workflowCitation") {
+
+        function "workflowCitation"
+
+        when {
+            function {
+                """
+                // define inputs of the function here. Example:
+                // input[0] = 1
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert function.success                  },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+    test("Test Function nfCoreLogo") {
+
+        function "nfCoreLogo"
+
+        when {
+            function {
+                """
+                input[0] = "9.9.9"
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert function.success                  },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+	
+
+    test("Test Function dashedLine") {
+
+        function "dashedLine"
+
+        when {
+            function {
+                """
+                // define inputs of the function here. Example:
+                // input[0] = 1
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert function.success                  },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+	
+
+    test("Test Function logColours") {
+
+        function "logColours"
+
+        when {
+            function {
+                """
+                // define inputs of the function here. Example:
+                // input[0] = 1
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert function.success                  },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test.snap b/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test.snap
new file mode 100644
index 00000000..3ea51f68
--- /dev/null
+++ b/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test.snap
@@ -0,0 +1,78 @@
+{
+    "Test Function logColours": {
+        "content": [
+            {
+                "reset": "\u001b[0m",
+                "bold": "\u001b[1m",
+                "dim": "\u001b[2m",
+                "underlined": "\u001b[4m",
+                "blink": "\u001b[5m",
+                "reverse": "\u001b[7m",
+                "hidden": "\u001b[8m",
+                "black": "\u001b[0;30m",
+                "red": "\u001b[0;31m",
+                "green": "\u001b[0;32m",
+                "yellow": "\u001b[0;33m",
+                "blue": "\u001b[0;34m",
+                "purple": "\u001b[0;35m",
+                "cyan": "\u001b[0;36m",
+                "white": "\u001b[0;37m",
+                "bblack": "\u001b[1;30m",
+                "bred": "\u001b[1;31m",
+                "bgreen": "\u001b[1;32m",
+                "byellow": "\u001b[1;33m",
+                "bblue": "\u001b[1;34m",
+                "bpurple": "\u001b[1;35m",
+                "bcyan": "\u001b[1;36m",
+                "bwhite": "\u001b[1;37m",
+                "ublack": "\u001b[4;30m",
+                "ured": "\u001b[4;31m",
+                "ugreen": "\u001b[4;32m",
+                "uyellow": "\u001b[4;33m",
+                "ublue": "\u001b[4;34m",
+                "upurple": "\u001b[4;35m",
+                "ucyan": "\u001b[4;36m",
+                "uwhite": "\u001b[4;37m",
+                "iblack": "\u001b[0;90m",
+                "ired": "\u001b[0;91m",
+                "igreen": "\u001b[0;92m",
+                "iyellow": "\u001b[0;93m",
+                "iblue": "\u001b[0;94m",
+                "ipurple": "\u001b[0;95m",
+                "icyan": "\u001b[0;96m",
+                "iwhite": "\u001b[0;97m",
+                "biblack": "\u001b[1;90m",
+                "bired": "\u001b[1;91m",
+                "bigreen": "\u001b[1;92m",
+                "biyellow": "\u001b[1;93m",
+                "biblue": "\u001b[1;94m",
+                "bipurple": "\u001b[1;95m",
+                "bicyan": "\u001b[1;96m",
+                "biwhite": "\u001b[1;97m"
+            }
+        ],
+        "timestamp": "2023-10-16T14:27:09.843064"
+    },
+    "Test Function checkConfigProvided": {
+        "content": null,
+        "timestamp": "2023-10-16T14:27:01.415849"
+    },
+    "Test Function nfCoreLogo": {
+        "content": [
+            "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n                                        \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m        ___     __   __   __   ___     \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \u001b[0;33m}  {\u001b[0m\n\u001b[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \u001b[0;32m\\`-._,-`-,\u001b[0m\n                                        \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m  nextflow_workflow 9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n"
+        ],
+        "timestamp": "2023-10-16T14:27:51.566211"
+    },
+    "Test Function workflowCitation": {
+        "content": [
+            "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n  https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n  https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n  https://github.com/nextflow_workflow/blob/master/CITATIONS.md"
+        ],
+        "timestamp": "2023-10-16T14:27:03.505737"
+    },
+    "Test Function dashedLine": {
+        "content": [
+            "-\u001b[2m----------------------------------------------------\u001b[0m-"
+        ],
+        "timestamp": "2023-10-16T14:27:07.721916"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.workflow.nf.test b/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.workflow.nf.test
new file mode 100644
index 00000000..ad7c73a8
--- /dev/null
+++ b/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.workflow.nf.test
@@ -0,0 +1,33 @@
+nextflow_workflow {
+
+    name "Test Workflow NFCORE_PIPELINE_UTILS"
+    script "../main.nf"
+    config "subworkflows/nf-core/nfcore_pipeline_utils/tests/nextflow.config"
+    workflow "NFCORE_PIPELINE_UTILS"
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "nfcorepipelineutils"
+    tag "subworkflows/nfcorepipelineutils"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                // define parameters here. Example:
+                // outdir = "tests/results"
+            }
+            workflow {
+                """
+                // define inputs of the workflow here. Example:
+                // input[0] = file("test-file.txt")
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
+}
diff --git a/subworkflows/nf-core/nfcore_pipeline_utils/tests/nextflow.config b/subworkflows/nf-core/nfcore_pipeline_utils/tests/nextflow.config
new file mode 100644
index 00000000..53574ffe
--- /dev/null
+++ b/subworkflows/nf-core/nfcore_pipeline_utils/tests/nextflow.config
@@ -0,0 +1,9 @@
+manifest {
+    name            = 'nextflow_workflow'
+    author          = """nf-core"""
+    homePage        = 'https://127.0.0.1'
+    description     = """Dummy pipeline"""
+    nextflowVersion  = '!>=23.04.0'
+    version         = '9.9.9'
+    doi             = 'https://doi.org/10.5281/zenodo.5070524'
+}
\ No newline at end of file

From 86cfae283941445a1d748a16669032e42cdee7e8 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 16 Oct 2023 16:12:01 +0200
Subject: [PATCH 563/852] Update nextflowpipelineutils

---
 modules.json                                                  | 2 +-
 .../nextflowpipelineutils/tests/main.functions.nf.test        | 1 +
 .../nextflowpipelineutils/tests/main.functions.nf.test.snap   | 4 ++--
 .../nf-core/nextflowpipelineutils/tests/nextflow.config       | 2 +-
 subworkflows/nf-core/nextflowpipelineutils/tests/tags.yml     | 2 --
 5 files changed, 5 insertions(+), 6 deletions(-)
 delete mode 100644 subworkflows/nf-core/nextflowpipelineutils/tests/tags.yml

diff --git a/modules.json b/modules.json
index 3cc9d6dd..ecd043f9 100644
--- a/modules.json
+++ b/modules.json
@@ -36,7 +36,7 @@
                     },
                     "nextflowpipelineutils": {
                         "branch": "master",
-                        "git_sha": "76cbb00305f6b045c15c1e202a5bdd516d6f64a3",
+                        "git_sha": "1405b3d5078f108f86a2c122846ed2797b4ec8bf",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test b/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test
index db757ed1..1a1577eb 100644
--- a/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test
+++ b/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test
@@ -3,6 +3,7 @@ nextflow_function {
 
     name "Test Functions"
     script "subworkflows/nf-core/nextflowpipelineutils/main.nf"
+    config "subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config"
     tag 'subworkflows'
     tag 'nextflowpipelineutils'
     tag 'subworkflows/nextflowpipelineutils'
diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test.snap b/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test.snap
index 956bfac7..939dbbad 100644
--- a/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test.snap
+++ b/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test.snap
@@ -1,9 +1,9 @@
 {
     "Test Function getWorkflowVersion": {
         "content": [
-            ""
+            "v9.9.9"
         ],
-        "timestamp": "2023-10-12T17:09:20.935733"
+        "timestamp": "2023-10-15T13:43:55.128868"
     },
     "Test Function checkCondaChannels": {
         "content": null,
diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config b/subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config
index 035c0f5d..53574ffe 100644
--- a/subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config
+++ b/subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config
@@ -3,7 +3,7 @@ manifest {
     author          = """nf-core"""
     homePage        = 'https://127.0.0.1'
     description     = """Dummy pipeline"""
-    nextflowVersion  = '!>=23.04.4'
+    nextflowVersion  = '!>=23.04.0'
     version         = '9.9.9'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/tags.yml b/subworkflows/nf-core/nextflowpipelineutils/tests/tags.yml
deleted file mode 100644
index 57127a2a..00000000
--- a/subworkflows/nf-core/nextflowpipelineutils/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-nextflowpipelineutils:
-  - subworkflows/nf-core/nextflowpipelineutils/**

From 4464c07f301ecafea93ae83a624c3730f290daca Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 16 Oct 2023 16:13:46 +0200
Subject: [PATCH 564/852] path fix

---
 subworkflows/local/nf_core_fetchngs_utils/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf
index f3035b58..b964ab5b 100644
--- a/subworkflows/local/nf_core_fetchngs_utils/main.nf
+++ b/subworkflows/local/nf_core_fetchngs_utils/main.nf
@@ -19,7 +19,7 @@ include {
     completionEmail; 
     completionSummary; 
     imNotification 
-} from '../../nf-core/nf_core_pipeline_utils'
+} from '../../nf-core/nfcore_pipeline_utils'
 
 /*
 ========================================================================================

From 52c4100dbc5ddb0d0950a8f68ff3a4a78cd2e847 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 16 Oct 2023 16:19:52 +0200
Subject: [PATCH 565/852] Update
 subworkflows/local/nf_core_fetchngs_utils/main.nf

Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
---
 subworkflows/local/nf_core_fetchngs_utils/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf
index b964ab5b..376f999e 100644
--- a/subworkflows/local/nf_core_fetchngs_utils/main.nf
+++ b/subworkflows/local/nf_core_fetchngs_utils/main.nf
@@ -9,7 +9,7 @@
 */
 
 include { CUSTOM_DUMPSOFTWAREVERSIONS                 } from '../../../modules/nf-core/custom/dumpsoftwareversions'
-include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion  } from '../../nf-core/nextflowpipelineutils/main'
+include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion } from '../../nf-core/nextflowpipelineutils/main'
 include { NF_VALIDATION_PLUGIN_UTILS                  } from '../nf_validation_plugin_utils'
 include { 
     NFCORE_PIPELINE_UTILS; 

From 16ce425f0afad8b0bb7f957704284fbfee0449b1 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 17 Oct 2023 16:15:35 +0200
Subject: [PATCH 566/852] update modules

---
 modules.json                                  | 23 ++++---
 .../sratoolsncbisettings/tests/tags.yml       |  2 +
 modules/nf-core/untar/main.nf                 | 63 +++++++++++++++++++
 modules/nf-core/untar/meta.yml                | 41 ++++++++++++
 4 files changed, 120 insertions(+), 9 deletions(-)
 create mode 100644 modules/nf-core/custom/sratoolsncbisettings/tests/tags.yml
 create mode 100644 modules/nf-core/untar/main.nf
 create mode 100644 modules/nf-core/untar/meta.yml

diff --git a/modules.json b/modules.json
index 7bf618ff..e5e6bbc6 100644
--- a/modules.json
+++ b/modules.json
@@ -7,23 +7,28 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0",
+                        "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5",
                         "installed_by": ["modules"]
                     },
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
-                        "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0",
+                        "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0",
+                        "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/prefetch": {
                         "branch": "master",
-                        "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0",
+                        "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
+                    },
+                    "untar": {
+                        "branch": "master",
+                        "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
+                        "installed_by": ["modules"]
                     }
                 }
             },
@@ -31,7 +36,7 @@
                 "nf-core": {
                     "fastq_download_prefetch_fasterqdump_sratools": {
                         "branch": "master",
-                        "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0",
+                        "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5",
                         "installed_by": ["subworkflows"]
                     },
                     "nextflowpipelineutils": {
@@ -39,14 +44,14 @@
                         "git_sha": "1405b3d5078f108f86a2c122846ed2797b4ec8bf",
                         "installed_by": ["subworkflows"]
                     },
-                    "nfvalidation_plugin_utils": {
+                    "nfcore_pipeline_utils": {
                         "branch": "master",
-                        "git_sha": "a8223a72def6cc46f4652a348feba21845ce68c6",
+                        "git_sha": "b1f3d31bbf14fe83959cc03f98db96c6b4f73b37",
                         "installed_by": ["subworkflows"]
                     },
-                    "nfcore_pipeline_utils": {
+                    "nfvalidation_plugin_utils": {
                         "branch": "master",
-                        "git_sha": "b1f3d31bbf14fe83959cc03f98db96c6b4f73b37",
+                        "git_sha": "a8223a72def6cc46f4652a348feba21845ce68c6",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/tags.yml b/modules/nf-core/custom/sratoolsncbisettings/tests/tags.yml
new file mode 100644
index 00000000..fb4a08a7
--- /dev/null
+++ b/modules/nf-core/custom/sratoolsncbisettings/tests/tags.yml
@@ -0,0 +1,2 @@
+custom/sratoolsncbisettings:
+  - modules/nf-core/custom/sratoolsncbisettings/**
diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf
new file mode 100644
index 00000000..61461c39
--- /dev/null
+++ b/modules/nf-core/untar/main.nf
@@ -0,0 +1,63 @@
+process UNTAR {
+    tag "$archive"
+    label 'process_single'
+
+    conda "conda-forge::sed=4.7 conda-forge::grep=3.11 conda-forge::tar=1.34"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'nf-core/ubuntu:20.04' }"
+
+    input:
+    tuple val(meta), path(archive)
+
+    output:
+    tuple val(meta), path("$prefix"), emit: untar
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args  = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    prefix    = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName.toString().replaceFirst(/\.tar$/, ""))
+
+    """
+    mkdir $prefix
+
+    ## Ensures --strip-components only applied when top level of tar contents is a directory
+    ## If just files or multiple directories, place all in prefix
+    if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then
+        tar \\
+            -C $prefix --strip-components 1 \\
+            -xavf \\
+            $args \\
+            $archive \\
+            $args2
+    else
+        tar \\
+            -C $prefix \\
+            -xavf \\
+            $args \\
+            $archive \\
+            $args2
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    prefix    = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, ""))
+    """
+    mkdir $prefix
+    touch ${prefix}/file.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml
new file mode 100644
index 00000000..db241a6e
--- /dev/null
+++ b/modules/nf-core/untar/meta.yml
@@ -0,0 +1,41 @@
+name: untar
+description: Extract files.
+keywords:
+  - untar
+  - uncompress
+  - extract
+tools:
+  - untar:
+      description: |
+        Extract tar.gz files.
+      documentation: https://www.gnu.org/software/tar/manual/
+      licence: ["GPL-3.0-or-later"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - archive:
+      type: file
+      description: File to be untar
+      pattern: "*.{tar}.{gz}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - untar:
+      type: directory
+      description: Directory containing contents of archive
+      pattern: "*/"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@matthdsm"
+  - "@jfy133"

From 5875c57588cafd1f9f3389be3a2842bbf33c0f00 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 17 Oct 2023 16:18:55 +0200
Subject: [PATCH 567/852] patch custom-dumpsoftwareversions snap

---
 .../custom-dumpsoftwareversions.diff          | 49 +++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff

diff --git a/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff b/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff
new file mode 100644
index 00000000..307c06ea
--- /dev/null
+++ b/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff
@@ -0,0 +1,49 @@
+Changes in module 'nf-core/custom/dumpsoftwareversions'
+--- /dev/null
++++ modules/nf-core/custom/dumpsoftwareversions/nextflow.config
+@@ -0,0 +1,10 @@
++process {
++    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
++        cache = false
++        publishDir = [
++            path: { "${params.outdir}/pipeline_info" },
++            mode: params.publish_dir_mode,
++            pattern: '*_versions.yml'
++        ]
++    }
++}
+--- modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
++++ modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
+@@ -3,25 +3,25 @@
+         "content": [
+             {
+                 "0": [
+-                    "software_versions.yml:md5,a027f820f30b8191a20ca16465daaf37"
++                    "software_versions.yml:md5,45e271267967cd582c53d2cc609f8e02"
+                 ],
+                 "1": [
+-                    "software_versions_mqc.yml:md5,ee4a1d028ad29987f9ac511f4668f17c"
++                    "software_versions_mqc.yml:md5,2b6b639f9edde0b032afcd9d2fcf6877"
+                 ],
+                 "2": [
+                     "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3"
+                 ],
+                 "mqc_yml": [
+-                    "software_versions_mqc.yml:md5,ee4a1d028ad29987f9ac511f4668f17c"
++                    "software_versions_mqc.yml:md5,2b6b639f9edde0b032afcd9d2fcf6877"
+                 ],
+                 "versions": [
+                     "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3"
+                 ],
+                 "yml": [
+-                    "software_versions.yml:md5,a027f820f30b8191a20ca16465daaf37"
++                    "software_versions.yml:md5,45e271267967cd582c53d2cc609f8e02"
+                 ]
+             }
+         ],
+-        "timestamp": "2023-10-11T17:10:02.930699"
++        "timestamp": "2023-10-17T16:16:58.324012"
+     }
+-}
++}
+************************************************************

From 4312b74fface24c1069826c402ac343719a991d6 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 17 Oct 2023 16:33:44 +0200
Subject: [PATCH 568/852] update snaps

---
 .../custom/dumpsoftwareversions/tests/main.nf.test.snap       | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
index 8713b921..c4e7a6d3 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
+++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
@@ -22,6 +22,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-11T17:10:02.930699"
+        "timestamp": "2023-10-17T16:16:58.324012"
     }
-}
+}
\ No newline at end of file

From 2f47befc1d66324ecbddd06bf184a5e2b645b1ae Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 17 Oct 2023 16:43:48 +0200
Subject: [PATCH 569/852] Replace CUSTOM_DUMPSOFTWAREVERSIONS with collectFile
 operator

---
 modules.json                                  |  13 +--
 .../custom/dumpsoftwareversions/main.nf       |  24 -----
 .../custom/dumpsoftwareversions/meta.yml      |  36 -------
 .../dumpsoftwareversions/nextflow.config      |  10 --
 .../templates/dumpsoftwareversions.py         | 101 ------------------
 .../dumpsoftwareversions/tests/main.nf.test   |  38 -------
 .../tests/main.nf.test.snap                   |  27 -----
 .../dumpsoftwareversions/tests/tags.yml       |   2 -
 .../local/nf_core_fetchngs_utils/main.nf      |  12 ++-
 9 files changed, 12 insertions(+), 251 deletions(-)
 delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/main.nf
 delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/meta.yml
 delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/nextflow.config
 delete mode 100755 modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
 delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
 delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
 delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml

diff --git a/modules.json b/modules.json
index 7bf618ff..81b6b318 100644
--- a/modules.json
+++ b/modules.json
@@ -5,11 +5,6 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
-                    "custom/dumpsoftwareversions": {
-                        "branch": "master",
-                        "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0",
-                        "installed_by": ["modules"]
-                    },
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
                         "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0",
@@ -39,14 +34,14 @@
                         "git_sha": "1405b3d5078f108f86a2c122846ed2797b4ec8bf",
                         "installed_by": ["subworkflows"]
                     },
-                    "nfvalidation_plugin_utils": {
+                    "nfcore_pipeline_utils": {
                         "branch": "master",
-                        "git_sha": "a8223a72def6cc46f4652a348feba21845ce68c6",
+                        "git_sha": "b1f3d31bbf14fe83959cc03f98db96c6b4f73b37",
                         "installed_by": ["subworkflows"]
                     },
-                    "nfcore_pipeline_utils": {
+                    "nfvalidation_plugin_utils": {
                         "branch": "master",
-                        "git_sha": "b1f3d31bbf14fe83959cc03f98db96c6b4f73b37",
+                        "git_sha": "a8223a72def6cc46f4652a348feba21845ce68c6",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
deleted file mode 100644
index c9d014b1..00000000
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ /dev/null
@@ -1,24 +0,0 @@
-process CUSTOM_DUMPSOFTWAREVERSIONS {
-    label 'process_single'
-
-    // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda "bioconda::multiqc=1.15"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.15--pyhdfd78af_0' }"
-
-    input:
-    path versions
-
-    output:
-    path "software_versions.yml"    , emit: yml
-    path "software_versions_mqc.yml", emit: mqc_yml
-    path "versions.yml"             , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    template 'dumpsoftwareversions.py'
-}
diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
deleted file mode 100644
index c32657de..00000000
--- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml
+++ /dev/null
@@ -1,36 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
-name: custom_dumpsoftwareversions
-description: Custom module used to dump software versions within the nf-core pipeline template
-keywords:
-  - custom
-  - dump
-  - version
-tools:
-  - custom:
-      description: Custom module used to dump software versions within the nf-core pipeline template
-      homepage: https://github.com/nf-core/tools
-      documentation: https://github.com/nf-core/tools
-      licence: ["MIT"]
-input:
-  - versions:
-      type: file
-      description: YML file containing software versions
-      pattern: "*.yml"
-
-output:
-  - yml:
-      type: file
-      description: Standard YML file containing software versions
-      pattern: "software_versions.yml"
-  - mqc_yml:
-      type: file
-      description: MultiQC custom content YML file containing software versions
-      pattern: "software_versions_mqc.yml"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-
-authors:
-  - "@drpatelh"
-  - "@grst"
diff --git a/modules/nf-core/custom/dumpsoftwareversions/nextflow.config b/modules/nf-core/custom/dumpsoftwareversions/nextflow.config
deleted file mode 100644
index 241654e7..00000000
--- a/modules/nf-core/custom/dumpsoftwareversions/nextflow.config
+++ /dev/null
@@ -1,10 +0,0 @@
-process {
-    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            pattern: '*_versions.yml'
-        ]
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
deleted file mode 100755
index da033408..00000000
--- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ /dev/null
@@ -1,101 +0,0 @@
-#!/usr/bin/env python
-
-
-"""Provide functions to merge multiple versions.yml files."""
-
-
-import yaml
-import platform
-from textwrap import dedent
-
-
-def _make_versions_html(versions):
-    """Generate a tabular HTML output of all versions for MultiQC."""
-    html = [
-        dedent(
-            """\\
-            <style>
-            #nf-core-versions tbody:nth-child(even) {
-                background-color: #f2f2f2;
-            }
-            </style>
-            <table class="table" style="width:100%" id="nf-core-versions">
-                <thead>
-                    <tr>
-                        <th> Process Name </th>
-                        <th> Software </th>
-                        <th> Version  </th>
-                    </tr>
-                </thead>
-            """
-        )
-    ]
-    for process, tmp_versions in sorted(versions.items()):
-        html.append("<tbody>")
-        for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
-            html.append(
-                dedent(
-                    f"""\\
-                    <tr>
-                        <td><samp>{process if (i == 0) else ''}</samp></td>
-                        <td><samp>{tool}</samp></td>
-                        <td><samp>{version}</samp></td>
-                    </tr>
-                    """
-                )
-            )
-        html.append("</tbody>")
-    html.append("</table>")
-    return "\\n".join(html)
-
-
-def main():
-    """Load all version files and generate merged output."""
-    versions_this_module = {}
-    versions_this_module["${task.process}"] = {
-        "python": platform.python_version(),
-        "yaml": yaml.__version__,
-    }
-
-    with open("$versions") as f:
-        versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
-
-    # aggregate versions by the module name (derived from fully-qualified process name)
-    versions_by_module = {}
-    for process, process_versions in versions_by_process.items():
-        module = process.split(":")[-1]
-        try:
-            if versions_by_module[module] != process_versions:
-                raise AssertionError(
-                    "We assume that software versions are the same between all modules. "
-                    "If you see this error-message it means you discovered an edge-case "
-                    "and should open an issue in nf-core/tools. "
-                )
-        except KeyError:
-            versions_by_module[module] = process_versions
-
-    versions_by_module["Workflow"] = {
-        "Nextflow": "$workflow.nextflow.version",
-        "$workflow.manifest.name": "$workflow.manifest.version",
-    }
-
-    versions_mqc = {
-        "id": "software_versions",
-        "section_name": "${workflow.manifest.name} Software Versions",
-        "section_href": "https://github.com/${workflow.manifest.name}",
-        "plot_type": "html",
-        "description": "are collected at run time from the software output.",
-        "data": _make_versions_html(versions_by_module),
-    }
-
-    with open("software_versions.yml", "w") as f:
-        yaml.dump(versions_by_module, f, default_flow_style=False)
-    with open("software_versions_mqc.yml", "w") as f:
-        yaml.dump(versions_mqc, f, default_flow_style=False)
-
-    with open("versions.yml", "w") as f:
-        yaml.dump(versions_this_module, f, default_flow_style=False)
-
-
-if __name__ == "__main__":
-    main()
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
deleted file mode 100644
index eec1db10..00000000
--- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
+++ /dev/null
@@ -1,38 +0,0 @@
-nextflow_process {
-
-    name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS"
-    script "../main.nf"
-    process "CUSTOM_DUMPSOFTWAREVERSIONS"
-    tag "modules"
-    tag "modules_nfcore"
-    tag "custom"
-    tag "dumpsoftwareversions"
-    tag "custom/dumpsoftwareversions"
-
-    test("Should run without failures") {
-        when {
-            process {
-                """
-                def tool1_version = '''
-                TOOL1:
-                    tool1: 0.11.9
-                '''.stripIndent()
-
-                def tool2_version = '''
-                TOOL2:
-                    tool2: 1.9
-                '''.stripIndent()
-
-                input[0] = Channel.of(tool1_version, tool2_version).collectFile()
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-}
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
deleted file mode 100644
index 8713b921..00000000
--- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
+++ /dev/null
@@ -1,27 +0,0 @@
-{
-    "Should run without failures": {
-        "content": [
-            {
-                "0": [
-                    "software_versions.yml:md5,a027f820f30b8191a20ca16465daaf37"
-                ],
-                "1": [
-                    "software_versions_mqc.yml:md5,ee4a1d028ad29987f9ac511f4668f17c"
-                ],
-                "2": [
-                    "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3"
-                ],
-                "mqc_yml": [
-                    "software_versions_mqc.yml:md5,ee4a1d028ad29987f9ac511f4668f17c"
-                ],
-                "versions": [
-                    "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3"
-                ],
-                "yml": [
-                    "software_versions.yml:md5,a027f820f30b8191a20ca16465daaf37"
-                ]
-            }
-        ],
-        "timestamp": "2023-10-11T17:10:02.930699"
-    }
-}
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml
deleted file mode 100644
index 405aa24a..00000000
--- a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-custom/dumpsoftwareversions:
-  - modules/nf-core/custom/dumpsoftwareversions/**
diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf
index eecc62e1..287ed0db 100644
--- a/subworkflows/local/nf_core_fetchngs_utils/main.nf
+++ b/subworkflows/local/nf_core_fetchngs_utils/main.nf
@@ -8,7 +8,6 @@
 ========================================================================================
 */
 
-include { CUSTOM_DUMPSOFTWAREVERSIONS                 } from '../../../modules/nf-core/custom/dumpsoftwareversions'
 include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion } from '../../nf-core/nextflowpipelineutils/main'
 include { NF_VALIDATION_PLUGIN_UTILS                  } from '../../nf-core/nfvalidation_plugin_utils/main.nf'
 include { 
@@ -113,9 +112,14 @@ workflow PIPELINE_COMPLETION {
     //
     // MODULE: Dump software versions for all tools used in the workflow
     //
-    CUSTOM_DUMPSOFTWAREVERSIONS (
-        versions.collectFile(name: 'collated_versions.yml')
-    )
+    pipeline_version_info = Channel.of("""
+    "Workflow":
+        "Nextflow": ${workflow.nextflow.version},
+        "${workflow.manifest.name}": ${workflow.manifest.version},
+    """.stripIndent())
+
+    versions = versions.mix(pipeline_version_info)
+    versions.collectFile(name: 'versions.yml', storeDir: "${params.outdir}/pipeline_info")
 
     //
     // Completion email and summary

From f941c4db34d66547ce2bcafd90638138ba3388d4 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 17 Oct 2023 16:46:28 +0200
Subject: [PATCH 570/852] fixup

---
 nextflow.config | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 3589e118..f7674569 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -65,9 +65,6 @@ try {
     System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
 }
 
-// Module specific configs
-includeConfig './modules/nf-core/custom/dumpsoftwareversions/nextflow.config'
-
 // Workflow specific configs
 if (params.input_type == 'sra') {
     includeConfig './workflows/sra/nextflow.config'

From ba1924327a061d594fed190b610ef2307a11f3d0 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 17 Oct 2023 17:10:23 +0200
Subject: [PATCH 571/852] gitignore

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index ff233cdb..ef809d7c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,6 +4,7 @@
 .nf-test.log
 data/
 nf-test
+.nf-test*
 results/
 test.xml
 testing*

From 364e6baf05fdcc3f60f963361cfcb9a999c8707a Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 17 Oct 2023 17:16:08 +0200
Subject: [PATCH 572/852] Use software versions file that matches MultiQC input

---
 subworkflows/local/nf_core_fetchngs_utils/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf
index 287ed0db..f07e7997 100644
--- a/subworkflows/local/nf_core_fetchngs_utils/main.nf
+++ b/subworkflows/local/nf_core_fetchngs_utils/main.nf
@@ -119,7 +119,7 @@ workflow PIPELINE_COMPLETION {
     """.stripIndent())
 
     versions = versions.mix(pipeline_version_info)
-    versions.collectFile(name: 'versions.yml', storeDir: "${params.outdir}/pipeline_info")
+    versions.collectFile(name: 'fetchngs_mqc_versions.yml', storeDir: "${params.outdir}/pipeline_info")
 
     //
     // Completion email and summary

From e6c79c557ab1ce39533c4fe063abcebf20a3b31e Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 17 Oct 2023 17:29:21 +0200
Subject: [PATCH 573/852] tidy

---
 subworkflows/local/nf_core_fetchngs_utils/main.nf | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf
index f07e7997..509a4473 100644
--- a/subworkflows/local/nf_core_fetchngs_utils/main.nf
+++ b/subworkflows/local/nf_core_fetchngs_utils/main.nf
@@ -112,10 +112,9 @@ workflow PIPELINE_COMPLETION {
     //
     // MODULE: Dump software versions for all tools used in the workflow
     //
-    pipeline_version_info = Channel.of("""
-    "Workflow":
-        "Nextflow": ${workflow.nextflow.version},
-        "${workflow.manifest.name}": ${workflow.manifest.version},
+    pipeline_version_info = Channel.of("""\"workflow\":
+        nextflow: ${workflow.nextflow.version}
+        ${workflow.manifest.name}: ${workflow.manifest.version}
     """.stripIndent())
 
     versions = versions.mix(pipeline_version_info)

From a9d8ae875c5797c137ca80eb6f8833299aff2ab9 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 17 Oct 2023 17:50:16 +0200
Subject: [PATCH 574/852] forgot patch

---
 modules.json | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules.json b/modules.json
index e5e6bbc6..4966f053 100644
--- a/modules.json
+++ b/modules.json
@@ -8,7 +8,8 @@
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff"
                     },
                     "custom/sratoolsncbisettings": {
                         "branch": "master",

From cedd600b2e8de83a5671d8b3c0fd803571039063 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 17 Oct 2023 17:57:37 +0200
Subject: [PATCH 575/852] add data

---
 conf/test_data.config | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/conf/test_data.config b/conf/test_data.config
index 68e84262..670115a8 100644
--- a/conf/test_data.config
+++ b/conf/test_data.config
@@ -24,6 +24,12 @@ params {
     }
 
     test_data {
+        'sarscov2'{
+            'illumina' {
+                SRR11140744_tar_gz                  = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR11140744.tar.gz"
+                SRR13255544_tar_gz                  = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR13255544.tar.gz"
+            }
+        }
         'generic' {
             'config' {
                 ncbi_user_settings                  = "${params.test_data_base}/data/generic/config/ncbi_user_settings.mkfg"

From 5884bba8db03ffb58fc6e2fb00e33d602e13fb1b Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 18 Oct 2023 10:32:07 +0200
Subject: [PATCH 576/852] tinier tests + patch fasterdump

---
 modules.json                                                | 3 ++-
 .../nf-core/sratools/fasterqdump/tests/main.nf.test.snap    | 4 ++--
 tests/sra_ids_test.csv                                      | 6 +-----
 workflows/sra/tests/main.nf.test                            | 2 +-
 workflows/sra/tests/sra_force_sratools_download.nf.test     | 2 +-
 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test    | 2 +-
 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test     | 2 +-
 .../sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test      | 2 +-
 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test | 2 +-
 workflows/sra/tests/sra_skip_fastq_download.nf.test         | 2 +-
 10 files changed, 12 insertions(+), 15 deletions(-)

diff --git a/modules.json b/modules.json
index 7fa9eaf0..81312b77 100644
--- a/modules.json
+++ b/modules.json
@@ -13,7 +13,8 @@
                     "sratools/fasterqdump": {
                         "branch": "master",
                         "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5",
-                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
+                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"],
+                        "patch": "modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff"
                     },
                     "sratools/prefetch": {
                         "branch": "master",
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
index d3bf90f7..77fd6c79 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
@@ -8,7 +8,7 @@
                             "id": "test_single_end",
                             "single_end": true
                         },
-                        "test_single_end.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82"
+                        "test_single_end_1.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82"
                     ]
                 ],
                 "1": [
@@ -20,7 +20,7 @@
                             "id": "test_single_end",
                             "single_end": true
                         },
-                        "test_single_end.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82"
+                        "test_single_end_1.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82"
                     ]
                 ],
                 "versions": [
diff --git a/tests/sra_ids_test.csv b/tests/sra_ids_test.csv
index ec8b5cc9..d9a20c22 100644
--- a/tests/sra_ids_test.csv
+++ b/tests/sra_ids_test.csv
@@ -1,7 +1,3 @@
-SRR9984183
-SRR13191702
 ERR1160846
-SRR12848126
-SRR14593545
-SRR14709033
 GSE214215
+SRR12848126
diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index c234e98f..ef5b7c9d 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -18,7 +18,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
+                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126')
                 """
             }
             params {
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index e2d4f54f..df751a6b 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -18,7 +18,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
+                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126')
                 """
             }
             params {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index 0e2fcac3..f4837f76 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -18,7 +18,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
+                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126')
                 """
             }
             params {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index 5f8d37a2..871207ab 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -18,7 +18,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
+                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126')
                 """
             }
             params {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index 95bbe2c8..995301dd 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -18,7 +18,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
+                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126')
                 """
             }
             params {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index 21c78ae7..4bf6a3f0 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -18,7 +18,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
+                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126')
                 """
             }
             params {
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index bcc4b697..705facbb 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -18,7 +18,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
+                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126')
                 """
             }
             params {

From b9a8609be309ce629073775baaf92a9de02457c5 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 18 Oct 2023 10:33:13 +0200
Subject: [PATCH 577/852] diff file

---
 .../fasterqdump/sratools-fasterqdump.diff     | 36 +++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff

diff --git a/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff b/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff
new file mode 100644
index 00000000..5275d3e4
--- /dev/null
+++ b/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff
@@ -0,0 +1,36 @@
+Changes in module 'nf-core/sratools/fasterqdump'
+--- /dev/null
++++ modules/nf-core/sratools/fasterqdump/nextflow.config
+@@ -0,0 +1,10 @@
++process {
++    withName: SRATOOLS_FASTERQDUMP {
++        ext.args = '--split-files --include-technical'
++        publishDir = [
++            path: { "${params.outdir}/fastq" },
++            mode: params.publish_dir_mode,
++            pattern: "*.fastq.gz"
++        ]
++    }
++}
+--- modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
++++ modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
+@@ -8,7 +8,7 @@
+                             "id": "test_single_end",
+                             "single_end": true
+                         },
+-                        "test_single_end.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82"
++                        "test_single_end_1.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82"
+                     ]
+                 ],
+                 "1": [
+@@ -20,7 +20,7 @@
+                             "id": "test_single_end",
+                             "single_end": true
+                         },
+-                        "test_single_end.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82"
++                        "test_single_end_1.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82"
+                     ]
+                 ],
+                 "versions": [
+
+************************************************************

From 0d5f1d00097695baaae733f9930532b7374a52a0 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 18 Oct 2023 10:33:27 +0200
Subject: [PATCH 578/852] one last test

---
 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index 62bb1999..62cabb7b 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -18,7 +18,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183')
+                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126')
                 """
             }
             params {

From b885d5252b5f0b30bde28615d58c82e666fbf2db Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Wed, 18 Oct 2023 11:35:25 +0200
Subject: [PATCH 579/852] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9fbb2013..8a9459c4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -24,7 +24,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 
 ### Enhancements & fixes
 
-- [PR #XXX](https://github.com/nf-core/fetchngs/pull/XXX) - Use nf-test for all pipeline testing
+- [PR #188](https://github.com/nf-core/fetchngs/pull/188) - Use nf-test for all pipeline testing
 
 ### Enhancements & fixes
 

From 79487642f2ecd8ef058f1104e59af9f184971960 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 18 Oct 2023 11:36:56 +0200
Subject: [PATCH 580/852] Prepare 1.11.0 RC

---
 CHANGELOG.md              | 2 +-
 assets/multiqc_config.yml | 4 ++--
 nextflow.config           | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c500efcc..4247dde3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unpublished Version / DEV]
+## [[1.11.0](https://github.com/nf-core/fetchngs/releases/tag/1.11.0)] - 2023-10-18
 
 ### Enhancements & fixes
 
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index a8974f98..21e8296b 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/fetchngs/releases/tag/dev" target="_blank">nf-core/fetchngs</a>
+  This report has been generated by the <a href="https://github.com/nf-core/fetchngs/releases/tag/1.11.0" target="_blank">nf-core/fetchngs</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/fetchngs/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/fetchngs/1.11.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-fetchngs-methods-description":
     order: -1000
diff --git a/nextflow.config b/nextflow.config
index 912ce43c..c7d78f99 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -220,7 +220,7 @@ manifest {
     description     = """Pipeline to fetch metadata and raw FastQ files from public databases"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.11.0dev'
+    version         = '1.11.0'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
 

From 833ad7eb79a67801d536c767f6c6272cc7fd566f Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Wed, 18 Oct 2023 09:51:04 +0000
Subject: [PATCH 581/852] qwqUpdate snaps

---
 workflows/sra/tests/main.nf.test.snap              | 14 +++++++-------
 .../sra_custom_ena_metadata_fields.nf.test.snap    | 14 +++++++-------
 .../tests/sra_force_sratools_download.nf.test.snap | 14 +++++++-------
 .../sra_nf_core_pipeline_atacseq.nf.test.snap      | 14 +++++++-------
 .../tests/sra_nf_core_pipeline_rnaseq.nf.test.snap | 14 +++++++-------
 .../sra_nf_core_pipeline_taxprofiler.nf.test.snap  | 14 +++++++-------
 .../sra_nf_core_pipeline_viralrecon.nf.test.snap   | 14 +++++++-------
 .../sra/tests/sra_skip_fastq_download.nf.test.snap | 14 +++++++-------
 8 files changed, 56 insertions(+), 56 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
index 4ba15917..885b7d6a 100644
--- a/workflows/sra/tests/main.nf.test.snap
+++ b/workflows/sra/tests/main.nf.test.snap
@@ -6,14 +6,14 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,5926f40ded37e0e6ce0b290c445772ac"
+                    "samplesheet.csv:md5,eda595eca3cb5ed450641565c38390c2"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
+                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
                 ],
                 "3": [
                     [
-                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
+                        "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
@@ -29,16 +29,16 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
+                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
                 ],
                 "sample_mappings": [
                     [
-                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
+                        "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,5926f40ded37e0e6ce0b290c445772ac"
+                    "samplesheet.csv:md5,eda595eca3cb5ed450641565c38390c2"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -50,6 +50,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-13T13:45:55.621951"
+        "timestamp": "2023-10-18T09:49:19.020482551"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
index 5e98f3b1..45e007d0 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
@@ -6,14 +6,14 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,4ea86d2a38bf25d025331afd1925a138"
+                    "samplesheet.csv:md5,a9e9da506288c364af14d46b86dafeb1"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,e581a9117ed2cc8e98e65c25fe7f34aa"
+                    "id_mappings.csv:md5,8ed2bd72d432eff4a8ed7d909af6f60c"
                 ],
                 "3": [
                     [
-                        "multiqc_config.yml:md5,0f18d574c7ddfa08cf444a593cb91cde",
+                        "multiqc_config.yml:md5,3bc981f0de28023083cdf13691d249d5",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
@@ -29,16 +29,16 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,e581a9117ed2cc8e98e65c25fe7f34aa"
+                    "id_mappings.csv:md5,8ed2bd72d432eff4a8ed7d909af6f60c"
                 ],
                 "sample_mappings": [
                     [
-                        "multiqc_config.yml:md5,0f18d574c7ddfa08cf444a593cb91cde",
+                        "multiqc_config.yml:md5,3bc981f0de28023083cdf13691d249d5",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,4ea86d2a38bf25d025331afd1925a138"
+                    "samplesheet.csv:md5,a9e9da506288c364af14d46b86dafeb1"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -50,6 +50,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-13T13:41:56.570144"
+        "timestamp": "2023-10-18T09:36:57.154883885"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
index 1c92c75d..f445296a 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
@@ -6,14 +6,14 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,461dfaa7b95f84210840347ef8cc93c2"
+                    "samplesheet.csv:md5,7e6a65057fe000f562132ae9e608e87b"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
+                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
                 ],
                 "3": [
                     [
-                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
+                        "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
@@ -28,16 +28,16 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
+                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
                 ],
                 "sample_mappings": [
                     [
-                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
+                        "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,461dfaa7b95f84210840347ef8cc93c2"
+                    "samplesheet.csv:md5,7e6a65057fe000f562132ae9e608e87b"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -48,6 +48,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-13T13:51:26.617172"
+        "timestamp": "2023-10-18T09:43:16.468494798"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
index cabe296e..3e9e7f31 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
@@ -6,14 +6,14 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,0deebc93328dcbb63762aa91d4fc9f35"
+                    "samplesheet.csv:md5,35292d2bea78b087d75c3333f6319b6b"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
+                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
                 ],
                 "3": [
                     [
-                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
+                        "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
@@ -29,16 +29,16 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
+                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
                 ],
                 "sample_mappings": [
                     [
-                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
+                        "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,0deebc93328dcbb63762aa91d4fc9f35"
+                    "samplesheet.csv:md5,35292d2bea78b087d75c3333f6319b6b"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -50,6 +50,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-13T13:37:42.486986"
+        "timestamp": "2023-10-18T09:47:56.240260295"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
index 111fe537..8805d3ac 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
@@ -6,14 +6,14 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,e20d0858b2ff04a62d50274a2527b913"
+                    "samplesheet.csv:md5,b7ac0ff84f5031daaa9405c736a37125"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
+                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
                 ],
                 "3": [
                     [
-                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
+                        "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
@@ -29,16 +29,16 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
+                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
                 ],
                 "sample_mappings": [
                     [
-                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
+                        "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,e20d0858b2ff04a62d50274a2527b913"
+                    "samplesheet.csv:md5,b7ac0ff84f5031daaa9405c736a37125"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -50,6 +50,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-13T13:43:56.980991"
+        "timestamp": "2023-10-18T09:40:15.590249346"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
index 14c38837..0853eef8 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
@@ -6,14 +6,14 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,c781b226b9aac812c1d38881145a74d6"
+                    "samplesheet.csv:md5,296836917bbdf34bda106a313424fa95"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
+                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
                 ],
                 "3": [
                     [
-                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
+                        "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
@@ -29,16 +29,16 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
+                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
                 ],
                 "sample_mappings": [
                     [
-                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
+                        "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,c781b226b9aac812c1d38881145a74d6"
+                    "samplesheet.csv:md5,296836917bbdf34bda106a313424fa95"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -50,6 +50,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-13T13:39:55.31037"
+        "timestamp": "2023-10-18T09:49:51.04235046"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
index d26dd1cc..e364b3a9 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
@@ -6,14 +6,14 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,5926f40ded37e0e6ce0b290c445772ac"
+                    "samplesheet.csv:md5,eda595eca3cb5ed450641565c38390c2"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
+                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
                 ],
                 "3": [
                     [
-                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
+                        "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
@@ -29,16 +29,16 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
+                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
                 ],
                 "sample_mappings": [
                     [
-                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
+                        "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,5926f40ded37e0e6ce0b290c445772ac"
+                    "samplesheet.csv:md5,eda595eca3cb5ed450641565c38390c2"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -50,6 +50,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-13T13:35:41.371352"
+        "timestamp": "2023-10-18T09:48:46.587502263"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
index f0bac51f..cdb0965c 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
@@ -6,14 +6,14 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,23d39235ed39f69cb8333322de77ed26"
+                    "samplesheet.csv:md5,0a9b99509bcc64ca245408b6bb634f15"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
+                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
                 ],
                 "3": [
                     [
-                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
+                        "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
@@ -27,16 +27,16 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f"
+                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
                 ],
                 "sample_mappings": [
                     [
-                        "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff",
+                        "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,23d39235ed39f69cb8333322de77ed26"
+                    "samplesheet.csv:md5,0a9b99509bcc64ca245408b6bb634f15"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -46,6 +46,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-13T13:46:11.136377"
+        "timestamp": "2023-10-18T09:50:04.300075498"
     }
 }
\ No newline at end of file

From 4d13a4470639a9ae6a84610f900f9d97e276ce03 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Wed, 18 Oct 2023 11:56:39 +0200
Subject: [PATCH 582/852] Update .github/workflows/ci.yml

Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
---
 .github/workflows/ci.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2268c794..53480a37 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -10,7 +10,6 @@ on:
     branches:
       - master
       - dev
-      - refactor
 
 env:
   NXF_ANSI_LOG: false

From bf2ab3ad270476558c21ba459748f0d265b03f42 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 27 Oct 2023 11:24:09 +0200
Subject: [PATCH 583/852] remove duplicate tests

---
 workflows/sra/tests/main.nf.test                             | 5 -----
 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test   | 5 -----
 workflows/sra/tests/sra_force_sratools_download.nf.test      | 5 -----
 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test     | 5 -----
 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test      | 5 -----
 workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test | 5 -----
 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test  | 5 -----
 workflows/sra/tests/sra_skip_fastq_download.nf.test          | 5 -----
 8 files changed, 40 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index ef5b7c9d..c8dce3c7 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -6,11 +6,6 @@ nextflow_workflow {
     tag "workflows"
     tag "workflows_sra"
     tag "multiqc_mappings_config"
-    tag "sra_fastq_ftp"
-    tag "sra_ids_to_runinfo"
-    tag "sra_merge_samplesheet"
-    tag "sra_runinfo_to_ftp"
-    tag "sra_to_samplesheet"
     tag "sra_default_parameters"
 
     test("Parameters: default") {
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index 62cabb7b..d4dd4141 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -6,11 +6,6 @@ nextflow_workflow {
     tag "workflows"
     tag "workflows_sra"
     tag "multiqc_mappings_config"
-    tag "sra_fastq_ftp"
-    tag "sra_ids_to_runinfo"
-    tag "sra_merge_samplesheet"
-    tag "sra_runinfo_to_ftp"
-    tag "sra_to_samplesheet"
     tag "sra_custom_ena_metadata_fields"
 
     test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") {
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index df751a6b..62adb9af 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -6,11 +6,6 @@ nextflow_workflow {
     tag "workflows"
     tag "workflows_sra"
     tag "multiqc_mappings_config"
-    tag "sra_fastq_ftp"
-    tag "sra_ids_to_runinfo"
-    tag "sra_merge_samplesheet"
-    tag "sra_runinfo_to_ftp"
-    tag "sra_to_samplesheet"
     tag "sra_force_sratools_download"
 
     test("Parameters: --force_sratools_download") {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index f4837f76..00f545b5 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -6,11 +6,6 @@ nextflow_workflow {
     tag "workflows"
     tag "workflows_sra"
     tag "multiqc_mappings_config"
-    tag "sra_fastq_ftp"
-    tag "sra_ids_to_runinfo"
-    tag "sra_merge_samplesheet"
-    tag "sra_runinfo_to_ftp"
-    tag "sra_to_samplesheet"
     tag "sra_nf_core_pipeline_atacseq"
 
     test("Parameters: --nf_core_pipeline atacseq") {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index 871207ab..62bd6380 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -6,11 +6,6 @@ nextflow_workflow {
     tag "workflows"
     tag "workflows_sra"
     tag "multiqc_mappings_config"
-    tag "sra_fastq_ftp"
-    tag "sra_ids_to_runinfo"
-    tag "sra_merge_samplesheet"
-    tag "sra_runinfo_to_ftp"
-    tag "sra_to_samplesheet"
     tag "sra_nf_core_pipeline_rnaseq"
 
     test("Parameters: --nf_core_pipeline rnaseq") {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index 995301dd..c5e2865f 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -6,11 +6,6 @@ nextflow_workflow {
     tag "workflows"
     tag "workflows_sra"
     tag "multiqc_mappings_config"
-    tag "sra_fastq_ftp"
-    tag "sra_ids_to_runinfo"
-    tag "sra_merge_samplesheet"
-    tag "sra_runinfo_to_ftp"
-    tag "sra_to_samplesheet"
     tag "sra_nf_core_pipeline_taxprofiler"
 
     test("Parameters: --nf_core_pipeline taxprofiler") {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index 4bf6a3f0..04485010 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -6,11 +6,6 @@ nextflow_workflow {
     tag "workflows"
     tag "workflows_sra"
     tag "multiqc_mappings_config"
-    tag "sra_fastq_ftp"
-    tag "sra_ids_to_runinfo"
-    tag "sra_merge_samplesheet"
-    tag "sra_runinfo_to_ftp"
-    tag "sra_to_samplesheet"
     tag "sra_nf_core_pipeline_viralrecon"
 
     test("Parameters: --nf_core_pipeline viralrecon") {
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index 705facbb..dd846643 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -6,11 +6,6 @@ nextflow_workflow {
     tag "workflows"
     tag "workflows_sra"
     tag "multiqc_mappings_config"
-    tag "sra_fastq_ftp"
-    tag "sra_ids_to_runinfo"
-    tag "sra_merge_samplesheet"
-    tag "sra_runinfo_to_ftp"
-    tag "sra_to_samplesheet"
     tag "sra_skip_fastq_download"
 
     test("Parameters: --skip_fastq_download") {

From ef9f1e71b5b0b22f70d220b3d90ce529983dd8fa Mon Sep 17 00:00:00 2001
From: "Blaessle,Dr.,Alexander (GCBDS) BIP-DE-B"
 <alexander.blaessle@boehringer-ingelheim.com>
Date: Tue, 7 Nov 2023 11:55:35 +0100
Subject: [PATCH 584/852] Resolved bug when prefetching large studies

Prefetching large studies resulted in error stated in issue

https://github.com/nf-core/fetchngs/issues/236

Resolved this by handing over text file with filepaths instead
of list of filepaths. Rewrote sra_merge_samplesheet accordingly.

Tested with study with ~25k samples.
---
 modules/local/sra_merge_samplesheet/main.nf | 24 +++++++++++----------
 workflows/sra/main.nf                       | 14 ++++++++++--
 2 files changed, 25 insertions(+), 13 deletions(-)

diff --git a/modules/local/sra_merge_samplesheet/main.nf b/modules/local/sra_merge_samplesheet/main.nf
index 1c2ee7df..3c4a076d 100644
--- a/modules/local/sra_merge_samplesheet/main.nf
+++ b/modules/local/sra_merge_samplesheet/main.nf
@@ -6,9 +6,11 @@ process SRA_MERGE_SAMPLESHEET {
         'nf-core/ubuntu:20.04' }"
 
     input:
-    path ('samplesheets/*')
-    path ('mappings/*')
-
+    // path ('samplesheets/*')
+    // path ('mappings/*')
+    path 'samplesheets.txt'
+    path 'mappings.txt'
+    
     output:
     path "samplesheet.csv", emit: samplesheet
     path "id_mappings.csv", emit: mappings
@@ -16,16 +18,16 @@ process SRA_MERGE_SAMPLESHEET {
 
     script:
     """
-    head -n 1 `ls ./samplesheets/* | head -n 1` > samplesheet.csv
-    for fileid in `ls ./samplesheets/*`; do
+    head -n 1 `head -n 1 samplesheets.txt` > samplesheet.csv
+    while read fileid; do
         awk 'NR>1' \$fileid >> samplesheet.csv
-    done
-
-    head -n 1 `ls ./mappings/* | head -n 1` > id_mappings.csv
-    for fileid in `ls ./mappings/*`; do
+    done < samplesheets.txt
+    
+    head -n 1 `head -n 1 mappings.txt` > id_mappings.csv
+    while read fileid; do
         awk 'NR>1' \$fileid >> id_mappings.csv
-    done
-
+    done < mappings.txt
+    
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index ddac096d..143e1f8f 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -118,14 +118,24 @@ workflow SRA {
         params.nf_core_rnaseq_strandedness ?: 'auto',
         params.sample_mapping_fields
     )
+    
+
+    // Combine all sample sheet/mapping paths into two files
+    ch_samplesheets=SRA_TO_SAMPLESHEET.out.samplesheet.map{it[1].toString()}.collectFile(name: 'samplesheets.txt', newLine: true)
+    ch_mappings=SRA_TO_SAMPLESHEET.out.mappings.map{it[1].toString()}.collectFile(name: 'mappings.txt', newLine: true)
 
     //
     // MODULE: Create a merged samplesheet across all samples for the pipeline
     //
+    // SRA_MERGE_SAMPLESHEET (
+    //     SRA_TO_SAMPLESHEET.out.samplesheet.collect{it[1]},
+    //     SRA_TO_SAMPLESHEET.out.mappings.collect{it[1]}
+    // )
     SRA_MERGE_SAMPLESHEET (
-        SRA_TO_SAMPLESHEET.out.samplesheet.collect{it[1]},
-        SRA_TO_SAMPLESHEET.out.mappings.collect{it[1]}
+        ch_samplesheets,
+        ch_mappings
     )
+
     ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions)
 
     //

From 5651ab5d689eaaa8d3d5a34d45d74fddc591aaac Mon Sep 17 00:00:00 2001
From: "Blaessle,Dr.,Alexander (GCBDS) BIP-DE-B"
 <alexander.blaessle@boehringer-ingelheim.com>
Date: Tue, 7 Nov 2023 12:19:13 +0100
Subject: [PATCH 585/852] Removed whitespaces/old code

---
 modules/local/sra_merge_samplesheet/main.nf | 8 +++-----
 workflows/sra/main.nf                       | 7 ++-----
 2 files changed, 5 insertions(+), 10 deletions(-)

diff --git a/modules/local/sra_merge_samplesheet/main.nf b/modules/local/sra_merge_samplesheet/main.nf
index 3c4a076d..c5704d81 100644
--- a/modules/local/sra_merge_samplesheet/main.nf
+++ b/modules/local/sra_merge_samplesheet/main.nf
@@ -6,11 +6,9 @@ process SRA_MERGE_SAMPLESHEET {
         'nf-core/ubuntu:20.04' }"
 
     input:
-    // path ('samplesheets/*')
-    // path ('mappings/*')
     path 'samplesheets.txt'
     path 'mappings.txt'
-    
+
     output:
     path "samplesheet.csv", emit: samplesheet
     path "id_mappings.csv", emit: mappings
@@ -22,12 +20,12 @@ process SRA_MERGE_SAMPLESHEET {
     while read fileid; do
         awk 'NR>1' \$fileid >> samplesheet.csv
     done < samplesheets.txt
-    
+
     head -n 1 `head -n 1 mappings.txt` > id_mappings.csv
     while read fileid; do
         awk 'NR>1' \$fileid >> id_mappings.csv
     done < mappings.txt
-    
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 143e1f8f..9605c217 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -118,7 +118,7 @@ workflow SRA {
         params.nf_core_rnaseq_strandedness ?: 'auto',
         params.sample_mapping_fields
     )
-    
+  
 
     // Combine all sample sheet/mapping paths into two files
     ch_samplesheets=SRA_TO_SAMPLESHEET.out.samplesheet.map{it[1].toString()}.collectFile(name: 'samplesheets.txt', newLine: true)
@@ -127,10 +127,7 @@ workflow SRA {
     //
     // MODULE: Create a merged samplesheet across all samples for the pipeline
     //
-    // SRA_MERGE_SAMPLESHEET (
-    //     SRA_TO_SAMPLESHEET.out.samplesheet.collect{it[1]},
-    //     SRA_TO_SAMPLESHEET.out.mappings.collect{it[1]}
-    // )
+
     SRA_MERGE_SAMPLESHEET (
         ch_samplesheets,
         ch_mappings

From 87c94c0d309e6c48d003f5f146313b23e9ad9237 Mon Sep 17 00:00:00 2001
From: "Blaessle,Dr.,Alexander (GCBDS) BIP-DE-B"
 <alexander.blaessle@boehringer-ingelheim.com>
Date: Mon, 13 Nov 2023 11:14:40 +0100
Subject: [PATCH 586/852] Substituted sra_merge_samplesheet module with
 collectFile statement

---
 modules/local/sra_merge_samplesheet/main.nf   | 34 -------------------
 .../sra_merge_samplesheet/nextflow.config     |  9 -----
 .../sra_merge_samplesheet/tests/main.nf.test  | 32 -----------------
 .../tests/main.nf.test.snap                   | 27 ---------------
 .../sra_merge_samplesheet/tests/tags.yml      |  2 --
 workflows/sra/main.nf                         | 22 +++---------
 workflows/sra/nextflow.config                 |  1 -
 7 files changed, 5 insertions(+), 122 deletions(-)
 delete mode 100644 modules/local/sra_merge_samplesheet/main.nf
 delete mode 100644 modules/local/sra_merge_samplesheet/nextflow.config
 delete mode 100644 modules/local/sra_merge_samplesheet/tests/main.nf.test
 delete mode 100644 modules/local/sra_merge_samplesheet/tests/main.nf.test.snap
 delete mode 100644 modules/local/sra_merge_samplesheet/tests/tags.yml

diff --git a/modules/local/sra_merge_samplesheet/main.nf b/modules/local/sra_merge_samplesheet/main.nf
deleted file mode 100644
index c5704d81..00000000
--- a/modules/local/sra_merge_samplesheet/main.nf
+++ /dev/null
@@ -1,34 +0,0 @@
-process SRA_MERGE_SAMPLESHEET {
-
-    conda "conda-forge::sed=4.7"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'nf-core/ubuntu:20.04' }"
-
-    input:
-    path 'samplesheets.txt'
-    path 'mappings.txt'
-
-    output:
-    path "samplesheet.csv", emit: samplesheet
-    path "id_mappings.csv", emit: mappings
-    path "versions.yml"   , emit: versions
-
-    script:
-    """
-    head -n 1 `head -n 1 samplesheets.txt` > samplesheet.csv
-    while read fileid; do
-        awk 'NR>1' \$fileid >> samplesheet.csv
-    done < samplesheets.txt
-
-    head -n 1 `head -n 1 mappings.txt` > id_mappings.csv
-    while read fileid; do
-        awk 'NR>1' \$fileid >> id_mappings.csv
-    done < mappings.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/sra_merge_samplesheet/nextflow.config b/modules/local/sra_merge_samplesheet/nextflow.config
deleted file mode 100644
index f2926529..00000000
--- a/modules/local/sra_merge_samplesheet/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-    withName: 'SRA_MERGE_SAMPLESHEET' {
-        publishDir = [
-            path: { "${params.outdir}/samplesheet" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-}
\ No newline at end of file
diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test b/modules/local/sra_merge_samplesheet/tests/main.nf.test
deleted file mode 100644
index b7c98622..00000000
--- a/modules/local/sra_merge_samplesheet/tests/main.nf.test
+++ /dev/null
@@ -1,32 +0,0 @@
-nextflow_process {
-
-    name "Test process: SRA_MERGE_SAMPLESHEET"
-    script "../main.nf"
-    process "SRA_MERGE_SAMPLESHEET"
-    tag "modules"
-    tag "modules_local"
-    tag "sra_merge_samplesheet"
-
-    test("Should run without failures") {
-
-        when {
-            params {
-                outdir = "$outputDir"
-            }
-
-            process {
-                """
-                input[0] = params.test_data['modules_local']['sra_merge_samplesheet_samplesheets'].collect { file(it, checkIfExists: true) }
-                input[1] = params.test_data['modules_local']['sra_merge_samplesheet_mappings'].collect { file(it, checkIfExists: true) }
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-}
diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap b/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap
deleted file mode 100644
index 203395ae..00000000
--- a/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap
+++ /dev/null
@@ -1,27 +0,0 @@
-{
-    "Should run without failures": {
-        "content": [
-            {
-                "0": [
-                    "samplesheet.csv:md5,ef756557b0735becd2574c2a3f5840b2"
-                ],
-                "1": [
-                    "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253"
-                ],
-                "2": [
-                    "versions.yml:md5,410006679d5e496d8c55e58e78ca6b34"
-                ],
-                "mappings": [
-                    "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253"
-                ],
-                "samplesheet": [
-                    "samplesheet.csv:md5,ef756557b0735becd2574c2a3f5840b2"
-                ],
-                "versions": [
-                    "versions.yml:md5,410006679d5e496d8c55e58e78ca6b34"
-                ]
-            }
-        ],
-        "timestamp": "2023-09-22T10:59:14.022116"
-    }
-}
\ No newline at end of file
diff --git a/modules/local/sra_merge_samplesheet/tests/tags.yml b/modules/local/sra_merge_samplesheet/tests/tags.yml
deleted file mode 100644
index a4292b70..00000000
--- a/modules/local/sra_merge_samplesheet/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-sra_merge_samplesheet:
-  - modules/local/sra_merge_samplesheet/**
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 9605c217..16408496 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -7,7 +7,6 @@
 include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_config'
 include { SRA_FASTQ_FTP           } from '../../modules/local/sra_fastq_ftp'
 include { SRA_IDS_TO_RUNINFO      } from '../../modules/local/sra_ids_to_runinfo'
-include { SRA_MERGE_SAMPLESHEET   } from '../../modules/local/sra_merge_samplesheet'
 include { SRA_RUNINFO_TO_FTP      } from '../../modules/local/sra_runinfo_to_ftp'
 include { SRA_TO_SAMPLESHEET      } from '../../modules/local/sra_to_samplesheet'
 
@@ -121,19 +120,8 @@ workflow SRA {
   
 
     // Combine all sample sheet/mapping paths into two files
-    ch_samplesheets=SRA_TO_SAMPLESHEET.out.samplesheet.map{it[1].toString()}.collectFile(name: 'samplesheets.txt', newLine: true)
-    ch_mappings=SRA_TO_SAMPLESHEET.out.mappings.map{it[1].toString()}.collectFile(name: 'mappings.txt', newLine: true)
-
-    //
-    // MODULE: Create a merged samplesheet across all samples for the pipeline
-    //
-
-    SRA_MERGE_SAMPLESHEET (
-        ch_samplesheets,
-        ch_mappings
-    )
-
-    ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions)
+    ch_samplesheet=SRA_TO_SAMPLESHEET.out.samplesheet.map{it[1]}.collectFile(name:'samplesheets.csv', newLine: true, keepHeader: true, storeDir:params.outdir)
+    ch_mappings=SRA_TO_SAMPLESHEET.out.samplesheet.map{it[1]}.collectFile(name:'id_mappings.csv', newLine: true, keepHeader: true, storeDir:params.outdir)
 
     //
     // MODULE: Create a MutiQC config file with sample name mappings
@@ -141,7 +129,7 @@ workflow SRA {
     ch_sample_mappings_yml = Channel.empty()
     if (params.sample_mapping_fields) {
         MULTIQC_MAPPINGS_CONFIG (
-            SRA_MERGE_SAMPLESHEET.out.mappings
+            ch_mappings
         )
         ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions)
         ch_sample_mappings_yml = MULTIQC_MAPPINGS_CONFIG.out.yml
@@ -149,8 +137,8 @@ workflow SRA {
 
     emit:
     fastq           = fastq_files
-    samplesheet     = SRA_MERGE_SAMPLESHEET.out.samplesheet
-    mappings        = SRA_MERGE_SAMPLESHEET.out.mappings
+    samplesheet     = ch_samplesheet
+    mappings        = ch_mappings
     sample_mappings = ch_sample_mappings_yml
     versions        = ch_versions.unique()
 }
diff --git a/workflows/sra/nextflow.config b/workflows/sra/nextflow.config
index 6b66fcd5..21b374c5 100644
--- a/workflows/sra/nextflow.config
+++ b/workflows/sra/nextflow.config
@@ -1,7 +1,6 @@
 includeConfig "../../modules/local/multiqc_mappings_config/nextflow.config"
 includeConfig "../../modules/local/sra_fastq_ftp/nextflow.config"
 includeConfig "../../modules/local/sra_ids_to_runinfo/nextflow.config"
-includeConfig "../../modules/local/sra_merge_samplesheet/nextflow.config"
 includeConfig "../../modules/local/sra_runinfo_to_ftp/nextflow.config"
 includeConfig "../../modules/local/sra_to_samplesheet/nextflow.config"
 includeConfig "../../modules/nf-core/sratools/prefetch/nextflow.config"

From 69f5bb9ac59d4de276e0fcc3cde40033453cbef2 Mon Sep 17 00:00:00 2001
From: nicolae06 <nicolae.gogelescu97@e-uvt.ro>
Date: Wed, 13 Dec 2023 23:00:08 +0200
Subject: [PATCH 587/852] merge fixed

---
 CHANGELOG.md                        |  15 ++-
 conf/modules.config                 | 171 ++++++++++++++++++++++++++++
 modules/local/sra_fastq_ftp/main.nf |  28 ++---
 3 files changed, 199 insertions(+), 15 deletions(-)
 create mode 100644 conf/modules.config

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5e484a7a..b99805c9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [[1.11.0](https://github.com/nf-core/fetchngs/releases/tag/1.11.0)] - 2023-10-18
+## [Unpublished Version / DEV]
 
 ### Credits
 
@@ -19,14 +20,26 @@ Special thanks to the following for their contributions to the release:
 - [Rob Syme](https://github.com/robsyme)
 - [Sateesh Peri](https://github.com/sateeshperi)
 - [Sebastian Schönherr](https://github.com/seppinho)
+- [Sebastian Uhrig](https://github.com/suhrig)
 
 Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
 
 ### Enhancements & fixes
 
 - [PR #188](https://github.com/nf-core/fetchngs/pull/188) - Use nf-test for all pipeline testing
+- [#169](https://github.com/nf-core/fetchngs/issues/173) - download of big files time out and don't resume
 
-### Enhancements & fixes
+### Software dependencies
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `wget`     |             | 1.20.1      |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+>
+> **NB:** Dependency has been **added** if just the new version information is present.
+>
+> **NB:** Dependency has been **removed** if new version information isn't present.
 
 ## [[1.10.1](https://github.com/nf-core/fetchngs/releases/tag/1.10.1)] - 2023-10-08
 
diff --git a/conf/modules.config b/conf/modules.config
new file mode 100644
index 00000000..1e8a4ca2
--- /dev/null
+++ b/conf/modules.config
@@ -0,0 +1,171 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+//
+// Generic process options for all workflows
+//
+process {
+
+    publishDir = [
+        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+    ]
+
+    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
+        publishDir = [
+            path: { "${params.outdir}/pipeline_info" },
+            mode: params.publish_dir_mode,
+            pattern: '*_versions.yml'
+        ]
+    }
+
+}
+
+//
+//  Process options for the SRA workflow
+//
+if (params.input_type == 'sra') {
+
+    process {
+
+        withName: SRA_IDS_TO_RUNINFO {
+            publishDir = [
+                path: { "${params.outdir}/metadata" },
+                enabled: false
+            ]
+        }
+
+        withName: SRA_RUNINFO_TO_FTP {
+            publishDir = [
+                path: { "${params.outdir}/metadata" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+        withName: SRA_FASTQ_FTP {
+            ext.args = '-t 5 -nv -c -T 60'
+            publishDir = [
+                [
+                    path: { "${params.outdir}/fastq" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.fastq.gz"
+                ],
+                [
+                    path: { "${params.outdir}/fastq/md5" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.md5"
+                ]
+            ]
+        }
+
+        withName: SRATOOLS_PREFETCH {
+            publishDir = [
+                path: { "${params.outdir}/sra" },
+                enabled: false
+            ]
+        }
+
+        withName: SRATOOLS_FASTERQDUMP {
+            ext.args = '--split-files --include-technical'
+            publishDir = [
+                path: { "${params.outdir}/fastq" },
+                mode: params.publish_dir_mode,
+                pattern: "*.fastq.gz"
+            ]
+        }
+
+        withName: SRA_TO_SAMPLESHEET {
+            publishDir = [
+                path: { "${params.outdir}/samplesheet" },
+                enabled: false
+            ]
+        }
+
+        withName: SRA_MERGE_SAMPLESHEET {
+            publishDir = [
+                path: { "${params.outdir}/samplesheet" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+        withName: MULTIQC_MAPPINGS_CONFIG {
+            publishDir = [
+                path: { "${params.outdir}/samplesheet" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+    }
+
+}
+
+//
+//  Process options for the Synapse workflow
+//
+if (params.input_type == 'synapse') {
+
+    process {
+
+        withName: SYNAPSE_LIST {
+            ext.args = '--long'
+            publishDir = [
+                path: { "${params.outdir}/metadata" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+        withName: SYNAPSE_GET {
+            publishDir = [
+                [
+                    path: { "${params.outdir}/fastq" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.fastq.gz"
+                ],
+                [
+                    path: { "${params.outdir}/fastq/md5" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.md5"
+                ]
+            ]
+        }
+
+        withName: SYNAPSE_SHOW {
+            publishDir = [
+                path: { "${params.outdir}/metadata" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+        withName: SYNAPSE_TO_SAMPLESHEET {
+            publishDir = [
+                path: { "${params.outdir}/samplesheet" },
+                enabled: false
+            ]
+        }
+
+        withName: SYNAPSE_MERGE_SAMPLESHEET {
+            publishDir = [
+                path: { "${params.outdir}/samplesheet" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+    }
+
+}
diff --git a/modules/local/sra_fastq_ftp/main.nf b/modules/local/sra_fastq_ftp/main.nf
index 2b7769ff..e2274d46 100644
--- a/modules/local/sra_fastq_ftp/main.nf
+++ b/modules/local/sra_fastq_ftp/main.nf
@@ -4,10 +4,10 @@ process SRA_FASTQ_FTP {
     label 'process_low'
     label 'error_retry'
 
-    conda "bioconda::sra-tools=2.11.0"
+    conda "conda-forge::wget=1.20.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' :
-        'biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
+        'https://depot.galaxyproject.org/singularity/wget:1.20.1' :
+        'biocontainers/wget:1.20.1' }"
 
     input:
     tuple val(meta), val(fastq)
@@ -21,40 +21,40 @@ process SRA_FASTQ_FTP {
     def args = task.ext.args ?: ''
     if (meta.single_end) {
         """
-        curl \\
+        wget \\
             $args \\
-            -L ${fastq[0]} \\
-            -o ${meta.id}.fastq.gz
+            -O ${meta.id}.fastq.gz \\
+            ${fastq[0]}
 
         echo "${meta.md5_1}  ${meta.id}.fastq.gz" > ${meta.id}.fastq.gz.md5
         md5sum -c ${meta.id}.fastq.gz.md5
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
-            curl: \$(echo \$(curl --version | head -n 1 | sed 's/^curl //; s/ .*\$//'))
+            wget: \$(echo \$(wget --version | head -n 1 | sed 's/^GNU Wget //; s/ .*\$//'))
         END_VERSIONS
         """
     } else {
         """
-        curl \\
+        wget \\
             $args \\
-            -L ${fastq[0]} \\
-            -o ${meta.id}_1.fastq.gz
+            -O ${meta.id}_1.fastq.gz \\
+            ${fastq[0]}
 
         echo "${meta.md5_1}  ${meta.id}_1.fastq.gz" > ${meta.id}_1.fastq.gz.md5
         md5sum -c ${meta.id}_1.fastq.gz.md5
 
-        curl \\
+        wget \\
             $args \\
-            -L ${fastq[1]} \\
-            -o ${meta.id}_2.fastq.gz
+            -O ${meta.id}_2.fastq.gz \\
+            ${fastq[1]}
 
         echo "${meta.md5_2}  ${meta.id}_2.fastq.gz" > ${meta.id}_2.fastq.gz.md5
         md5sum -c ${meta.id}_2.fastq.gz.md5
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
-            curl: \$(echo \$(curl --version | head -n 1 | sed 's/^curl //; s/ .*\$//'))
+            wget: \$(echo \$(wget --version | head -n 1 | sed 's/^GNU Wget //; s/ .*\$//'))
         END_VERSIONS
         """
     }

From 508b7109119ab21bfbaf21ec9fe097794383a009 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Tue, 19 Dec 2023 10:56:52 +0100
Subject: [PATCH 588/852] Update CHANGELOG.md

---
 CHANGELOG.md | 39 ++++++++++++++++++++++++---------------
 1 file changed, 24 insertions(+), 15 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b99805c9..73a22661 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,31 +3,19 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[1.11.0](https://github.com/nf-core/fetchngs/releases/tag/1.11.0)] - 2023-10-18
 ## [Unpublished Version / DEV]
 
 ### Credits
 
 Special thanks to the following for their contributions to the release:
 
-- [Adam Talbot](https://github.com/adamrtalbot)
-- [Edmund Miller](https://github.com/Emiller88)
-- [Esha Joshi](https://github.com/ejseqera)
-- [Harshil Patel](https://github.com/drpatelh)
-- [Lukas Forer](https://github.com/lukfor)
-- [James Fellows Yates](https://github.com/jfy133)
-- [Maxime Garcia](https://github.com/maxulysse)
-- [Rob Syme](https://github.com/robsyme)
-- [Sateesh Peri](https://github.com/sateeshperi)
-- [Sebastian Schönherr](https://github.com/seppinho)
 - [Sebastian Uhrig](https://github.com/suhrig)
 
-Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
-
 ### Enhancements & fixes
 
-- [PR #188](https://github.com/nf-core/fetchngs/pull/188) - Use nf-test for all pipeline testing
-- [#169](https://github.com/nf-core/fetchngs/issues/173) - download of big files time out and don't resume
+- [PR #241](https://github.com/nf-core/fetchngs/pull/241) - download of big files time out and don't resume
+
+## [[1.11.0](https://github.com/nf-core/fetchngs/releases/tag/1.11.0)] - 2023-10-18
 
 ### Software dependencies
 
@@ -41,6 +29,27 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 >
 > **NB:** Dependency has been **removed** if new version information isn't present.
 
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Adam Talbot](https://github.com/adamrtalbot)
+- [Edmund Miller](https://github.com/Emiller88)
+- [Esha Joshi](https://github.com/ejseqera)
+- [Harshil Patel](https://github.com/drpatelh)
+- [Lukas Forer](https://github.com/lukfor)
+- [James Fellows Yates](https://github.com/jfy133)
+- [Maxime Garcia](https://github.com/maxulysse)
+- [Rob Syme](https://github.com/robsyme)
+- [Sateesh Peri](https://github.com/sateeshperi)
+- [Sebastian Schönherr](https://github.com/seppinho)
+
+Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
+
+### Enhancements & fixes
+
+- [PR #188](https://github.com/nf-core/fetchngs/pull/188) - Use nf-test for all pipeline testing
+
 ## [[1.10.1](https://github.com/nf-core/fetchngs/releases/tag/1.10.1)] - 2023-10-08
 
 ### Credits

From 14fe71de3be87cb50416ba97ae5c70ddeb1ddba8 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Tue, 19 Dec 2023 10:57:19 +0100
Subject: [PATCH 589/852] Update CHANGELOG.md

---
 CHANGELOG.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 73a22661..5f2a1de5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,8 +15,6 @@ Special thanks to the following for their contributions to the release:
 
 - [PR #241](https://github.com/nf-core/fetchngs/pull/241) - download of big files time out and don't resume
 
-## [[1.11.0](https://github.com/nf-core/fetchngs/releases/tag/1.11.0)] - 2023-10-18
-
 ### Software dependencies
 
 | Dependency | Old version | New version |
@@ -29,6 +27,8 @@ Special thanks to the following for their contributions to the release:
 >
 > **NB:** Dependency has been **removed** if new version information isn't present.
 
+## [[1.11.0](https://github.com/nf-core/fetchngs/releases/tag/1.11.0)] - 2023-10-18
+
 ### Credits
 
 Special thanks to the following for their contributions to the release:

From 4c40784196c0f380d45cdaa73d9a01a44d171acc Mon Sep 17 00:00:00 2001
From: nicolae06 <nicolae.gogelescu97@e-uvt.ro>
Date: Tue, 19 Dec 2023 23:46:09 +0200
Subject: [PATCH 590/852] snapshot file updated

---
 .../sra_fastq_ftp/tests/main.nf.test.snap     | 58 +++----------------
 1 file changed, 7 insertions(+), 51 deletions(-)

diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap
index fb815455..a2d24d65 100644
--- a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap
+++ b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap
@@ -3,69 +3,25 @@
         "content": [
             {
                 "0": [
-                    [
-                        {
-                            "id": "SRX9626017_SRR13191702",
-                            "single_end": false,
-                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
-                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
-                        },
-                        [
-                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
-                        ]
-                    ]
+                    
                 ],
                 "1": [
-                    [
-                        {
-                            "id": "SRX9626017_SRR13191702",
-                            "single_end": false,
-                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
-                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
-                        },
-                        [
-                            "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
-                            "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
-                        ]
-                    ]
+                    
                 ],
                 "2": [
-                    "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b"
+                    
                 ],
                 "fastq": [
-                    [
-                        {
-                            "id": "SRX9626017_SRR13191702",
-                            "single_end": false,
-                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
-                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
-                        },
-                        [
-                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
-                        ]
-                    ]
+                    
                 ],
                 "md5": [
-                    [
-                        {
-                            "id": "SRX9626017_SRR13191702",
-                            "single_end": false,
-                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
-                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
-                        },
-                        [
-                            "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
-                            "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
-                        ]
-                    ]
+                    
                 ],
                 "versions": [
-                    "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b"
+                    
                 ]
             }
         ],
-        "timestamp": "2023-09-22T10:58:46.998421"
+        "timestamp": "2023-12-19T21:44:01.92664"
     }
 }
\ No newline at end of file

From e192e49d8567c1a80f3705b94aa94a06297e157b Mon Sep 17 00:00:00 2001
From: nicolae06 <nicolae.gogelescu97@e-uvt.ro>
Date: Wed, 20 Dec 2023 23:38:56 +0200
Subject: [PATCH 591/852] nextflow.config these arguments are not compatible
 with wget.

---
 modules/local/sra_fastq_ftp/nextflow.config   |  2 +-
 .../sra_fastq_ftp/tests/main.nf.test.snap     | 58 ++++++++++++++++---
 2 files changed, 52 insertions(+), 8 deletions(-)

diff --git a/modules/local/sra_fastq_ftp/nextflow.config b/modules/local/sra_fastq_ftp/nextflow.config
index 7b5ebf70..b73c3729 100644
--- a/modules/local/sra_fastq_ftp/nextflow.config
+++ b/modules/local/sra_fastq_ftp/nextflow.config
@@ -1,6 +1,6 @@
 process {
     withName: 'SRA_FASTQ_FTP' {
-        ext.args = '--retry 5 --continue-at - --max-time 1200'
+
         publishDir = [
             [
                 path: { "${params.outdir}/fastq" },
diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap
index a2d24d65..531a5ec3 100644
--- a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap
+++ b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap
@@ -3,25 +3,69 @@
         "content": [
             {
                 "0": [
-                    
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,baaaea61cba4294ec696fdfea1610848",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,8e43ad99049fabb6526a4b846da01c32"
+                        ]
+                    ]
                 ],
                 "1": [
-                    
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
+                            "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
+                        ]
+                    ]
                 ],
                 "2": [
-                    
+                    "versions.yml:md5,6b60ed6d5805271a1b97798e29c0635c"
                 ],
                 "fastq": [
-                    
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,baaaea61cba4294ec696fdfea1610848",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,8e43ad99049fabb6526a4b846da01c32"
+                        ]
+                    ]
                 ],
                 "md5": [
-                    
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
+                            "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
+                        ]
+                    ]
                 ],
                 "versions": [
-                    
+                    "versions.yml:md5,6b60ed6d5805271a1b97798e29c0635c"
                 ]
             }
         ],
-        "timestamp": "2023-12-19T21:44:01.92664"
+        "timestamp": "2023-12-20T23:33:35.159073"
     }
 }
\ No newline at end of file

From ecd957b9858d37ad85d7dc05f5b43c18d8cc823b Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Thu, 4 Jan 2024 15:44:12 +0100
Subject: [PATCH 592/852] Update CHANGELOG.md

---
 CHANGELOG.md | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5f2a1de5..2bfacdc2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,11 +9,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 Special thanks to the following for their contributions to the release:
 
+- [Alexandru Mizeranschi](https://github.com/nicolae06)
 - [Sebastian Uhrig](https://github.com/suhrig)
 
+Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
+
 ### Enhancements & fixes
 
-- [PR #241](https://github.com/nf-core/fetchngs/pull/241) - download of big files time out and don't resume
+- [PR #241](https://github.com/nf-core/fetchngs/pull/241) - Download of big files time out and don't resume ([#169](https://github.com/nf-core/fetchngs/issues/169))
 
 ### Software dependencies
 

From b138070974849bd6524f063e50102f29c84a72b5 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Thu, 4 Jan 2024 15:45:25 +0100
Subject: [PATCH 593/852] Delete conf/modules.config

---
 conf/modules.config | 171 --------------------------------------------
 1 file changed, 171 deletions(-)
 delete mode 100644 conf/modules.config

diff --git a/conf/modules.config b/conf/modules.config
deleted file mode 100644
index 1e8a4ca2..00000000
--- a/conf/modules.config
+++ /dev/null
@@ -1,171 +0,0 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Config file for defining DSL2 per module options and publishing paths
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Available keys to override module options:
-        ext.args   = Additional arguments appended to command in module.
-        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
-        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
-        ext.prefix = File name prefix for output files.
-----------------------------------------------------------------------------------------
-*/
-
-//
-// Generic process options for all workflows
-//
-process {
-
-    publishDir = [
-        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-    ]
-
-    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            pattern: '*_versions.yml'
-        ]
-    }
-
-}
-
-//
-//  Process options for the SRA workflow
-//
-if (params.input_type == 'sra') {
-
-    process {
-
-        withName: SRA_IDS_TO_RUNINFO {
-            publishDir = [
-                path: { "${params.outdir}/metadata" },
-                enabled: false
-            ]
-        }
-
-        withName: SRA_RUNINFO_TO_FTP {
-            publishDir = [
-                path: { "${params.outdir}/metadata" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
-        withName: SRA_FASTQ_FTP {
-            ext.args = '-t 5 -nv -c -T 60'
-            publishDir = [
-                [
-                    path: { "${params.outdir}/fastq" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.fastq.gz"
-                ],
-                [
-                    path: { "${params.outdir}/fastq/md5" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.md5"
-                ]
-            ]
-        }
-
-        withName: SRATOOLS_PREFETCH {
-            publishDir = [
-                path: { "${params.outdir}/sra" },
-                enabled: false
-            ]
-        }
-
-        withName: SRATOOLS_FASTERQDUMP {
-            ext.args = '--split-files --include-technical'
-            publishDir = [
-                path: { "${params.outdir}/fastq" },
-                mode: params.publish_dir_mode,
-                pattern: "*.fastq.gz"
-            ]
-        }
-
-        withName: SRA_TO_SAMPLESHEET {
-            publishDir = [
-                path: { "${params.outdir}/samplesheet" },
-                enabled: false
-            ]
-        }
-
-        withName: SRA_MERGE_SAMPLESHEET {
-            publishDir = [
-                path: { "${params.outdir}/samplesheet" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
-        withName: MULTIQC_MAPPINGS_CONFIG {
-            publishDir = [
-                path: { "${params.outdir}/samplesheet" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
-    }
-
-}
-
-//
-//  Process options for the Synapse workflow
-//
-if (params.input_type == 'synapse') {
-
-    process {
-
-        withName: SYNAPSE_LIST {
-            ext.args = '--long'
-            publishDir = [
-                path: { "${params.outdir}/metadata" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
-        withName: SYNAPSE_GET {
-            publishDir = [
-                [
-                    path: { "${params.outdir}/fastq" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.fastq.gz"
-                ],
-                [
-                    path: { "${params.outdir}/fastq/md5" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.md5"
-                ]
-            ]
-        }
-
-        withName: SYNAPSE_SHOW {
-            publishDir = [
-                path: { "${params.outdir}/metadata" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
-        withName: SYNAPSE_TO_SAMPLESHEET {
-            publishDir = [
-                path: { "${params.outdir}/samplesheet" },
-                enabled: false
-            ]
-        }
-
-        withName: SYNAPSE_MERGE_SAMPLESHEET {
-            publishDir = [
-                path: { "${params.outdir}/samplesheet" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
-    }
-
-}

From 9c3a086597af22e2008c06a79517d607257c588e Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Thu, 4 Jan 2024 15:48:03 +0100
Subject: [PATCH 594/852] Update nextflow.config

---
 modules/local/sra_fastq_ftp/nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/sra_fastq_ftp/nextflow.config b/modules/local/sra_fastq_ftp/nextflow.config
index b73c3729..56e43959 100644
--- a/modules/local/sra_fastq_ftp/nextflow.config
+++ b/modules/local/sra_fastq_ftp/nextflow.config
@@ -1,6 +1,6 @@
 process {
     withName: 'SRA_FASTQ_FTP' {
-
+        ext.args = '-t 5 -nv -c -T 60'
         publishDir = [
             [
                 path: { "${params.outdir}/fastq" },

From 47a54919ed0690e41cb3716dd38029d3aab9186c Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 4 Jan 2024 18:02:22 +0000
Subject: [PATCH 595/852] Use double quotes for closure around projectDir

---
 conf/test.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/test.config b/conf/test.config
index c09a571c..9bfd2adc 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -20,7 +20,7 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input  = '${projectDir}/tests/sra_ids_test.csv'
+    input = "${projectDir}/tests/sra_ids_test.csv"
 
     validationSchemaIgnoreParams = 'test_data_base,merge_samplesheet_ids,fastq_ftp_ids,test_data'
 }

From 7afee7689ab0a75a8554b0a298d368b7e70419bc Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 4 Jan 2024 18:02:40 +0000
Subject: [PATCH 596/852] Remove test data for sra_merge_samplesheet process

---
 conf/test_data.config | 30 ++++++++----------------------
 1 file changed, 8 insertions(+), 22 deletions(-)

diff --git a/conf/test_data.config b/conf/test_data.config
index 670115a8..167dff83 100644
--- a/conf/test_data.config
+++ b/conf/test_data.config
@@ -2,19 +2,7 @@ params {
     // Base directory for test data
     test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs"
 
-    merge_samplesheet_ids = [ "DRX024467_DRR026872", "SRX11047067_SRR14709033", "SRX9504942_SRR13055517", "DRX026011_DRR028935", "SRX17709227_SRR21711856", "SRX9504942_SRR13055518", "ERX1188904_ERR1109373", "SRX17709228_SRR21711855", "SRX9504942_SRR13055519", "ERX1234253_ERR1160846", "SRX6725035_SRR9984183", "SRX9504942_SRR13055520", "SRX10940790_SRR14593545", "SRX9315476_SRR12848126", "SRX9626017_SRR13191702" ]
-
-    def merge_samplesheet_url  = "${params.test_data_base}/modules/local/sra_merge_samplesheet/samplesheets/"
-    def merge_mappings_url     = "${params.test_data_base}/modules/local/sra_merge_samplesheet/mappings/"
-    def merge_samplesheet_urls = []
-    def merge_mappings_urls    = []
-
-    merge_samplesheet_ids.each { id ->
-        merge_samplesheet_urls += "${merge_samplesheet_url}${id}.samplesheet.csv"
-        merge_mappings_urls    += "${merge_mappings_url}/${id}.mappings.csv"
-    }
-
-    fastq_ftp_ids      = ["SRR13191702"]
+    fastq_ftp_ids = ["SRR13191702"]
     def fastq_ftp_url  = "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/"
     def fastq_ftp_urls = []
 
@@ -26,22 +14,20 @@ params {
     test_data {
         'sarscov2'{
             'illumina' {
-                SRR11140744_tar_gz                  = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR11140744.tar.gz"
-                SRR13255544_tar_gz                  = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR13255544.tar.gz"
+                SRR11140744_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR11140744.tar.gz"
+                SRR13255544_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR13255544.tar.gz"
             }
         }
         'generic' {
             'config' {
-                ncbi_user_settings                  = "${params.test_data_base}/data/generic/config/ncbi_user_settings.mkfg"
+                ncbi_user_settings = "${params.test_data_base}/data/generic/config/ncbi_user_settings.mkfg"
             }
         }
         'modules_local' {
-                multiqc_mappings_config             = "${params.test_data_base}/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv"
-                sra_merge_samplesheet_samplesheets  = merge_samplesheet_urls
-                sra_merge_samplesheet_mappings      = merge_mappings_urls
-                sra_to_samplesheet                  = "${params.test_data_base}/modules/local/sra_to_samplesheet/SRX9626017_SRR13191702.mappings.csv"
-                sra_fastq_ftp                       = fastq_ftp_urls
-                sra_runinfo_to_ftp                  = "${params.test_data_base}/modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv"
+                multiqc_mappings_config = "${params.test_data_base}/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv"
+                sra_to_samplesheet      = "${params.test_data_base}/modules/local/sra_to_samplesheet/SRX9626017_SRR13191702.mappings.csv"
+                sra_fastq_ftp           = fastq_ftp_urls
+                sra_runinfo_to_ftp      = "${params.test_data_base}/modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv"
         }
     }
 }

From 209a7a4cc81c99e98dc4cf13c5158653d2b962a7 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 4 Jan 2024 18:03:56 +0000
Subject: [PATCH 597/852] Fix bugs with samplesheet merging from PR #238

---
 workflows/sra/main.nf | 22 ++++++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 16408496..de2d4d5d 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -118,10 +118,24 @@ workflow SRA {
         params.sample_mapping_fields
     )
   
-
-    // Combine all sample sheet/mapping paths into two files
-    ch_samplesheet=SRA_TO_SAMPLESHEET.out.samplesheet.map{it[1]}.collectFile(name:'samplesheets.csv', newLine: true, keepHeader: true, storeDir:params.outdir)
-    ch_mappings=SRA_TO_SAMPLESHEET.out.samplesheet.map{it[1]}.collectFile(name:'id_mappings.csv', newLine: true, keepHeader: true, storeDir:params.outdir)
+    // Merge samplesheets and mapping files across all samples
+    SRA_TO_SAMPLESHEET
+        .out
+        .samplesheet
+        .map { it[1] }
+        .collectFile(name:'tmp_samplesheet.csv', newLine: true, keepHeader: true)
+        .map { it.text.tokenize('\n').join('\n') }
+        .collectFile(name:'samplesheet.csv', storeDir: "${params.outdir}/samplesheet")
+        .set { ch_samplesheet }
+
+    SRA_TO_SAMPLESHEET
+        .out
+        .mappings
+        .map { it[1] }
+        .collectFile(name:'tmp_id_mappings.csv', newLine: true, keepHeader: true)
+        .map { it.text.tokenize('\n').join('\n') }
+        .collectFile(name:'id_mappings.csv', storeDir: "${params.outdir}/samplesheet")
+        .set { ch_mappings }
 
     //
     // MODULE: Create a MutiQC config file with sample name mappings

From ec8585c7256c41db61b52f20f7fbb89136c2222e Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 4 Jan 2024 18:07:13 +0000
Subject: [PATCH 598/852] Update CHANGELOG

---
 CHANGELOG.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2bfacdc2..8ade0c4c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,13 +10,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 Special thanks to the following for their contributions to the release:
 
 - [Alexandru Mizeranschi](https://github.com/nicolae06)
+- [Alexander Blaessle](https://github.com/alexblaessle)
 - [Sebastian Uhrig](https://github.com/suhrig)
 
 Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
 
 ### Enhancements & fixes
 
+- [PR #238](https://github.com/nf-core/fetchngs/pull/238) - Resolved bug when prefetching large studies ([#236](https://github.com/nf-core/fetchngs/issues/236))
 - [PR #241](https://github.com/nf-core/fetchngs/pull/241) - Download of big files time out and don't resume ([#169](https://github.com/nf-core/fetchngs/issues/169))
+- [PR #243](https://github.com/nf-core/fetchngs/pull/243) - Fixes for [PR #238](https://github.com/nf-core/fetchngs/pull/238)
 
 ### Software dependencies
 

From da88dc6a32ef82098031ace5a8e01c056b8b5066 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 4 Jan 2024 18:10:23 +0000
Subject: [PATCH 599/852] Fix nf-core lint until template updates are merged in

---
 .nf-core.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.nf-core.yml b/.nf-core.yml
index 0e89cae9..2a36eda4 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -17,3 +17,6 @@ lint:
     - .gitignore
     - assets/sendmail_template.txt
     - lib/NfcoreTemplate.groovy
+    - .github/CONTRIBUTING.md
+    - .github/PULL_REQUEST_TEMPLATE.md                                         │
+    - .github/workflows/linting.yml
\ No newline at end of file

From 05b993e8ca0388e5ad34030cb359e50830dc6d1c Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 4 Jan 2024 18:12:34 +0000
Subject: [PATCH 600/852] Fix prettier

---
 .nf-core.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index 2a36eda4..cc0541e3 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -19,4 +19,4 @@ lint:
     - lib/NfcoreTemplate.groovy
     - .github/CONTRIBUTING.md
     - .github/PULL_REQUEST_TEMPLATE.md                                         │
-    - .github/workflows/linting.yml
\ No newline at end of file
+    - .github/workflows/linting.yml

From 8fc57d909dcd185017d8920afe38a61b9321de19 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 4 Jan 2024 18:13:28 +0000
Subject: [PATCH 601/852] Fix prettier

---
 .nf-core.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index cc0541e3..47379ac6 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -18,5 +18,5 @@ lint:
     - assets/sendmail_template.txt
     - lib/NfcoreTemplate.groovy
     - .github/CONTRIBUTING.md
-    - .github/PULL_REQUEST_TEMPLATE.md                                         │
+    - .github/PULL_REQUEST_TEMPLATE.md
     - .github/workflows/linting.yml

From fb07b32552c552147686799f2b6832aca886944e Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 4 Jan 2024 19:59:54 +0000
Subject: [PATCH 602/852] Fix nf-test for sra_skip_fastq_download

---
 bin/multiqc_mappings_config.py                       |  5 +++--
 .../sra/tests/sra_skip_fastq_download.nf.test.snap   | 12 +++++-------
 2 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/bin/multiqc_mappings_config.py b/bin/multiqc_mappings_config.py
index 2fcdb49a..5b60f2e0 100755
--- a/bin/multiqc_mappings_config.py
+++ b/bin/multiqc_mappings_config.py
@@ -7,6 +7,7 @@
     config = "sample_names_rename_buttons:\n"
     config += "\n".join(["  - " + x.strip('"') for x in header])
     config += "sample_names_rename:\n"
+    rename = []
     for line in fin:
-        config += f"  - [{', '.join(line.strip().split(','))}]\n"
-    fout.write(config)
+        rename.append(f"  - [{', '.join(line.strip().split(','))}]")
+    fout.write(config + '\n'.join(sorted(rename)) + '\n')
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
index cdb0965c..c7835acb 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,0a9b99509bcc64ca245408b6bb634f15"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "3": [
                     [
@@ -20,14 +20,13 @@
                 "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ],
                 "fastq": [
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "sample_mappings": [
                     [
@@ -36,16 +35,15 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,0a9b99509bcc64ca245408b6bb634f15"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ]
             }
         ],
-        "timestamp": "2023-10-18T09:50:04.300075498"
+        "timestamp": "2024-01-04T19:59:06.257582"
     }
 }
\ No newline at end of file

From 7e5687a6b4e7c48fcc1e897cb5975bb79a390194 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 5 Jan 2024 10:23:24 +0000
Subject: [PATCH 603/852] Change workDir to .nf-test

---
 nf-test.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf-test.config b/nf-test.config
index cb656b94..0799cb40 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -3,7 +3,7 @@ config {
     testsDir "."
 
     // nf-test directory including temporary files for each test
-    workDir "/tmp"
+    workDir ".nf-test"
 
     // location of library folder that is added automatically to the classpath
     libDir "lib/"

From 0193bce55205fb453be5d8a22edb878591e8c64d Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 5 Jan 2024 10:40:57 +0000
Subject: [PATCH 604/852] Fix Black lint

---
 bin/multiqc_mappings_config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/multiqc_mappings_config.py b/bin/multiqc_mappings_config.py
index 5b60f2e0..3ffe35ec 100755
--- a/bin/multiqc_mappings_config.py
+++ b/bin/multiqc_mappings_config.py
@@ -10,4 +10,4 @@
     rename = []
     for line in fin:
         rename.append(f"  - [{', '.join(line.strip().split(','))}]")
-    fout.write(config + '\n'.join(sorted(rename)) + '\n')
+    fout.write(config + "\n".join(sorted(rename)) + "\n")

From c642adf8bf4d0701dd3ecd8a6bede8af0153d61f Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 5 Jan 2024 10:53:04 +0000
Subject: [PATCH 605/852] Update CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2bfacdc2..7307bdd8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 ### Enhancements & fixes
 
 - [PR #241](https://github.com/nf-core/fetchngs/pull/241) - Download of big files time out and don't resume ([#169](https://github.com/nf-core/fetchngs/issues/169))
+- [PR #242](https://github.com/nf-core/fetchngs/pull/242) - Template update for nf-core/tools v2.11
 
 ### Software dependencies
 

From 06cfcc8ffd54a8207ec8ecdada29f4359ef48d33 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 5 Jan 2024 12:20:22 +0000
Subject: [PATCH 606/852] Update snapshots and remove dot from nf-test workDir

---
 nf-test.config                                |  2 +-
 workflows/sra/tests/main.nf.test.snap         | 20 +++++++++----------
 ...ra_custom_ena_metadata_fields.nf.test.snap | 20 +++++++++----------
 .../sra_force_sratools_download.nf.test.snap  | 12 +++++------
 .../sra_nf_core_pipeline_atacseq.nf.test.snap | 20 +++++++++----------
 .../sra_nf_core_pipeline_rnaseq.nf.test.snap  | 20 +++++++++----------
 ..._nf_core_pipeline_taxprofiler.nf.test.snap | 20 +++++++++----------
 ...a_nf_core_pipeline_viralrecon.nf.test.snap | 20 +++++++++----------
 8 files changed, 60 insertions(+), 74 deletions(-)

diff --git a/nf-test.config b/nf-test.config
index 0799cb40..76aab204 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -3,7 +3,7 @@ config {
     testsDir "."
 
     // nf-test directory including temporary files for each test
-    workDir ".nf-test"
+    workDir "nf-test"
 
     // location of library folder that is added automatically to the classpath
     libDir "lib/"
diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
index 885b7d6a..ce70041b 100644
--- a/workflows/sra/tests/main.nf.test.snap
+++ b/workflows/sra/tests/main.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,eda595eca3cb5ed450641565c38390c2"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "3": [
                     [
@@ -20,16 +20,15 @@
                 "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ],
                 "fastq": [
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "sample_mappings": [
                     [
@@ -38,18 +37,17 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,eda595eca3cb5ed450641565c38390c2"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ]
             }
         ],
-        "timestamp": "2023-10-18T09:49:19.020482551"
+        "timestamp": "2024-01-05T11:53:53.509361"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
index 45e007d0..294a7951 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,a9e9da506288c364af14d46b86dafeb1"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,8ed2bd72d432eff4a8ed7d909af6f60c"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "3": [
                     [
@@ -20,16 +20,15 @@
                 "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ],
                 "fastq": [
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,8ed2bd72d432eff4a8ed7d909af6f60c"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "sample_mappings": [
                     [
@@ -38,18 +37,17 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,a9e9da506288c364af14d46b86dafeb1"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ]
             }
         ],
-        "timestamp": "2023-10-18T09:36:57.154883885"
+        "timestamp": "2024-01-05T12:00:54.018925"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
index f445296a..b2df7434 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,7e6a65057fe000f562132ae9e608e87b"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "3": [
                     [
@@ -21,14 +21,13 @@
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ],
                 "fastq": [
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "sample_mappings": [
                     [
@@ -37,17 +36,16 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,7e6a65057fe000f562132ae9e608e87b"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ]
             }
         ],
-        "timestamp": "2023-10-18T09:43:16.468494798"
+        "timestamp": "2024-01-05T11:57:59.429567"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
index 3e9e7f31..687d857d 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,35292d2bea78b087d75c3333f6319b6b"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "3": [
                     [
@@ -20,16 +20,15 @@
                 "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ],
                 "fastq": [
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "sample_mappings": [
                     [
@@ -38,18 +37,17 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,35292d2bea78b087d75c3333f6319b6b"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ]
             }
         ],
-        "timestamp": "2023-10-18T09:47:56.240260295"
+        "timestamp": "2024-01-05T12:11:46.580901"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
index 8805d3ac..fc41c497 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,b7ac0ff84f5031daaa9405c736a37125"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "3": [
                     [
@@ -20,16 +20,15 @@
                 "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ],
                 "fastq": [
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "sample_mappings": [
                     [
@@ -38,18 +37,17 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,b7ac0ff84f5031daaa9405c736a37125"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ]
             }
         ],
-        "timestamp": "2023-10-18T09:40:15.590249346"
+        "timestamp": "2024-01-05T12:14:34.129435"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
index 0853eef8..8a83465f 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,296836917bbdf34bda106a313424fa95"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "3": [
                     [
@@ -20,16 +20,15 @@
                 "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ],
                 "fastq": [
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "sample_mappings": [
                     [
@@ -38,18 +37,17 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,296836917bbdf34bda106a313424fa95"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ]
             }
         ],
-        "timestamp": "2023-10-18T09:49:51.04235046"
+        "timestamp": "2024-01-05T12:19:15.913569"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
index e364b3a9..1c946943 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,eda595eca3cb5ed450641565c38390c2"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "3": [
                     [
@@ -20,16 +20,15 @@
                 "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ],
                 "fastq": [
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "sample_mappings": [
                     [
@@ -38,18 +37,17 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,eda595eca3cb5ed450641565c38390c2"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
+                    "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,e977678bd13a54fc9c31addf135be15e"
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ]
             }
         ],
-        "timestamp": "2023-10-18T09:48:46.587502263"
+        "timestamp": "2024-01-05T12:06:14.563473"
     }
 }
\ No newline at end of file

From 39f40e9e1a1f7c148f9823dff2b1a24c4167b1d2 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 5 Jan 2024 13:59:27 +0000
Subject: [PATCH 607/852] Update files ignored from lintint

---
 .nf-core.yml | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index 0e89cae9..51a92309 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -2,18 +2,11 @@ repository_type: pipeline
 lint:
   actions_ci: false
   files_exist:
-    - .github/workflows/awsfulltest.yml
-    - .github/workflows/awstest.yml
-    - assets/multiqc_config.yml
-    - conf/igenomes.config
     - conf/modules.config
     - lib/NfcoreTemplate.groovy
     - lib/Utils.groovy
-    - lib/WorkflowFetchngs.groovy
     - lib/WorkflowMain.groovy
     - lib/nfcore_external_java_deps.jar
   files_unchanged:
-    - .gitattributes
     - .gitignore
     - assets/sendmail_template.txt
-    - lib/NfcoreTemplate.groovy

From a4f7a4ac0333509b25ec7a8566b329c6f4db6eae Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 5 Jan 2024 13:59:44 +0000
Subject: [PATCH 608/852] Use double quotes for closure around projectDir

---
 conf/test.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/test.config b/conf/test.config
index c09a571c..05b58689 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -20,7 +20,7 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input  = '${projectDir}/tests/sra_ids_test.csv'
+    input  = "${projectDir}/tests/sra_ids_test.csv"
 
     validationSchemaIgnoreParams = 'test_data_base,merge_samplesheet_ids,fastq_ftp_ids,test_data'
 }

From 5fbe7f045823ed21ff020f759914279e40693a0b Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 5 Jan 2024 14:00:14 +0000
Subject: [PATCH 609/852] Bump pipeline version to 1.12.0dev

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 0f867a95..e81dac71 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -234,7 +234,7 @@ manifest {
     description     = """Pipeline to fetch metadata and raw FastQ files from public databases"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.11.0'
+    version         = '1.12.0dev'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
 

From 1544d3fc65c99e7e296fb0f71efd13bd97a5d1b4 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 5 Jan 2024 15:24:33 +0000
Subject: [PATCH 610/852] Use @adamrtalbot Docker runOptions fix to get nf-test
 running

---
 nf-test.config        | 2 +-
 tests/nextflow.config | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)
 create mode 100644 tests/nextflow.config

diff --git a/nf-test.config b/nf-test.config
index 76aab204..c880f88a 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -9,7 +9,7 @@ config {
     libDir "lib/"
 
     // location of an optional nextflow.config file specific for executing tests
-    configFile "nextflow.config"
+    configFile "tests/nextflow.config"
 
     // run all test with the defined docker profile from the main nextflow.config
     profile ""
diff --git a/tests/nextflow.config b/tests/nextflow.config
new file mode 100644
index 00000000..c9ea8473
--- /dev/null
+++ b/tests/nextflow.config
@@ -0,0 +1 @@
+docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64 -v $HOME:$HOME'
\ No newline at end of file

From e94ed03c49711ca425a93928b75c718954231a81 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 5 Jan 2024 16:16:53 +0000
Subject: [PATCH 611/852] Bump nf-test version to 0.8.2 in CI tests

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1a5fe7f7..5c06c5ce 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -13,7 +13,7 @@ on:
 
 env:
   NXF_ANSI_LOG: false
-  NFTEST_VER: "0.8.1"
+  NFTEST_VER: "0.8.2"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"

From 0b738edc859864c59f49590e27d653b35e22e0d3 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 5 Jan 2024 16:27:20 +0000
Subject: [PATCH 612/852] Test adding docker.runOptions to pipeline
 nextflow.config

---
 nextflow.config       | 2 +-
 nf-test.config        | 2 +-
 tests/nextflow.config | 1 -
 3 files changed, 2 insertions(+), 3 deletions(-)
 delete mode 100644 tests/nextflow.config

diff --git a/nextflow.config b/nextflow.config
index 0f867a95..76ca8a36 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -114,7 +114,7 @@ profiles {
         shifter.enabled        = false
         charliecloud.enabled   = false
         apptainer.enabled      = false
-        runOptions             = '-u $(id -u):$(id -g)'
+        runOptions             = '-u $(id -u):$(id -g) -v $HOME:$HOME'
     }
     arm {
         docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
diff --git a/nf-test.config b/nf-test.config
index c880f88a..76aab204 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -9,7 +9,7 @@ config {
     libDir "lib/"
 
     // location of an optional nextflow.config file specific for executing tests
-    configFile "tests/nextflow.config"
+    configFile "nextflow.config"
 
     // run all test with the defined docker profile from the main nextflow.config
     profile ""
diff --git a/tests/nextflow.config b/tests/nextflow.config
deleted file mode 100644
index c9ea8473..00000000
--- a/tests/nextflow.config
+++ /dev/null
@@ -1 +0,0 @@
-docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64 -v $HOME:$HOME'
\ No newline at end of file

From 0a89ccbe93b687de06cfca9dbaebdd2cb22607b9 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 5 Jan 2024 16:38:33 +0000
Subject: [PATCH 613/852] Idiot...add docker in front of runOptions

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 76ca8a36..c849b9b8 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -114,7 +114,7 @@ profiles {
         shifter.enabled        = false
         charliecloud.enabled   = false
         apptainer.enabled      = false
-        runOptions             = '-u $(id -u):$(id -g) -v $HOME:$HOME'
+        docker.runOptions      = '-u $(id -u):$(id -g) -v $HOME:$HOME'
     }
     arm {
         docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'

From 1f70b27de019c14ec1581f5c243a8a5756cdc1a6 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 5 Jan 2024 17:10:22 +0000
Subject: [PATCH 614/852] Add sort logic to collectFile operator

---
 workflows/sra/main.nf                                  |  4 ++--
 workflows/sra/tests/sra_skip_fastq_download.nf.test    |  2 +-
 .../sra/tests/sra_skip_fastq_download.nf.test.snap     | 10 +++++-----
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index de2d4d5d..106041a4 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -123,7 +123,7 @@ workflow SRA {
         .out
         .samplesheet
         .map { it[1] }
-        .collectFile(name:'tmp_samplesheet.csv', newLine: true, keepHeader: true)
+        .collectFile(name:'tmp_samplesheet.csv', newLine: true, keepHeader: true, sort: { it.baseName })
         .map { it.text.tokenize('\n').join('\n') }
         .collectFile(name:'samplesheet.csv', storeDir: "${params.outdir}/samplesheet")
         .set { ch_samplesheet }
@@ -132,7 +132,7 @@ workflow SRA {
         .out
         .mappings
         .map { it[1] }
-        .collectFile(name:'tmp_id_mappings.csv', newLine: true, keepHeader: true)
+        .collectFile(name:'tmp_id_mappings.csv', newLine: true, keepHeader: true, sort: { it.baseName })
         .map { it.text.tokenize('\n').join('\n') }
         .collectFile(name:'id_mappings.csv', storeDir: "${params.outdir}/samplesheet")
         .set { ch_mappings }
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index dd846643..c9217606 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "results"
+                outdir = "$outputDir"
                 skip_fastq_download = true
             }
         }
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
index c7835acb..3631113e 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,eb18025bb1cb97a4fe399ca16757d2db"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "3": [
                     [
@@ -26,7 +26,7 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "sample_mappings": [
                     [
@@ -35,7 +35,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,eb18025bb1cb97a4fe399ca16757d2db"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -44,6 +44,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-04T19:59:06.257582"
+        "timestamp": "2024-01-05T17:08:15.42871"
     }
 }
\ No newline at end of file

From 12597f1796d0c594f1f2b530b1306ea486a7b024 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 5 Jan 2024 17:48:20 +0000
Subject: [PATCH 615/852] Update all workflow snapshots and use outputDir by
 default

---
 workflows/sra/tests/main.nf.test                       |  2 +-
 workflows/sra/tests/main.nf.test.snap                  | 10 +++++-----
 .../sra/tests/sra_custom_ena_metadata_fields.nf.test   |  2 +-
 .../tests/sra_custom_ena_metadata_fields.nf.test.snap  | 10 +++++-----
 .../sra/tests/sra_force_sratools_download.nf.test      |  2 +-
 .../sra/tests/sra_force_sratools_download.nf.test.snap | 10 +++++-----
 .../sra/tests/sra_nf_core_pipeline_atacseq.nf.test     |  2 +-
 .../tests/sra_nf_core_pipeline_atacseq.nf.test.snap    | 10 +++++-----
 .../sra/tests/sra_nf_core_pipeline_rnaseq.nf.test      |  2 +-
 .../sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap | 10 +++++-----
 .../sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test |  2 +-
 .../sra_nf_core_pipeline_taxprofiler.nf.test.snap      | 10 +++++-----
 .../sra/tests/sra_nf_core_pipeline_viralrecon.nf.test  |  2 +-
 .../tests/sra_nf_core_pipeline_viralrecon.nf.test.snap | 10 +++++-----
 14 files changed, 42 insertions(+), 42 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index c8dce3c7..072c2ebb 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "results"
+                outdir = "$outputDir"
             }
         }
 
diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
index ce70041b..ffdf20cc 100644
--- a/workflows/sra/tests/main.nf.test.snap
+++ b/workflows/sra/tests/main.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,d252b222b8ef94670117780d43498b86"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "3": [
                     [
@@ -28,7 +28,7 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "sample_mappings": [
                     [
@@ -37,7 +37,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,d252b222b8ef94670117780d43498b86"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -48,6 +48,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-05T11:53:53.509361"
+        "timestamp": "2024-01-05T17:31:06.996066"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index d4dd4141..262cedef 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "results"
+                outdir = "$outputDir"
                 nf_core_pipeline = "rnaseq"
                 ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5"
                 sample_mapping_fields = "run_accession,library_layout"
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
index 294a7951..56c0505c 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,7cc8031f595157c6ac13ba5067e4bcfb"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,7ee50def039a942e0ac8ca63292c8368"
                 ],
                 "3": [
                     [
@@ -28,7 +28,7 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,7ee50def039a942e0ac8ca63292c8368"
                 ],
                 "sample_mappings": [
                     [
@@ -37,7 +37,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,7cc8031f595157c6ac13ba5067e4bcfb"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -48,6 +48,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-05T12:00:54.018925"
+        "timestamp": "2024-01-05T17:27:38.720872"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index 62adb9af..453ab328 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "results"
+                outdir = "$outputDir"
                 force_sratools_download = true
             }
         }
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
index b2df7434..895d79b1 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,0f2c0516990774b5d7d76a7ddf763f55"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "3": [
                     [
@@ -27,7 +27,7 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "sample_mappings": [
                     [
@@ -36,7 +36,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,0f2c0516990774b5d7d76a7ddf763f55"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -46,6 +46,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-05T11:57:59.429567"
+        "timestamp": "2024-01-05T17:19:30.088408"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index 00f545b5..3bb70fe6 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "results"
+                outdir = "$outputDir"
                 nf_core_pipeline = "atacseq"
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
index 687d857d..30de9de2 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,8f985e9dd993b9c826ea095bd377d34a"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "3": [
                     [
@@ -28,7 +28,7 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "sample_mappings": [
                     [
@@ -37,7 +37,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,8f985e9dd993b9c826ea095bd377d34a"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -48,6 +48,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-05T12:11:46.580901"
+        "timestamp": "2024-01-05T17:42:19.033613"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index 62bd6380..a64d4348 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "results"
+                outdir = "$outputDir"
                 nf_core_pipeline = "rnaseq"
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
index fc41c497..97772a53 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,c0f7d7b70e884c78f90630c695703d7b"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "3": [
                     [
@@ -28,7 +28,7 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "sample_mappings": [
                     [
@@ -37,7 +37,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,c0f7d7b70e884c78f90630c695703d7b"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -48,6 +48,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-05T12:14:34.129435"
+        "timestamp": "2024-01-05T17:45:04.403125"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index c5e2865f..1befdba2 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "results"
+                outdir = "$outputDir"
                 nf_core_pipeline = "taxprofiler"
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
index 8a83465f..1d882f8e 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,fe3c7ba9e7b7debe07291d6125f9edc7"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "3": [
                     [
@@ -28,7 +28,7 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "sample_mappings": [
                     [
@@ -37,7 +37,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,fe3c7ba9e7b7debe07291d6125f9edc7"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -48,6 +48,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-05T12:19:15.913569"
+        "timestamp": "2024-01-05T17:47:55.191319"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index 04485010..ba185097 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "results"
+                outdir = "$outputDir"
                 nf_core_pipeline = "viralrecon"
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
index 1c946943..0b63f33d 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,99a3fd9fe3c7cad8184b1bbeadd89c45"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "3": [
                     [
@@ -28,7 +28,7 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "sample_mappings": [
                     [
@@ -37,7 +37,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,99a3fd9fe3c7cad8184b1bbeadd89c45"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -48,6 +48,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-05T12:06:14.563473"
+        "timestamp": "2024-01-05T17:35:26.463757"
     }
 }
\ No newline at end of file

From dd67624668b3ec89da299664e019235d554c208b Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 5 Jan 2024 18:07:18 +0000
Subject: [PATCH 616/852] Use icdiff tool to show nf-test snapshot diff in
 Github Actions output

---
 .github/workflows/ci.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 5c06c5ce..861dd018 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -14,6 +14,8 @@ on:
 env:
   NXF_ANSI_LOG: false
   NFTEST_VER: "0.8.2"
+  NFT_DIFF: "icdiff"
+  NFT_DIFF_ARGS: "-N --cols 200 -L expected -L observed -t"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
@@ -88,6 +90,10 @@ jobs:
         run: |
           wget -qO- https://code.askimed.com/install/nf-test | bash
           sudo mv nf-test /usr/local/bin/
+      
+      - name: Install icdiff for nf-test diff viewing
+        run: |
+          sudo apt install icdiff
 
       - name: Run nf-test
         run: |

From b8d43bee4f8fed9876643c514e1bf834d34b697c Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 5 Jan 2024 18:08:26 +0000
Subject: [PATCH 617/852] Fix prettier

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 861dd018..074b577d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -90,7 +90,7 @@ jobs:
         run: |
           wget -qO- https://code.askimed.com/install/nf-test | bash
           sudo mv nf-test /usr/local/bin/
-      
+
       - name: Install icdiff for nf-test diff viewing
         run: |
           sudo apt install icdiff

From 300cb2e6a27fcb5e83a9c09389325ab19d0d3f99 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 6 Jan 2024 20:03:54 +0000
Subject: [PATCH 618/852] Bump nf-test version to 0.8.3 and remove Docker home
 mounts

---
 .github/workflows/ci.yml | 2 +-
 nextflow.config          | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 074b577d..b89823fc 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -13,7 +13,7 @@ on:
 
 env:
   NXF_ANSI_LOG: false
-  NFTEST_VER: "0.8.2"
+  NFTEST_VER: "0.8.3"
   NFT_DIFF: "icdiff"
   NFT_DIFF_ARGS: "-N --cols 200 -L expected -L observed -t"
 
diff --git a/nextflow.config b/nextflow.config
index c849b9b8..ad11a3fc 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -114,7 +114,7 @@ profiles {
         shifter.enabled        = false
         charliecloud.enabled   = false
         apptainer.enabled      = false
-        docker.runOptions      = '-u $(id -u):$(id -g) -v $HOME:$HOME'
+        docker.runOptions      = '-u $(id -u):$(id -g)'
     }
     arm {
         docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'

From db9d949982f7edc64a705da5efb2445bb58cf92c Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 6 Jan 2024 20:11:45 +0000
Subject: [PATCH 619/852] Add ch_ prefix to fastq_files channel

---
 workflows/sra/main.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 106041a4..d6fc8ce4 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -61,7 +61,7 @@ workflow SRA {
         .unique()
         .set { ch_sra_metadata }
 
-    fastq_files = Channel.empty()
+    ch_fastq_files = Channel.empty()
     if (!params.skip_fastq_download) {
 
         ch_sra_metadata
@@ -93,7 +93,7 @@ workflow SRA {
         ch_versions = ch_versions.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.versions.first())
 
         // Isolate FASTQ channel which will be added to emit block
-        fastq_files
+        ch_fastq_files
             .mix(SRA_FASTQ_FTP.out.fastq, FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads)
             .map {
                 meta, fastq ->
@@ -150,7 +150,7 @@ workflow SRA {
     }
 
     emit:
-    fastq           = fastq_files
+    fastq           = ch_fastq_files
     samplesheet     = ch_samplesheet
     mappings        = ch_mappings
     sample_mappings = ch_sample_mappings_yml

From 44aa79c5e21375a729dd9eea427b5fda84db1fef Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 6 Jan 2024 20:34:30 +0000
Subject: [PATCH 620/852] Use --verbose parameter by default with nf-test

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b89823fc..8917a345 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -97,7 +97,7 @@ jobs:
 
       - name: Run nf-test
         run: |
-          nf-test test --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml
+          nf-test test --verbose --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml
 
       - name: Output log on failure
         if: failure()

From 584fb2d44d7040ad62c02b2739b89c27e3b21c6c Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 6 Jan 2024 20:35:30 +0000
Subject: [PATCH 621/852] Use relative path for --outdir because outputDir will
 be unique path

---
 .../sra/tests/sra_custom_ena_metadata_fields.nf.test   |  2 +-
 .../sra/tests/sra_force_sratools_download.nf.test      |  2 +-
 .../sra/tests/sra_force_sratools_download.nf.test.snap | 10 +++++-----
 .../sra/tests/sra_nf_core_pipeline_atacseq.nf.test     |  2 +-
 .../sra/tests/sra_nf_core_pipeline_rnaseq.nf.test      |  2 +-
 .../sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test |  2 +-
 .../sra/tests/sra_nf_core_pipeline_viralrecon.nf.test  |  2 +-
 workflows/sra/tests/sra_skip_fastq_download.nf.test    |  2 +-
 8 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index 262cedef..d4dd4141 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
+                outdir = "results"
                 nf_core_pipeline = "rnaseq"
                 ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5"
                 sample_mapping_fields = "run_accession,library_layout"
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index 453ab328..62adb9af 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
+                outdir = "results"
                 force_sratools_download = true
             }
         }
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
index 895d79b1..07cf1871 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,0f2c0516990774b5d7d76a7ddf763f55"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "3": [
                     [
@@ -27,7 +27,7 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "sample_mappings": [
                     [
@@ -36,7 +36,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,0f2c0516990774b5d7d76a7ddf763f55"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -46,6 +46,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-05T17:19:30.088408"
+        "timestamp": "2024-01-06T20:32:48.107479"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index 3bb70fe6..00f545b5 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
+                outdir = "results"
                 nf_core_pipeline = "atacseq"
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index a64d4348..62bd6380 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
+                outdir = "results"
                 nf_core_pipeline = "rnaseq"
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index 1befdba2..c5e2865f 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
+                outdir = "results"
                 nf_core_pipeline = "taxprofiler"
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index ba185097..04485010 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
+                outdir = "results"
                 nf_core_pipeline = "viralrecon"
             }
         }
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index c9217606..dd846643 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
+                outdir = "results"
                 skip_fastq_download = true
             }
         }

From 18a7c272f07e1c1b414c2ea3df11f51d4f01554f Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sat, 6 Jan 2024 20:50:03 +0000
Subject: [PATCH 622/852] Update snapshots

---
 .../tests/sra_custom_ena_metadata_fields.nf.test.snap  | 10 +++++-----
 .../tests/sra_nf_core_pipeline_atacseq.nf.test.snap    | 10 +++++-----
 .../sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap | 10 +++++-----
 .../sra_nf_core_pipeline_taxprofiler.nf.test.snap      | 10 +++++-----
 .../tests/sra_nf_core_pipeline_viralrecon.nf.test.snap | 10 +++++-----
 .../sra/tests/sra_skip_fastq_download.nf.test.snap     | 10 +++++-----
 6 files changed, 30 insertions(+), 30 deletions(-)

diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
index 56c0505c..ad611ee2 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,7cc8031f595157c6ac13ba5067e4bcfb"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,7ee50def039a942e0ac8ca63292c8368"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "3": [
                     [
@@ -28,7 +28,7 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,7ee50def039a942e0ac8ca63292c8368"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "sample_mappings": [
                     [
@@ -37,7 +37,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,7cc8031f595157c6ac13ba5067e4bcfb"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -48,6 +48,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-05T17:27:38.720872"
+        "timestamp": "2024-01-06T20:36:14.475733"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
index 30de9de2..3c616c12 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,8f985e9dd993b9c826ea095bd377d34a"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "3": [
                     [
@@ -28,7 +28,7 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "sample_mappings": [
                     [
@@ -37,7 +37,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,8f985e9dd993b9c826ea095bd377d34a"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -48,6 +48,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-05T17:42:19.033613"
+        "timestamp": "2024-01-06T20:45:29.760739"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
index 97772a53..2ad3280d 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,c0f7d7b70e884c78f90630c695703d7b"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "3": [
                     [
@@ -28,7 +28,7 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "sample_mappings": [
                     [
@@ -37,7 +37,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,c0f7d7b70e884c78f90630c695703d7b"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -48,6 +48,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-05T17:45:04.403125"
+        "timestamp": "2024-01-06T20:47:23.837927"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
index 1d882f8e..031014c4 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,fe3c7ba9e7b7debe07291d6125f9edc7"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "3": [
                     [
@@ -28,7 +28,7 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "sample_mappings": [
                     [
@@ -37,7 +37,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,fe3c7ba9e7b7debe07291d6125f9edc7"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -48,6 +48,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-05T17:47:55.191319"
+        "timestamp": "2024-01-06T20:49:22.636476"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
index 0b63f33d..15043ffd 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,99a3fd9fe3c7cad8184b1bbeadd89c45"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "3": [
                     [
@@ -28,7 +28,7 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "sample_mappings": [
                     [
@@ -37,7 +37,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,99a3fd9fe3c7cad8184b1bbeadd89c45"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -48,6 +48,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-05T17:35:26.463757"
+        "timestamp": "2024-01-06T20:40:07.74118"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
index 3631113e..a402abdf 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
@@ -6,10 +6,10 @@
                     
                 ],
                 "1": [
-                    "samplesheet.csv:md5,eb18025bb1cb97a4fe399ca16757d2db"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "2": [
-                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "3": [
                     [
@@ -26,7 +26,7 @@
                     
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
+                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
                 "sample_mappings": [
                     [
@@ -35,7 +35,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,eb18025bb1cb97a4fe399ca16757d2db"
+                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
@@ -44,6 +44,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-05T17:08:15.42871"
+        "timestamp": "2024-01-06T20:43:31.440219"
     }
 }
\ No newline at end of file

From 95b30a62b2822fef37ad67dbfe47e0d3fdd84d5d Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 7 Jan 2024 14:13:14 +0000
Subject: [PATCH 623/852] Update snapshots and replace with explicit tests

---
 workflows/sra/main.nf                         |   9 +-
 workflows/sra/tests/main.nf.test.snap         | 328 +++++++++++++++++-
 .../sra_custom_ena_metadata_fields.nf.test    |  28 +-
 ...ra_custom_ena_metadata_fields.nf.test.snap | 120 ++++++-
 .../tests/sra_force_sratools_download.nf.test |  28 +-
 .../sra_force_sratools_download.nf.test.snap  | 328 +++++++++++++++++-
 .../sra_nf_core_pipeline_atacseq.nf.test      |  28 +-
 .../sra_nf_core_pipeline_atacseq.nf.test.snap | 328 +++++++++++++++++-
 .../tests/sra_nf_core_pipeline_rnaseq.nf.test |  28 +-
 .../sra_nf_core_pipeline_rnaseq.nf.test.snap  | 328 +++++++++++++++++-
 .../sra_nf_core_pipeline_taxprofiler.nf.test  |  28 +-
 ..._nf_core_pipeline_taxprofiler.nf.test.snap | 328 +++++++++++++++++-
 .../sra_nf_core_pipeline_viralrecon.nf.test   |  28 +-
 ...a_nf_core_pipeline_viralrecon.nf.test.snap | 328 +++++++++++++++++-
 .../sra/tests/sra_skip_fastq_download.nf.test |  28 +-
 .../sra_skip_fastq_download.nf.test.snap      | 328 +++++++++++++++++-
 16 files changed, 2517 insertions(+), 104 deletions(-)

diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index d6fc8ce4..3d487431 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -61,7 +61,6 @@ workflow SRA {
         .unique()
         .set { ch_sra_metadata }
 
-    ch_fastq_files = Channel.empty()
     if (!params.skip_fastq_download) {
 
         ch_sra_metadata
@@ -93,8 +92,10 @@ workflow SRA {
         ch_versions = ch_versions.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.versions.first())
 
         // Isolate FASTQ channel which will be added to emit block
-        ch_fastq_files
-            .mix(SRA_FASTQ_FTP.out.fastq, FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads)
+        SRA_FASTQ_FTP
+            .out
+            .fastq
+            .mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads)
             .map {
                 meta, fastq ->
                     def reads = fastq instanceof List ? fastq.flatten() : [ fastq ]
@@ -150,10 +151,10 @@ workflow SRA {
     }
 
     emit:
-    fastq           = ch_fastq_files
     samplesheet     = ch_samplesheet
     mappings        = ch_mappings
     sample_mappings = ch_sample_mappings_yml
+    sra_metadata    = ch_sra_metadata
     versions        = ch_versions.unique()
 }
 
diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
index ffdf20cc..f525d55d 100644
--- a/workflows/sra/tests/main.nf.test.snap
+++ b/workflows/sra/tests/main.nf.test.snap
@@ -3,29 +3,181 @@
         "content": [
             {
                 "0": [
-                    
-                ],
-                "1": [
                     "samplesheet.csv:md5,d252b222b8ef94670117780d43498b86"
                 ],
-                "2": [
+                "1": [
                     "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
-                "3": [
+                "2": [
                     [
                         "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
+                "3": [
+                    {
+                        "base_count": "35658",
+                        "experiment_accession": "ERX1234253",
+                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_bytes": "18077",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "id": "ERX1234253_ERR1160846",
+                        "instrument_model": "Illumina HiSeq 2500",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "10317.BLANK.93.3E.r22",
+                        "library_selection": "PCR",
+                        "library_source": "METAGENOMIC",
+                        "library_strategy": "AMPLICON",
+                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "md5_2": "",
+                        "read_count": "283",
+                        "run_accession": "ERR1160846",
+                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                        "sample_accession": "SAMEA3687214",
+                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                        "sample_description": "American Gut control",
+                        "sample_title": "10317.BLANK.93.3E.r22",
+                        "scientific_name": "metagenome",
+                        "secondary_sample_accession": "ERS994363",
+                        "secondary_study_accession": "ERP012803",
+                        "single_end": true,
+                        "study_accession": "PRJEB11419",
+                        "study_alias": "qiita_sid_10317",
+                        "study_title": "American Gut Project",
+                        "submission_accession": "ERA541392",
+                        "tax_id": "256318"
+                    },
+                    {
+                        "base_count": "431758",
+                        "experiment_accession": "SRX9315476",
+                        "experiment_alias": "F11-N1-05",
+                        "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381",
+                        "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb",
+                        "fastq_aspera": "",
+                        "fastq_bytes": "",
+                        "fastq_ftp": "",
+                        "fastq_galaxy": "",
+                        "fastq_md5": "",
+                        "id": "SRX9315476_SRR12848126",
+                        "instrument_model": "Illumina HiSeq 3000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "PAIRED",
+                        "library_name": "F11-N1-05",
+                        "library_selection": "RANDOM PCR",
+                        "library_source": "GENOMIC",
+                        "library_strategy": "Synthetic-Long-Read",
+                        "md5_1": "",
+                        "md5_2": "",
+                        "read_count": "2954",
+                        "run_accession": "SRR12848126",
+                        "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam",
+                        "sample_accession": "SAMN16455283",
+                        "sample_alias": "F11-N1-05",
+                        "sample_description": "F11-N1-05",
+                        "sample_title": "Longshanks_F11-N1-05",
+                        "scientific_name": "Mus musculus domesticus",
+                        "secondary_sample_accession": "SRS7540262",
+                        "secondary_study_accession": "SRP287769",
+                        "single_end": false,
+                        "study_accession": "PRJNA670070",
+                        "study_alias": "PRJNA670070",
+                        "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "submission_accession": "SRA1145417",
+                        "tax_id": "10092"
+                    },
+                    {
+                        "base_count": "573417800",
+                        "experiment_accession": "SRX17709227",
+                        "experiment_alias": "GSM6601460_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_bytes": "447377777",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
+                        "id": "SRX17709227_SRR21711856",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601460",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "7cd1402155befc87be338132d1f31f64",
+                        "md5_2": "",
+                        "read_count": "11468356",
+                        "run_accession": "SRR21711856",
+                        "run_alias": "GSM6601460_r1",
+                        "sample_accession": "SAMN31021823",
+                        "sample_alias": "GSM6601460",
+                        "sample_description": "sham-treated worms in day 5",
+                        "sample_title": "sham-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239723",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    },
+                    {
+                        "base_count": "677912850",
+                        "experiment_accession": "SRX17709228",
+                        "experiment_alias": "GSM6601461_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_bytes": "529798447",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "id": "SRX17709228_SRR21711855",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601461",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "md5_2": "",
+                        "read_count": "13558257",
+                        "run_accession": "SRR21711855",
+                        "run_alias": "GSM6601461_r1",
+                        "sample_accession": "SAMN31021822",
+                        "sample_alias": "GSM6601461",
+                        "sample_description": "PM2.5-treated worms in day 5",
+                        "sample_title": "PM2.5-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239724",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    }
+                ],
                 "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
-                ],
-                "fastq": [
-                    
                 ],
                 "mappings": [
                     "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
@@ -39,6 +191,164 @@
                 "samplesheet": [
                     "samplesheet.csv:md5,d252b222b8ef94670117780d43498b86"
                 ],
+                "sra_metadata": [
+                    {
+                        "base_count": "35658",
+                        "experiment_accession": "ERX1234253",
+                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_bytes": "18077",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "id": "ERX1234253_ERR1160846",
+                        "instrument_model": "Illumina HiSeq 2500",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "10317.BLANK.93.3E.r22",
+                        "library_selection": "PCR",
+                        "library_source": "METAGENOMIC",
+                        "library_strategy": "AMPLICON",
+                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "md5_2": "",
+                        "read_count": "283",
+                        "run_accession": "ERR1160846",
+                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                        "sample_accession": "SAMEA3687214",
+                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                        "sample_description": "American Gut control",
+                        "sample_title": "10317.BLANK.93.3E.r22",
+                        "scientific_name": "metagenome",
+                        "secondary_sample_accession": "ERS994363",
+                        "secondary_study_accession": "ERP012803",
+                        "single_end": true,
+                        "study_accession": "PRJEB11419",
+                        "study_alias": "qiita_sid_10317",
+                        "study_title": "American Gut Project",
+                        "submission_accession": "ERA541392",
+                        "tax_id": "256318"
+                    },
+                    {
+                        "base_count": "431758",
+                        "experiment_accession": "SRX9315476",
+                        "experiment_alias": "F11-N1-05",
+                        "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381",
+                        "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb",
+                        "fastq_aspera": "",
+                        "fastq_bytes": "",
+                        "fastq_ftp": "",
+                        "fastq_galaxy": "",
+                        "fastq_md5": "",
+                        "id": "SRX9315476_SRR12848126",
+                        "instrument_model": "Illumina HiSeq 3000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "PAIRED",
+                        "library_name": "F11-N1-05",
+                        "library_selection": "RANDOM PCR",
+                        "library_source": "GENOMIC",
+                        "library_strategy": "Synthetic-Long-Read",
+                        "md5_1": "",
+                        "md5_2": "",
+                        "read_count": "2954",
+                        "run_accession": "SRR12848126",
+                        "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam",
+                        "sample_accession": "SAMN16455283",
+                        "sample_alias": "F11-N1-05",
+                        "sample_description": "F11-N1-05",
+                        "sample_title": "Longshanks_F11-N1-05",
+                        "scientific_name": "Mus musculus domesticus",
+                        "secondary_sample_accession": "SRS7540262",
+                        "secondary_study_accession": "SRP287769",
+                        "single_end": false,
+                        "study_accession": "PRJNA670070",
+                        "study_alias": "PRJNA670070",
+                        "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "submission_accession": "SRA1145417",
+                        "tax_id": "10092"
+                    },
+                    {
+                        "base_count": "573417800",
+                        "experiment_accession": "SRX17709227",
+                        "experiment_alias": "GSM6601460_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_bytes": "447377777",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
+                        "id": "SRX17709227_SRR21711856",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601460",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "7cd1402155befc87be338132d1f31f64",
+                        "md5_2": "",
+                        "read_count": "11468356",
+                        "run_accession": "SRR21711856",
+                        "run_alias": "GSM6601460_r1",
+                        "sample_accession": "SAMN31021823",
+                        "sample_alias": "GSM6601460",
+                        "sample_description": "sham-treated worms in day 5",
+                        "sample_title": "sham-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239723",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    },
+                    {
+                        "base_count": "677912850",
+                        "experiment_accession": "SRX17709228",
+                        "experiment_alias": "GSM6601461_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_bytes": "529798447",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "id": "SRX17709228_SRR21711855",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601461",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "md5_2": "",
+                        "read_count": "13558257",
+                        "run_accession": "SRR21711855",
+                        "run_alias": "GSM6601461_r1",
+                        "sample_accession": "SAMN31021822",
+                        "sample_alias": "GSM6601461",
+                        "sample_description": "PM2.5-treated worms in day 5",
+                        "sample_title": "PM2.5-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239724",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    }
+                ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
@@ -48,6 +358,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-05T17:31:06.996066"
+        "timestamp": "2024-01-07T13:27:35.094044"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index d4dd4141..356128c6 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -25,10 +25,30 @@ nextflow_workflow {
         }
 
         then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(workflow.out).match() }
-            )
+            assert workflow.success
+
+            with(workflow.out.samplesheet) {
+                assert path(get(0)).readLines().size() == 5
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+            }
+
+            with(workflow.out.mappings) {
+                assert path(get(0)).readLines().size() == 5
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+            }
+
+            with(workflow.out.sample_mappings) {
+                assert path(get(0)[0]).md5 == "3bc981f0de28023083cdf13691d249d5"
+            }
+
+            with(workflow.out.sra_metadata) {
+                assert get(0).get('experiment_accession') == 'ERX1234253'
+                assert get(1).get('experiment_accession') == 'SRX17709227'
+                assert get(2).get('experiment_accession') == 'SRX17709228'
+                assert get(3).get('experiment_accession') == 'SRX9315476'
+            }
         }
     }
 }
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
index ad611ee2..f182f555 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
@@ -3,29 +3,77 @@
         "content": [
             {
                 "0": [
-                    
-                ],
-                "1": [
                     "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
-                "2": [
+                "1": [
                     "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
-                "3": [
+                "2": [
                     [
                         "multiqc_config.yml:md5,3bc981f0de28023083cdf13691d249d5",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
+                "3": [
+                    {
+                        "experiment_accession": "ERX1234253",
+                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                        "fastq_2": "",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "id": "ERX1234253_ERR1160846",
+                        "library_layout": "SINGLE",
+                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "md5_2": "",
+                        "run_accession": "ERR1160846",
+                        "single_end": true
+                    },
+                    {
+                        "experiment_accession": "SRX17709227",
+                        "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2",
+                        "fastq_2": "",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
+                        "id": "SRX17709227_SRR21711856",
+                        "library_layout": "SINGLE",
+                        "md5_1": "7cd1402155befc87be338132d1f31f64",
+                        "md5_2": "",
+                        "run_accession": "SRR21711856",
+                        "single_end": true
+                    },
+                    {
+                        "experiment_accession": "SRX17709228",
+                        "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a",
+                        "fastq_2": "",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "id": "SRX17709228_SRR21711855",
+                        "library_layout": "SINGLE",
+                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "md5_2": "",
+                        "run_accession": "SRR21711855",
+                        "single_end": true
+                    },
+                    {
+                        "experiment_accession": "SRX9315476",
+                        "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381",
+                        "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb",
+                        "fastq_ftp": "",
+                        "fastq_md5": "",
+                        "id": "SRX9315476_SRR12848126",
+                        "library_layout": "PAIRED",
+                        "md5_1": "",
+                        "md5_2": "",
+                        "run_accession": "SRR12848126",
+                        "single_end": false
+                    }
+                ],
                 "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
-                ],
-                "fastq": [
-                    
                 ],
                 "mappings": [
                     "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
@@ -39,6 +87,60 @@
                 "samplesheet": [
                     "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
+                "sra_metadata": [
+                    {
+                        "experiment_accession": "ERX1234253",
+                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                        "fastq_2": "",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "id": "ERX1234253_ERR1160846",
+                        "library_layout": "SINGLE",
+                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "md5_2": "",
+                        "run_accession": "ERR1160846",
+                        "single_end": true
+                    },
+                    {
+                        "experiment_accession": "SRX17709227",
+                        "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2",
+                        "fastq_2": "",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
+                        "id": "SRX17709227_SRR21711856",
+                        "library_layout": "SINGLE",
+                        "md5_1": "7cd1402155befc87be338132d1f31f64",
+                        "md5_2": "",
+                        "run_accession": "SRR21711856",
+                        "single_end": true
+                    },
+                    {
+                        "experiment_accession": "SRX17709228",
+                        "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a",
+                        "fastq_2": "",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "id": "SRX17709228_SRR21711855",
+                        "library_layout": "SINGLE",
+                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "md5_2": "",
+                        "run_accession": "SRR21711855",
+                        "single_end": true
+                    },
+                    {
+                        "experiment_accession": "SRX9315476",
+                        "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381",
+                        "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb",
+                        "fastq_ftp": "",
+                        "fastq_md5": "",
+                        "id": "SRX9315476_SRR12848126",
+                        "library_layout": "PAIRED",
+                        "md5_1": "",
+                        "md5_2": "",
+                        "run_accession": "SRR12848126",
+                        "single_end": false
+                    }
+                ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
@@ -48,6 +150,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-06T20:36:14.475733"
+        "timestamp": "2024-01-07T13:22:50.246795"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index 62adb9af..3180d720 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -23,10 +23,30 @@ nextflow_workflow {
         }
 
         then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(workflow.out).match() }
-            )
+            assert workflow.success
+
+            with(workflow.out.samplesheet) {
+                assert path(get(0)).readLines().size() == 5
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+            }
+
+            with(workflow.out.mappings) {
+                assert path(get(0)).readLines().size() == 5
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+            }
+
+            with(workflow.out.sample_mappings) {
+                assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c"
+            }
+
+            with(workflow.out.sra_metadata) {
+                assert get(0).get('experiment_accession') == 'ERX1234253'
+                assert get(1).get('experiment_accession') == 'SRX17709227'
+                assert get(2).get('experiment_accession') == 'SRX17709228'
+                assert get(3).get('experiment_accession') == 'SRX9315476'
+            }
         }
     }
 }
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
index 07cf1871..2dcf052c 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
@@ -3,28 +3,180 @@
         "content": [
             {
                 "0": [
-                    
-                ],
-                "1": [
                     "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
-                "2": [
+                "1": [
                     "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
-                "3": [
+                "2": [
                     [
                         "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
+                "3": [
+                    {
+                        "base_count": "35658",
+                        "experiment_accession": "ERX1234253",
+                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_bytes": "18077",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "id": "ERX1234253_ERR1160846",
+                        "instrument_model": "Illumina HiSeq 2500",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "10317.BLANK.93.3E.r22",
+                        "library_selection": "PCR",
+                        "library_source": "METAGENOMIC",
+                        "library_strategy": "AMPLICON",
+                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "md5_2": "",
+                        "read_count": "283",
+                        "run_accession": "ERR1160846",
+                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                        "sample_accession": "SAMEA3687214",
+                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                        "sample_description": "American Gut control",
+                        "sample_title": "10317.BLANK.93.3E.r22",
+                        "scientific_name": "metagenome",
+                        "secondary_sample_accession": "ERS994363",
+                        "secondary_study_accession": "ERP012803",
+                        "single_end": true,
+                        "study_accession": "PRJEB11419",
+                        "study_alias": "qiita_sid_10317",
+                        "study_title": "American Gut Project",
+                        "submission_accession": "ERA541392",
+                        "tax_id": "256318"
+                    },
+                    {
+                        "base_count": "431758",
+                        "experiment_accession": "SRX9315476",
+                        "experiment_alias": "F11-N1-05",
+                        "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381",
+                        "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb",
+                        "fastq_aspera": "",
+                        "fastq_bytes": "",
+                        "fastq_ftp": "",
+                        "fastq_galaxy": "",
+                        "fastq_md5": "",
+                        "id": "SRX9315476_SRR12848126",
+                        "instrument_model": "Illumina HiSeq 3000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "PAIRED",
+                        "library_name": "F11-N1-05",
+                        "library_selection": "RANDOM PCR",
+                        "library_source": "GENOMIC",
+                        "library_strategy": "Synthetic-Long-Read",
+                        "md5_1": "",
+                        "md5_2": "",
+                        "read_count": "2954",
+                        "run_accession": "SRR12848126",
+                        "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam",
+                        "sample_accession": "SAMN16455283",
+                        "sample_alias": "F11-N1-05",
+                        "sample_description": "F11-N1-05",
+                        "sample_title": "Longshanks_F11-N1-05",
+                        "scientific_name": "Mus musculus domesticus",
+                        "secondary_sample_accession": "SRS7540262",
+                        "secondary_study_accession": "SRP287769",
+                        "single_end": false,
+                        "study_accession": "PRJNA670070",
+                        "study_alias": "PRJNA670070",
+                        "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "submission_accession": "SRA1145417",
+                        "tax_id": "10092"
+                    },
+                    {
+                        "base_count": "573417800",
+                        "experiment_accession": "SRX17709227",
+                        "experiment_alias": "GSM6601460_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "results/fastq/SRX17709227_SRR21711856_1.fastq.gz",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_bytes": "447377777",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
+                        "id": "SRX17709227_SRR21711856",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601460",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "7cd1402155befc87be338132d1f31f64",
+                        "md5_2": "",
+                        "read_count": "11468356",
+                        "run_accession": "SRR21711856",
+                        "run_alias": "GSM6601460_r1",
+                        "sample_accession": "SAMN31021823",
+                        "sample_alias": "GSM6601460",
+                        "sample_description": "sham-treated worms in day 5",
+                        "sample_title": "sham-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239723",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    },
+                    {
+                        "base_count": "677912850",
+                        "experiment_accession": "SRX17709228",
+                        "experiment_alias": "GSM6601461_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "results/fastq/SRX17709228_SRR21711855_1.fastq.gz",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_bytes": "529798447",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "id": "SRX17709228_SRR21711855",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601461",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "md5_2": "",
+                        "read_count": "13558257",
+                        "run_accession": "SRR21711855",
+                        "run_alias": "GSM6601461_r1",
+                        "sample_accession": "SAMN31021822",
+                        "sample_alias": "GSM6601461",
+                        "sample_description": "PM2.5-treated worms in day 5",
+                        "sample_title": "PM2.5-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239724",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    }
+                ],
                 "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
-                ],
-                "fastq": [
-                    
                 ],
                 "mappings": [
                     "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
@@ -38,6 +190,164 @@
                 "samplesheet": [
                     "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
+                "sra_metadata": [
+                    {
+                        "base_count": "35658",
+                        "experiment_accession": "ERX1234253",
+                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_bytes": "18077",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "id": "ERX1234253_ERR1160846",
+                        "instrument_model": "Illumina HiSeq 2500",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "10317.BLANK.93.3E.r22",
+                        "library_selection": "PCR",
+                        "library_source": "METAGENOMIC",
+                        "library_strategy": "AMPLICON",
+                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "md5_2": "",
+                        "read_count": "283",
+                        "run_accession": "ERR1160846",
+                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                        "sample_accession": "SAMEA3687214",
+                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                        "sample_description": "American Gut control",
+                        "sample_title": "10317.BLANK.93.3E.r22",
+                        "scientific_name": "metagenome",
+                        "secondary_sample_accession": "ERS994363",
+                        "secondary_study_accession": "ERP012803",
+                        "single_end": true,
+                        "study_accession": "PRJEB11419",
+                        "study_alias": "qiita_sid_10317",
+                        "study_title": "American Gut Project",
+                        "submission_accession": "ERA541392",
+                        "tax_id": "256318"
+                    },
+                    {
+                        "base_count": "431758",
+                        "experiment_accession": "SRX9315476",
+                        "experiment_alias": "F11-N1-05",
+                        "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381",
+                        "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb",
+                        "fastq_aspera": "",
+                        "fastq_bytes": "",
+                        "fastq_ftp": "",
+                        "fastq_galaxy": "",
+                        "fastq_md5": "",
+                        "id": "SRX9315476_SRR12848126",
+                        "instrument_model": "Illumina HiSeq 3000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "PAIRED",
+                        "library_name": "F11-N1-05",
+                        "library_selection": "RANDOM PCR",
+                        "library_source": "GENOMIC",
+                        "library_strategy": "Synthetic-Long-Read",
+                        "md5_1": "",
+                        "md5_2": "",
+                        "read_count": "2954",
+                        "run_accession": "SRR12848126",
+                        "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam",
+                        "sample_accession": "SAMN16455283",
+                        "sample_alias": "F11-N1-05",
+                        "sample_description": "F11-N1-05",
+                        "sample_title": "Longshanks_F11-N1-05",
+                        "scientific_name": "Mus musculus domesticus",
+                        "secondary_sample_accession": "SRS7540262",
+                        "secondary_study_accession": "SRP287769",
+                        "single_end": false,
+                        "study_accession": "PRJNA670070",
+                        "study_alias": "PRJNA670070",
+                        "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "submission_accession": "SRA1145417",
+                        "tax_id": "10092"
+                    },
+                    {
+                        "base_count": "573417800",
+                        "experiment_accession": "SRX17709227",
+                        "experiment_alias": "GSM6601460_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "results/fastq/SRX17709227_SRR21711856_1.fastq.gz",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_bytes": "447377777",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
+                        "id": "SRX17709227_SRR21711856",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601460",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "7cd1402155befc87be338132d1f31f64",
+                        "md5_2": "",
+                        "read_count": "11468356",
+                        "run_accession": "SRR21711856",
+                        "run_alias": "GSM6601460_r1",
+                        "sample_accession": "SAMN31021823",
+                        "sample_alias": "GSM6601460",
+                        "sample_description": "sham-treated worms in day 5",
+                        "sample_title": "sham-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239723",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    },
+                    {
+                        "base_count": "677912850",
+                        "experiment_accession": "SRX17709228",
+                        "experiment_alias": "GSM6601461_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "results/fastq/SRX17709228_SRR21711855_1.fastq.gz",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_bytes": "529798447",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "id": "SRX17709228_SRR21711855",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601461",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "md5_2": "",
+                        "read_count": "13558257",
+                        "run_accession": "SRR21711855",
+                        "run_alias": "GSM6601461_r1",
+                        "sample_accession": "SAMN31021822",
+                        "sample_alias": "GSM6601461",
+                        "sample_description": "PM2.5-treated worms in day 5",
+                        "sample_title": "PM2.5-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239724",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    }
+                ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
@@ -46,6 +356,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-06T20:32:48.107479"
+        "timestamp": "2024-01-07T13:36:22.094035"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index 00f545b5..1bcbbf72 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -23,10 +23,30 @@ nextflow_workflow {
         }
 
         then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(workflow.out).match() }
-            )
+            assert workflow.success
+
+            with(workflow.out.samplesheet) {
+                assert path(get(0)).readLines().size() == 5
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+            }
+
+            with(workflow.out.mappings) {
+                assert path(get(0)).readLines().size() == 5
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+            }
+
+            with(workflow.out.sample_mappings) {
+                assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c"
+            }
+
+            with(workflow.out.sra_metadata) {
+                assert get(0).get('experiment_accession') == 'ERX1234253'
+                assert get(1).get('experiment_accession') == 'SRX17709227'
+                assert get(2).get('experiment_accession') == 'SRX17709228'
+                assert get(3).get('experiment_accession') == 'SRX9315476'
+            }
         }
     }
 }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
index 3c616c12..5dd675d3 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
@@ -3,29 +3,181 @@
         "content": [
             {
                 "0": [
-                    
-                ],
-                "1": [
                     "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
-                "2": [
+                "1": [
                     "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
-                "3": [
+                "2": [
                     [
                         "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
+                "3": [
+                    {
+                        "base_count": "35658",
+                        "experiment_accession": "ERX1234253",
+                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_bytes": "18077",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "id": "ERX1234253_ERR1160846",
+                        "instrument_model": "Illumina HiSeq 2500",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "10317.BLANK.93.3E.r22",
+                        "library_selection": "PCR",
+                        "library_source": "METAGENOMIC",
+                        "library_strategy": "AMPLICON",
+                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "md5_2": "",
+                        "read_count": "283",
+                        "run_accession": "ERR1160846",
+                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                        "sample_accession": "SAMEA3687214",
+                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                        "sample_description": "American Gut control",
+                        "sample_title": "10317.BLANK.93.3E.r22",
+                        "scientific_name": "metagenome",
+                        "secondary_sample_accession": "ERS994363",
+                        "secondary_study_accession": "ERP012803",
+                        "single_end": true,
+                        "study_accession": "PRJEB11419",
+                        "study_alias": "qiita_sid_10317",
+                        "study_title": "American Gut Project",
+                        "submission_accession": "ERA541392",
+                        "tax_id": "256318"
+                    },
+                    {
+                        "base_count": "431758",
+                        "experiment_accession": "SRX9315476",
+                        "experiment_alias": "F11-N1-05",
+                        "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381",
+                        "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb",
+                        "fastq_aspera": "",
+                        "fastq_bytes": "",
+                        "fastq_ftp": "",
+                        "fastq_galaxy": "",
+                        "fastq_md5": "",
+                        "id": "SRX9315476_SRR12848126",
+                        "instrument_model": "Illumina HiSeq 3000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "PAIRED",
+                        "library_name": "F11-N1-05",
+                        "library_selection": "RANDOM PCR",
+                        "library_source": "GENOMIC",
+                        "library_strategy": "Synthetic-Long-Read",
+                        "md5_1": "",
+                        "md5_2": "",
+                        "read_count": "2954",
+                        "run_accession": "SRR12848126",
+                        "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam",
+                        "sample_accession": "SAMN16455283",
+                        "sample_alias": "F11-N1-05",
+                        "sample_description": "F11-N1-05",
+                        "sample_title": "Longshanks_F11-N1-05",
+                        "scientific_name": "Mus musculus domesticus",
+                        "secondary_sample_accession": "SRS7540262",
+                        "secondary_study_accession": "SRP287769",
+                        "single_end": false,
+                        "study_accession": "PRJNA670070",
+                        "study_alias": "PRJNA670070",
+                        "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "submission_accession": "SRA1145417",
+                        "tax_id": "10092"
+                    },
+                    {
+                        "base_count": "573417800",
+                        "experiment_accession": "SRX17709227",
+                        "experiment_alias": "GSM6601460_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_bytes": "447377777",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
+                        "id": "SRX17709227_SRR21711856",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601460",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "7cd1402155befc87be338132d1f31f64",
+                        "md5_2": "",
+                        "read_count": "11468356",
+                        "run_accession": "SRR21711856",
+                        "run_alias": "GSM6601460_r1",
+                        "sample_accession": "SAMN31021823",
+                        "sample_alias": "GSM6601460",
+                        "sample_description": "sham-treated worms in day 5",
+                        "sample_title": "sham-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239723",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    },
+                    {
+                        "base_count": "677912850",
+                        "experiment_accession": "SRX17709228",
+                        "experiment_alias": "GSM6601461_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_bytes": "529798447",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "id": "SRX17709228_SRR21711855",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601461",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "md5_2": "",
+                        "read_count": "13558257",
+                        "run_accession": "SRR21711855",
+                        "run_alias": "GSM6601461_r1",
+                        "sample_accession": "SAMN31021822",
+                        "sample_alias": "GSM6601461",
+                        "sample_description": "PM2.5-treated worms in day 5",
+                        "sample_title": "PM2.5-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239724",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    }
+                ],
                 "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
-                ],
-                "fastq": [
-                    
                 ],
                 "mappings": [
                     "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
@@ -39,6 +191,164 @@
                 "samplesheet": [
                     "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
+                "sra_metadata": [
+                    {
+                        "base_count": "35658",
+                        "experiment_accession": "ERX1234253",
+                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_bytes": "18077",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "id": "ERX1234253_ERR1160846",
+                        "instrument_model": "Illumina HiSeq 2500",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "10317.BLANK.93.3E.r22",
+                        "library_selection": "PCR",
+                        "library_source": "METAGENOMIC",
+                        "library_strategy": "AMPLICON",
+                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "md5_2": "",
+                        "read_count": "283",
+                        "run_accession": "ERR1160846",
+                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                        "sample_accession": "SAMEA3687214",
+                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                        "sample_description": "American Gut control",
+                        "sample_title": "10317.BLANK.93.3E.r22",
+                        "scientific_name": "metagenome",
+                        "secondary_sample_accession": "ERS994363",
+                        "secondary_study_accession": "ERP012803",
+                        "single_end": true,
+                        "study_accession": "PRJEB11419",
+                        "study_alias": "qiita_sid_10317",
+                        "study_title": "American Gut Project",
+                        "submission_accession": "ERA541392",
+                        "tax_id": "256318"
+                    },
+                    {
+                        "base_count": "431758",
+                        "experiment_accession": "SRX9315476",
+                        "experiment_alias": "F11-N1-05",
+                        "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381",
+                        "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb",
+                        "fastq_aspera": "",
+                        "fastq_bytes": "",
+                        "fastq_ftp": "",
+                        "fastq_galaxy": "",
+                        "fastq_md5": "",
+                        "id": "SRX9315476_SRR12848126",
+                        "instrument_model": "Illumina HiSeq 3000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "PAIRED",
+                        "library_name": "F11-N1-05",
+                        "library_selection": "RANDOM PCR",
+                        "library_source": "GENOMIC",
+                        "library_strategy": "Synthetic-Long-Read",
+                        "md5_1": "",
+                        "md5_2": "",
+                        "read_count": "2954",
+                        "run_accession": "SRR12848126",
+                        "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam",
+                        "sample_accession": "SAMN16455283",
+                        "sample_alias": "F11-N1-05",
+                        "sample_description": "F11-N1-05",
+                        "sample_title": "Longshanks_F11-N1-05",
+                        "scientific_name": "Mus musculus domesticus",
+                        "secondary_sample_accession": "SRS7540262",
+                        "secondary_study_accession": "SRP287769",
+                        "single_end": false,
+                        "study_accession": "PRJNA670070",
+                        "study_alias": "PRJNA670070",
+                        "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "submission_accession": "SRA1145417",
+                        "tax_id": "10092"
+                    },
+                    {
+                        "base_count": "573417800",
+                        "experiment_accession": "SRX17709227",
+                        "experiment_alias": "GSM6601460_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_bytes": "447377777",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
+                        "id": "SRX17709227_SRR21711856",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601460",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "7cd1402155befc87be338132d1f31f64",
+                        "md5_2": "",
+                        "read_count": "11468356",
+                        "run_accession": "SRR21711856",
+                        "run_alias": "GSM6601460_r1",
+                        "sample_accession": "SAMN31021823",
+                        "sample_alias": "GSM6601460",
+                        "sample_description": "sham-treated worms in day 5",
+                        "sample_title": "sham-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239723",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    },
+                    {
+                        "base_count": "677912850",
+                        "experiment_accession": "SRX17709228",
+                        "experiment_alias": "GSM6601461_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_bytes": "529798447",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "id": "SRX17709228_SRR21711855",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601461",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "md5_2": "",
+                        "read_count": "13558257",
+                        "run_accession": "SRR21711855",
+                        "run_alias": "GSM6601461_r1",
+                        "sample_accession": "SAMN31021822",
+                        "sample_alias": "GSM6601461",
+                        "sample_description": "PM2.5-treated worms in day 5",
+                        "sample_title": "PM2.5-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239724",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    }
+                ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
@@ -48,6 +358,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-06T20:45:29.760739"
+        "timestamp": "2024-01-07T13:38:47.906835"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index 62bd6380..c8be765b 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -23,10 +23,30 @@ nextflow_workflow {
         }
 
         then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(workflow.out).match() }
-            )
+            assert workflow.success
+
+            with(workflow.out.samplesheet) {
+                assert path(get(0)).readLines().size() == 5
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+            }
+
+            with(workflow.out.mappings) {
+                assert path(get(0)).readLines().size() == 5
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+            }
+
+            with(workflow.out.sample_mappings) {
+                assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c"
+            }
+
+            with(workflow.out.sra_metadata) {
+                assert get(0).get('experiment_accession') == 'ERX1234253'
+                assert get(1).get('experiment_accession') == 'SRX17709227'
+                assert get(2).get('experiment_accession') == 'SRX17709228'
+                assert get(3).get('experiment_accession') == 'SRX9315476'
+            }
         }
     }
 }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
index 2ad3280d..b831fe54 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
@@ -3,29 +3,181 @@
         "content": [
             {
                 "0": [
-                    
-                ],
-                "1": [
                     "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
-                "2": [
+                "1": [
                     "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
-                "3": [
+                "2": [
                     [
                         "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
+                "3": [
+                    {
+                        "base_count": "35658",
+                        "experiment_accession": "ERX1234253",
+                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_bytes": "18077",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "id": "ERX1234253_ERR1160846",
+                        "instrument_model": "Illumina HiSeq 2500",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "10317.BLANK.93.3E.r22",
+                        "library_selection": "PCR",
+                        "library_source": "METAGENOMIC",
+                        "library_strategy": "AMPLICON",
+                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "md5_2": "",
+                        "read_count": "283",
+                        "run_accession": "ERR1160846",
+                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                        "sample_accession": "SAMEA3687214",
+                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                        "sample_description": "American Gut control",
+                        "sample_title": "10317.BLANK.93.3E.r22",
+                        "scientific_name": "metagenome",
+                        "secondary_sample_accession": "ERS994363",
+                        "secondary_study_accession": "ERP012803",
+                        "single_end": true,
+                        "study_accession": "PRJEB11419",
+                        "study_alias": "qiita_sid_10317",
+                        "study_title": "American Gut Project",
+                        "submission_accession": "ERA541392",
+                        "tax_id": "256318"
+                    },
+                    {
+                        "base_count": "431758",
+                        "experiment_accession": "SRX9315476",
+                        "experiment_alias": "F11-N1-05",
+                        "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381",
+                        "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb",
+                        "fastq_aspera": "",
+                        "fastq_bytes": "",
+                        "fastq_ftp": "",
+                        "fastq_galaxy": "",
+                        "fastq_md5": "",
+                        "id": "SRX9315476_SRR12848126",
+                        "instrument_model": "Illumina HiSeq 3000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "PAIRED",
+                        "library_name": "F11-N1-05",
+                        "library_selection": "RANDOM PCR",
+                        "library_source": "GENOMIC",
+                        "library_strategy": "Synthetic-Long-Read",
+                        "md5_1": "",
+                        "md5_2": "",
+                        "read_count": "2954",
+                        "run_accession": "SRR12848126",
+                        "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam",
+                        "sample_accession": "SAMN16455283",
+                        "sample_alias": "F11-N1-05",
+                        "sample_description": "F11-N1-05",
+                        "sample_title": "Longshanks_F11-N1-05",
+                        "scientific_name": "Mus musculus domesticus",
+                        "secondary_sample_accession": "SRS7540262",
+                        "secondary_study_accession": "SRP287769",
+                        "single_end": false,
+                        "study_accession": "PRJNA670070",
+                        "study_alias": "PRJNA670070",
+                        "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "submission_accession": "SRA1145417",
+                        "tax_id": "10092"
+                    },
+                    {
+                        "base_count": "573417800",
+                        "experiment_accession": "SRX17709227",
+                        "experiment_alias": "GSM6601460_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_bytes": "447377777",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
+                        "id": "SRX17709227_SRR21711856",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601460",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "7cd1402155befc87be338132d1f31f64",
+                        "md5_2": "",
+                        "read_count": "11468356",
+                        "run_accession": "SRR21711856",
+                        "run_alias": "GSM6601460_r1",
+                        "sample_accession": "SAMN31021823",
+                        "sample_alias": "GSM6601460",
+                        "sample_description": "sham-treated worms in day 5",
+                        "sample_title": "sham-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239723",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    },
+                    {
+                        "base_count": "677912850",
+                        "experiment_accession": "SRX17709228",
+                        "experiment_alias": "GSM6601461_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_bytes": "529798447",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "id": "SRX17709228_SRR21711855",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601461",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "md5_2": "",
+                        "read_count": "13558257",
+                        "run_accession": "SRR21711855",
+                        "run_alias": "GSM6601461_r1",
+                        "sample_accession": "SAMN31021822",
+                        "sample_alias": "GSM6601461",
+                        "sample_description": "PM2.5-treated worms in day 5",
+                        "sample_title": "PM2.5-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239724",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    }
+                ],
                 "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
-                ],
-                "fastq": [
-                    
                 ],
                 "mappings": [
                     "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
@@ -39,6 +191,164 @@
                 "samplesheet": [
                     "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
+                "sra_metadata": [
+                    {
+                        "base_count": "35658",
+                        "experiment_accession": "ERX1234253",
+                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_bytes": "18077",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "id": "ERX1234253_ERR1160846",
+                        "instrument_model": "Illumina HiSeq 2500",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "10317.BLANK.93.3E.r22",
+                        "library_selection": "PCR",
+                        "library_source": "METAGENOMIC",
+                        "library_strategy": "AMPLICON",
+                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "md5_2": "",
+                        "read_count": "283",
+                        "run_accession": "ERR1160846",
+                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                        "sample_accession": "SAMEA3687214",
+                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                        "sample_description": "American Gut control",
+                        "sample_title": "10317.BLANK.93.3E.r22",
+                        "scientific_name": "metagenome",
+                        "secondary_sample_accession": "ERS994363",
+                        "secondary_study_accession": "ERP012803",
+                        "single_end": true,
+                        "study_accession": "PRJEB11419",
+                        "study_alias": "qiita_sid_10317",
+                        "study_title": "American Gut Project",
+                        "submission_accession": "ERA541392",
+                        "tax_id": "256318"
+                    },
+                    {
+                        "base_count": "431758",
+                        "experiment_accession": "SRX9315476",
+                        "experiment_alias": "F11-N1-05",
+                        "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381",
+                        "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb",
+                        "fastq_aspera": "",
+                        "fastq_bytes": "",
+                        "fastq_ftp": "",
+                        "fastq_galaxy": "",
+                        "fastq_md5": "",
+                        "id": "SRX9315476_SRR12848126",
+                        "instrument_model": "Illumina HiSeq 3000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "PAIRED",
+                        "library_name": "F11-N1-05",
+                        "library_selection": "RANDOM PCR",
+                        "library_source": "GENOMIC",
+                        "library_strategy": "Synthetic-Long-Read",
+                        "md5_1": "",
+                        "md5_2": "",
+                        "read_count": "2954",
+                        "run_accession": "SRR12848126",
+                        "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam",
+                        "sample_accession": "SAMN16455283",
+                        "sample_alias": "F11-N1-05",
+                        "sample_description": "F11-N1-05",
+                        "sample_title": "Longshanks_F11-N1-05",
+                        "scientific_name": "Mus musculus domesticus",
+                        "secondary_sample_accession": "SRS7540262",
+                        "secondary_study_accession": "SRP287769",
+                        "single_end": false,
+                        "study_accession": "PRJNA670070",
+                        "study_alias": "PRJNA670070",
+                        "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "submission_accession": "SRA1145417",
+                        "tax_id": "10092"
+                    },
+                    {
+                        "base_count": "573417800",
+                        "experiment_accession": "SRX17709227",
+                        "experiment_alias": "GSM6601460_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_bytes": "447377777",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
+                        "id": "SRX17709227_SRR21711856",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601460",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "7cd1402155befc87be338132d1f31f64",
+                        "md5_2": "",
+                        "read_count": "11468356",
+                        "run_accession": "SRR21711856",
+                        "run_alias": "GSM6601460_r1",
+                        "sample_accession": "SAMN31021823",
+                        "sample_alias": "GSM6601460",
+                        "sample_description": "sham-treated worms in day 5",
+                        "sample_title": "sham-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239723",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    },
+                    {
+                        "base_count": "677912850",
+                        "experiment_accession": "SRX17709228",
+                        "experiment_alias": "GSM6601461_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_bytes": "529798447",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "id": "SRX17709228_SRR21711855",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601461",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "md5_2": "",
+                        "read_count": "13558257",
+                        "run_accession": "SRR21711855",
+                        "run_alias": "GSM6601461_r1",
+                        "sample_accession": "SAMN31021822",
+                        "sample_alias": "GSM6601461",
+                        "sample_description": "PM2.5-treated worms in day 5",
+                        "sample_title": "PM2.5-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239724",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    }
+                ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
@@ -48,6 +358,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-06T20:47:23.837927"
+        "timestamp": "2024-01-07T13:42:36.795022"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index c5e2865f..17ec98da 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -23,10 +23,30 @@ nextflow_workflow {
         }
 
         then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(workflow.out).match() }
-            )
+            assert workflow.success
+
+            with(workflow.out.samplesheet) {
+                assert path(get(0)).readLines().size() == 5
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+            }
+
+            with(workflow.out.mappings) {
+                assert path(get(0)).readLines().size() == 5
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+            }
+
+            with(workflow.out.sample_mappings) {
+                assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c"
+            }
+
+            with(workflow.out.sra_metadata) {
+                assert get(0).get('experiment_accession') == 'ERX1234253'
+                assert get(1).get('experiment_accession') == 'SRX17709227'
+                assert get(2).get('experiment_accession') == 'SRX17709228'
+                assert get(3).get('experiment_accession') == 'SRX9315476'
+            }
         }
     }
 }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
index 031014c4..d7463e04 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
@@ -3,29 +3,181 @@
         "content": [
             {
                 "0": [
-                    
-                ],
-                "1": [
                     "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
-                "2": [
+                "1": [
                     "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
-                "3": [
+                "2": [
                     [
                         "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
+                "3": [
+                    {
+                        "base_count": "35658",
+                        "experiment_accession": "ERX1234253",
+                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_bytes": "18077",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "id": "ERX1234253_ERR1160846",
+                        "instrument_model": "Illumina HiSeq 2500",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "10317.BLANK.93.3E.r22",
+                        "library_selection": "PCR",
+                        "library_source": "METAGENOMIC",
+                        "library_strategy": "AMPLICON",
+                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "md5_2": "",
+                        "read_count": "283",
+                        "run_accession": "ERR1160846",
+                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                        "sample_accession": "SAMEA3687214",
+                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                        "sample_description": "American Gut control",
+                        "sample_title": "10317.BLANK.93.3E.r22",
+                        "scientific_name": "metagenome",
+                        "secondary_sample_accession": "ERS994363",
+                        "secondary_study_accession": "ERP012803",
+                        "single_end": true,
+                        "study_accession": "PRJEB11419",
+                        "study_alias": "qiita_sid_10317",
+                        "study_title": "American Gut Project",
+                        "submission_accession": "ERA541392",
+                        "tax_id": "256318"
+                    },
+                    {
+                        "base_count": "431758",
+                        "experiment_accession": "SRX9315476",
+                        "experiment_alias": "F11-N1-05",
+                        "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381",
+                        "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb",
+                        "fastq_aspera": "",
+                        "fastq_bytes": "",
+                        "fastq_ftp": "",
+                        "fastq_galaxy": "",
+                        "fastq_md5": "",
+                        "id": "SRX9315476_SRR12848126",
+                        "instrument_model": "Illumina HiSeq 3000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "PAIRED",
+                        "library_name": "F11-N1-05",
+                        "library_selection": "RANDOM PCR",
+                        "library_source": "GENOMIC",
+                        "library_strategy": "Synthetic-Long-Read",
+                        "md5_1": "",
+                        "md5_2": "",
+                        "read_count": "2954",
+                        "run_accession": "SRR12848126",
+                        "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam",
+                        "sample_accession": "SAMN16455283",
+                        "sample_alias": "F11-N1-05",
+                        "sample_description": "F11-N1-05",
+                        "sample_title": "Longshanks_F11-N1-05",
+                        "scientific_name": "Mus musculus domesticus",
+                        "secondary_sample_accession": "SRS7540262",
+                        "secondary_study_accession": "SRP287769",
+                        "single_end": false,
+                        "study_accession": "PRJNA670070",
+                        "study_alias": "PRJNA670070",
+                        "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "submission_accession": "SRA1145417",
+                        "tax_id": "10092"
+                    },
+                    {
+                        "base_count": "573417800",
+                        "experiment_accession": "SRX17709227",
+                        "experiment_alias": "GSM6601460_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_bytes": "447377777",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
+                        "id": "SRX17709227_SRR21711856",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601460",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "7cd1402155befc87be338132d1f31f64",
+                        "md5_2": "",
+                        "read_count": "11468356",
+                        "run_accession": "SRR21711856",
+                        "run_alias": "GSM6601460_r1",
+                        "sample_accession": "SAMN31021823",
+                        "sample_alias": "GSM6601460",
+                        "sample_description": "sham-treated worms in day 5",
+                        "sample_title": "sham-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239723",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    },
+                    {
+                        "base_count": "677912850",
+                        "experiment_accession": "SRX17709228",
+                        "experiment_alias": "GSM6601461_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_bytes": "529798447",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "id": "SRX17709228_SRR21711855",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601461",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "md5_2": "",
+                        "read_count": "13558257",
+                        "run_accession": "SRR21711855",
+                        "run_alias": "GSM6601461_r1",
+                        "sample_accession": "SAMN31021822",
+                        "sample_alias": "GSM6601461",
+                        "sample_description": "PM2.5-treated worms in day 5",
+                        "sample_title": "PM2.5-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239724",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    }
+                ],
                 "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
-                ],
-                "fastq": [
-                    
                 ],
                 "mappings": [
                     "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
@@ -39,6 +191,164 @@
                 "samplesheet": [
                     "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
+                "sra_metadata": [
+                    {
+                        "base_count": "35658",
+                        "experiment_accession": "ERX1234253",
+                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_bytes": "18077",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "id": "ERX1234253_ERR1160846",
+                        "instrument_model": "Illumina HiSeq 2500",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "10317.BLANK.93.3E.r22",
+                        "library_selection": "PCR",
+                        "library_source": "METAGENOMIC",
+                        "library_strategy": "AMPLICON",
+                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "md5_2": "",
+                        "read_count": "283",
+                        "run_accession": "ERR1160846",
+                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                        "sample_accession": "SAMEA3687214",
+                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                        "sample_description": "American Gut control",
+                        "sample_title": "10317.BLANK.93.3E.r22",
+                        "scientific_name": "metagenome",
+                        "secondary_sample_accession": "ERS994363",
+                        "secondary_study_accession": "ERP012803",
+                        "single_end": true,
+                        "study_accession": "PRJEB11419",
+                        "study_alias": "qiita_sid_10317",
+                        "study_title": "American Gut Project",
+                        "submission_accession": "ERA541392",
+                        "tax_id": "256318"
+                    },
+                    {
+                        "base_count": "431758",
+                        "experiment_accession": "SRX9315476",
+                        "experiment_alias": "F11-N1-05",
+                        "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381",
+                        "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb",
+                        "fastq_aspera": "",
+                        "fastq_bytes": "",
+                        "fastq_ftp": "",
+                        "fastq_galaxy": "",
+                        "fastq_md5": "",
+                        "id": "SRX9315476_SRR12848126",
+                        "instrument_model": "Illumina HiSeq 3000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "PAIRED",
+                        "library_name": "F11-N1-05",
+                        "library_selection": "RANDOM PCR",
+                        "library_source": "GENOMIC",
+                        "library_strategy": "Synthetic-Long-Read",
+                        "md5_1": "",
+                        "md5_2": "",
+                        "read_count": "2954",
+                        "run_accession": "SRR12848126",
+                        "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam",
+                        "sample_accession": "SAMN16455283",
+                        "sample_alias": "F11-N1-05",
+                        "sample_description": "F11-N1-05",
+                        "sample_title": "Longshanks_F11-N1-05",
+                        "scientific_name": "Mus musculus domesticus",
+                        "secondary_sample_accession": "SRS7540262",
+                        "secondary_study_accession": "SRP287769",
+                        "single_end": false,
+                        "study_accession": "PRJNA670070",
+                        "study_alias": "PRJNA670070",
+                        "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "submission_accession": "SRA1145417",
+                        "tax_id": "10092"
+                    },
+                    {
+                        "base_count": "573417800",
+                        "experiment_accession": "SRX17709227",
+                        "experiment_alias": "GSM6601460_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_bytes": "447377777",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
+                        "id": "SRX17709227_SRR21711856",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601460",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "7cd1402155befc87be338132d1f31f64",
+                        "md5_2": "",
+                        "read_count": "11468356",
+                        "run_accession": "SRR21711856",
+                        "run_alias": "GSM6601460_r1",
+                        "sample_accession": "SAMN31021823",
+                        "sample_alias": "GSM6601460",
+                        "sample_description": "sham-treated worms in day 5",
+                        "sample_title": "sham-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239723",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    },
+                    {
+                        "base_count": "677912850",
+                        "experiment_accession": "SRX17709228",
+                        "experiment_alias": "GSM6601461_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_bytes": "529798447",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "id": "SRX17709228_SRR21711855",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601461",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "md5_2": "",
+                        "read_count": "13558257",
+                        "run_accession": "SRR21711855",
+                        "run_alias": "GSM6601461_r1",
+                        "sample_accession": "SAMN31021822",
+                        "sample_alias": "GSM6601461",
+                        "sample_description": "PM2.5-treated worms in day 5",
+                        "sample_title": "PM2.5-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239724",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    }
+                ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
@@ -48,6 +358,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-06T20:49:22.636476"
+        "timestamp": "2024-01-07T13:46:25.989024"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index 04485010..09f2a9d1 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -23,10 +23,30 @@ nextflow_workflow {
         }
 
         then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(workflow.out).match() }
-            )
+            assert workflow.success
+
+            with(workflow.out.samplesheet) {
+                assert path(get(0)).readLines().size() == 5
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+            }
+
+            with(workflow.out.mappings) {
+                assert path(get(0)).readLines().size() == 5
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+            }
+
+            with(workflow.out.sample_mappings) {
+                assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c"
+            }
+
+            with(workflow.out.sra_metadata) {
+                assert get(0).get('experiment_accession') == 'ERX1234253'
+                assert get(1).get('experiment_accession') == 'SRX17709227'
+                assert get(2).get('experiment_accession') == 'SRX17709228'
+                assert get(3).get('experiment_accession') == 'SRX9315476'
+            }
         }
     }
 }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
index 15043ffd..a8f29a95 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
@@ -3,29 +3,181 @@
         "content": [
             {
                 "0": [
-                    
-                ],
-                "1": [
                     "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
-                "2": [
+                "1": [
                     "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
-                "3": [
+                "2": [
                     [
                         "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
+                "3": [
+                    {
+                        "base_count": "35658",
+                        "experiment_accession": "ERX1234253",
+                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_bytes": "18077",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "id": "ERX1234253_ERR1160846",
+                        "instrument_model": "Illumina HiSeq 2500",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "10317.BLANK.93.3E.r22",
+                        "library_selection": "PCR",
+                        "library_source": "METAGENOMIC",
+                        "library_strategy": "AMPLICON",
+                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "md5_2": "",
+                        "read_count": "283",
+                        "run_accession": "ERR1160846",
+                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                        "sample_accession": "SAMEA3687214",
+                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                        "sample_description": "American Gut control",
+                        "sample_title": "10317.BLANK.93.3E.r22",
+                        "scientific_name": "metagenome",
+                        "secondary_sample_accession": "ERS994363",
+                        "secondary_study_accession": "ERP012803",
+                        "single_end": true,
+                        "study_accession": "PRJEB11419",
+                        "study_alias": "qiita_sid_10317",
+                        "study_title": "American Gut Project",
+                        "submission_accession": "ERA541392",
+                        "tax_id": "256318"
+                    },
+                    {
+                        "base_count": "431758",
+                        "experiment_accession": "SRX9315476",
+                        "experiment_alias": "F11-N1-05",
+                        "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381",
+                        "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb",
+                        "fastq_aspera": "",
+                        "fastq_bytes": "",
+                        "fastq_ftp": "",
+                        "fastq_galaxy": "",
+                        "fastq_md5": "",
+                        "id": "SRX9315476_SRR12848126",
+                        "instrument_model": "Illumina HiSeq 3000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "PAIRED",
+                        "library_name": "F11-N1-05",
+                        "library_selection": "RANDOM PCR",
+                        "library_source": "GENOMIC",
+                        "library_strategy": "Synthetic-Long-Read",
+                        "md5_1": "",
+                        "md5_2": "",
+                        "read_count": "2954",
+                        "run_accession": "SRR12848126",
+                        "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam",
+                        "sample_accession": "SAMN16455283",
+                        "sample_alias": "F11-N1-05",
+                        "sample_description": "F11-N1-05",
+                        "sample_title": "Longshanks_F11-N1-05",
+                        "scientific_name": "Mus musculus domesticus",
+                        "secondary_sample_accession": "SRS7540262",
+                        "secondary_study_accession": "SRP287769",
+                        "single_end": false,
+                        "study_accession": "PRJNA670070",
+                        "study_alias": "PRJNA670070",
+                        "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "submission_accession": "SRA1145417",
+                        "tax_id": "10092"
+                    },
+                    {
+                        "base_count": "573417800",
+                        "experiment_accession": "SRX17709227",
+                        "experiment_alias": "GSM6601460_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_bytes": "447377777",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
+                        "id": "SRX17709227_SRR21711856",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601460",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "7cd1402155befc87be338132d1f31f64",
+                        "md5_2": "",
+                        "read_count": "11468356",
+                        "run_accession": "SRR21711856",
+                        "run_alias": "GSM6601460_r1",
+                        "sample_accession": "SAMN31021823",
+                        "sample_alias": "GSM6601460",
+                        "sample_description": "sham-treated worms in day 5",
+                        "sample_title": "sham-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239723",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    },
+                    {
+                        "base_count": "677912850",
+                        "experiment_accession": "SRX17709228",
+                        "experiment_alias": "GSM6601461_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_bytes": "529798447",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "id": "SRX17709228_SRR21711855",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601461",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "md5_2": "",
+                        "read_count": "13558257",
+                        "run_accession": "SRR21711855",
+                        "run_alias": "GSM6601461_r1",
+                        "sample_accession": "SAMN31021822",
+                        "sample_alias": "GSM6601461",
+                        "sample_description": "PM2.5-treated worms in day 5",
+                        "sample_title": "PM2.5-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239724",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    }
+                ],
                 "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
                     "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
-                ],
-                "fastq": [
-                    
                 ],
                 "mappings": [
                     "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
@@ -39,6 +191,164 @@
                 "samplesheet": [
                     "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
+                "sra_metadata": [
+                    {
+                        "base_count": "35658",
+                        "experiment_accession": "ERX1234253",
+                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_bytes": "18077",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "id": "ERX1234253_ERR1160846",
+                        "instrument_model": "Illumina HiSeq 2500",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "10317.BLANK.93.3E.r22",
+                        "library_selection": "PCR",
+                        "library_source": "METAGENOMIC",
+                        "library_strategy": "AMPLICON",
+                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "md5_2": "",
+                        "read_count": "283",
+                        "run_accession": "ERR1160846",
+                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                        "sample_accession": "SAMEA3687214",
+                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                        "sample_description": "American Gut control",
+                        "sample_title": "10317.BLANK.93.3E.r22",
+                        "scientific_name": "metagenome",
+                        "secondary_sample_accession": "ERS994363",
+                        "secondary_study_accession": "ERP012803",
+                        "single_end": true,
+                        "study_accession": "PRJEB11419",
+                        "study_alias": "qiita_sid_10317",
+                        "study_title": "American Gut Project",
+                        "submission_accession": "ERA541392",
+                        "tax_id": "256318"
+                    },
+                    {
+                        "base_count": "431758",
+                        "experiment_accession": "SRX9315476",
+                        "experiment_alias": "F11-N1-05",
+                        "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381",
+                        "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb",
+                        "fastq_aspera": "",
+                        "fastq_bytes": "",
+                        "fastq_ftp": "",
+                        "fastq_galaxy": "",
+                        "fastq_md5": "",
+                        "id": "SRX9315476_SRR12848126",
+                        "instrument_model": "Illumina HiSeq 3000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "PAIRED",
+                        "library_name": "F11-N1-05",
+                        "library_selection": "RANDOM PCR",
+                        "library_source": "GENOMIC",
+                        "library_strategy": "Synthetic-Long-Read",
+                        "md5_1": "",
+                        "md5_2": "",
+                        "read_count": "2954",
+                        "run_accession": "SRR12848126",
+                        "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam",
+                        "sample_accession": "SAMN16455283",
+                        "sample_alias": "F11-N1-05",
+                        "sample_description": "F11-N1-05",
+                        "sample_title": "Longshanks_F11-N1-05",
+                        "scientific_name": "Mus musculus domesticus",
+                        "secondary_sample_accession": "SRS7540262",
+                        "secondary_study_accession": "SRP287769",
+                        "single_end": false,
+                        "study_accession": "PRJNA670070",
+                        "study_alias": "PRJNA670070",
+                        "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "submission_accession": "SRA1145417",
+                        "tax_id": "10092"
+                    },
+                    {
+                        "base_count": "573417800",
+                        "experiment_accession": "SRX17709227",
+                        "experiment_alias": "GSM6601460_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_bytes": "447377777",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
+                        "id": "SRX17709227_SRR21711856",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601460",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "7cd1402155befc87be338132d1f31f64",
+                        "md5_2": "",
+                        "read_count": "11468356",
+                        "run_accession": "SRR21711856",
+                        "run_alias": "GSM6601460_r1",
+                        "sample_accession": "SAMN31021823",
+                        "sample_alias": "GSM6601460",
+                        "sample_description": "sham-treated worms in day 5",
+                        "sample_title": "sham-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239723",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    },
+                    {
+                        "base_count": "677912850",
+                        "experiment_accession": "SRX17709228",
+                        "experiment_alias": "GSM6601461_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_bytes": "529798447",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "id": "SRX17709228_SRR21711855",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601461",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "md5_2": "",
+                        "read_count": "13558257",
+                        "run_accession": "SRR21711855",
+                        "run_alias": "GSM6601461_r1",
+                        "sample_accession": "SAMN31021822",
+                        "sample_alias": "GSM6601461",
+                        "sample_description": "PM2.5-treated worms in day 5",
+                        "sample_title": "PM2.5-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239724",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    }
+                ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
@@ -48,6 +358,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-06T20:40:07.74118"
+        "timestamp": "2024-01-07T13:31:16.501443"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index dd846643..363e246c 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -23,10 +23,30 @@ nextflow_workflow {
         }
 
         then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(workflow.out).match() }
-            )
+            assert workflow.success
+
+            with(workflow.out.samplesheet) {
+                assert path(get(0)).readLines().size() == 5
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+            }
+
+            with(workflow.out.mappings) {
+                assert path(get(0)).readLines().size() == 5
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+            }
+
+            with(workflow.out.sample_mappings) {
+                assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c"
+            }
+
+            with(workflow.out.sra_metadata) {
+                assert get(0).get('experiment_accession') == 'ERX1234253'
+                assert get(1).get('experiment_accession') == 'SRX17709227'
+                assert get(2).get('experiment_accession') == 'SRX17709228'
+                assert get(3).get('experiment_accession') == 'SRX9315476'
+            }
         }
     }
 }
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
index a402abdf..22e9fefc 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
@@ -3,27 +3,179 @@
         "content": [
             {
                 "0": [
-                    
-                ],
-                "1": [
                     "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
-                "2": [
+                "1": [
                     "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
                 ],
-                "3": [
+                "2": [
                     [
                         "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
                         "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
                     ]
                 ],
+                "3": [
+                    {
+                        "base_count": "35658",
+                        "experiment_accession": "ERX1234253",
+                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_bytes": "18077",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "id": "ERX1234253_ERR1160846",
+                        "instrument_model": "Illumina HiSeq 2500",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "10317.BLANK.93.3E.r22",
+                        "library_selection": "PCR",
+                        "library_source": "METAGENOMIC",
+                        "library_strategy": "AMPLICON",
+                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "md5_2": "",
+                        "read_count": "283",
+                        "run_accession": "ERR1160846",
+                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                        "sample_accession": "SAMEA3687214",
+                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                        "sample_description": "American Gut control",
+                        "sample_title": "10317.BLANK.93.3E.r22",
+                        "scientific_name": "metagenome",
+                        "secondary_sample_accession": "ERS994363",
+                        "secondary_study_accession": "ERP012803",
+                        "single_end": true,
+                        "study_accession": "PRJEB11419",
+                        "study_alias": "qiita_sid_10317",
+                        "study_title": "American Gut Project",
+                        "submission_accession": "ERA541392",
+                        "tax_id": "256318"
+                    },
+                    {
+                        "base_count": "431758",
+                        "experiment_accession": "SRX9315476",
+                        "experiment_alias": "F11-N1-05",
+                        "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "fastq_1": "",
+                        "fastq_2": "",
+                        "fastq_aspera": "",
+                        "fastq_bytes": "",
+                        "fastq_ftp": "",
+                        "fastq_galaxy": "",
+                        "fastq_md5": "",
+                        "id": "SRX9315476_SRR12848126",
+                        "instrument_model": "Illumina HiSeq 3000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "PAIRED",
+                        "library_name": "F11-N1-05",
+                        "library_selection": "RANDOM PCR",
+                        "library_source": "GENOMIC",
+                        "library_strategy": "Synthetic-Long-Read",
+                        "md5_1": "",
+                        "md5_2": "",
+                        "read_count": "2954",
+                        "run_accession": "SRR12848126",
+                        "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam",
+                        "sample_accession": "SAMN16455283",
+                        "sample_alias": "F11-N1-05",
+                        "sample_description": "F11-N1-05",
+                        "sample_title": "Longshanks_F11-N1-05",
+                        "scientific_name": "Mus musculus domesticus",
+                        "secondary_sample_accession": "SRS7540262",
+                        "secondary_study_accession": "SRP287769",
+                        "single_end": false,
+                        "study_accession": "PRJNA670070",
+                        "study_alias": "PRJNA670070",
+                        "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "submission_accession": "SRA1145417",
+                        "tax_id": "10092"
+                    },
+                    {
+                        "base_count": "573417800",
+                        "experiment_accession": "SRX17709227",
+                        "experiment_alias": "GSM6601460_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_bytes": "447377777",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
+                        "id": "SRX17709227_SRR21711856",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601460",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "7cd1402155befc87be338132d1f31f64",
+                        "md5_2": "",
+                        "read_count": "11468356",
+                        "run_accession": "SRR21711856",
+                        "run_alias": "GSM6601460_r1",
+                        "sample_accession": "SAMN31021823",
+                        "sample_alias": "GSM6601460",
+                        "sample_description": "sham-treated worms in day 5",
+                        "sample_title": "sham-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239723",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    },
+                    {
+                        "base_count": "677912850",
+                        "experiment_accession": "SRX17709228",
+                        "experiment_alias": "GSM6601461_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_bytes": "529798447",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "id": "SRX17709228_SRR21711855",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601461",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "md5_2": "",
+                        "read_count": "13558257",
+                        "run_accession": "SRR21711855",
+                        "run_alias": "GSM6601461_r1",
+                        "sample_accession": "SAMN31021822",
+                        "sample_alias": "GSM6601461",
+                        "sample_description": "PM2.5-treated worms in day 5",
+                        "sample_title": "PM2.5-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239724",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    }
+                ],
                 "4": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
-                ],
-                "fastq": [
-                    
                 ],
                 "mappings": [
                     "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
@@ -37,6 +189,164 @@
                 "samplesheet": [
                     "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
                 ],
+                "sra_metadata": [
+                    {
+                        "base_count": "35658",
+                        "experiment_accession": "ERX1234253",
+                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_bytes": "18077",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "id": "ERX1234253_ERR1160846",
+                        "instrument_model": "Illumina HiSeq 2500",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "10317.BLANK.93.3E.r22",
+                        "library_selection": "PCR",
+                        "library_source": "METAGENOMIC",
+                        "library_strategy": "AMPLICON",
+                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "md5_2": "",
+                        "read_count": "283",
+                        "run_accession": "ERR1160846",
+                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                        "sample_accession": "SAMEA3687214",
+                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                        "sample_description": "American Gut control",
+                        "sample_title": "10317.BLANK.93.3E.r22",
+                        "scientific_name": "metagenome",
+                        "secondary_sample_accession": "ERS994363",
+                        "secondary_study_accession": "ERP012803",
+                        "single_end": true,
+                        "study_accession": "PRJEB11419",
+                        "study_alias": "qiita_sid_10317",
+                        "study_title": "American Gut Project",
+                        "submission_accession": "ERA541392",
+                        "tax_id": "256318"
+                    },
+                    {
+                        "base_count": "431758",
+                        "experiment_accession": "SRX9315476",
+                        "experiment_alias": "F11-N1-05",
+                        "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "fastq_1": "",
+                        "fastq_2": "",
+                        "fastq_aspera": "",
+                        "fastq_bytes": "",
+                        "fastq_ftp": "",
+                        "fastq_galaxy": "",
+                        "fastq_md5": "",
+                        "id": "SRX9315476_SRR12848126",
+                        "instrument_model": "Illumina HiSeq 3000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "PAIRED",
+                        "library_name": "F11-N1-05",
+                        "library_selection": "RANDOM PCR",
+                        "library_source": "GENOMIC",
+                        "library_strategy": "Synthetic-Long-Read",
+                        "md5_1": "",
+                        "md5_2": "",
+                        "read_count": "2954",
+                        "run_accession": "SRR12848126",
+                        "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam",
+                        "sample_accession": "SAMN16455283",
+                        "sample_alias": "F11-N1-05",
+                        "sample_description": "F11-N1-05",
+                        "sample_title": "Longshanks_F11-N1-05",
+                        "scientific_name": "Mus musculus domesticus",
+                        "secondary_sample_accession": "SRS7540262",
+                        "secondary_study_accession": "SRP287769",
+                        "single_end": false,
+                        "study_accession": "PRJNA670070",
+                        "study_alias": "PRJNA670070",
+                        "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
+                        "submission_accession": "SRA1145417",
+                        "tax_id": "10092"
+                    },
+                    {
+                        "base_count": "573417800",
+                        "experiment_accession": "SRX17709227",
+                        "experiment_alias": "GSM6601460_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_bytes": "447377777",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
+                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
+                        "id": "SRX17709227_SRR21711856",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601460",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "7cd1402155befc87be338132d1f31f64",
+                        "md5_2": "",
+                        "read_count": "11468356",
+                        "run_accession": "SRR21711856",
+                        "run_alias": "GSM6601460_r1",
+                        "sample_accession": "SAMN31021823",
+                        "sample_alias": "GSM6601460",
+                        "sample_description": "sham-treated worms in day 5",
+                        "sample_title": "sham-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239723",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    },
+                    {
+                        "base_count": "677912850",
+                        "experiment_accession": "SRX17709228",
+                        "experiment_alias": "GSM6601461_r1",
+                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
+                        "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_bytes": "529798447",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
+                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "id": "SRX17709228_SRR21711855",
+                        "instrument_model": "Illumina HiSeq 4000",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "GSM6601461",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
+                        "md5_2": "",
+                        "read_count": "13558257",
+                        "run_accession": "SRR21711855",
+                        "run_alias": "GSM6601461_r1",
+                        "sample_accession": "SAMN31021822",
+                        "sample_alias": "GSM6601461",
+                        "sample_description": "PM2.5-treated worms in day 5",
+                        "sample_title": "PM2.5-treated worms in day 5",
+                        "scientific_name": "Caenorhabditis elegans",
+                        "secondary_sample_accession": "SRS15239724",
+                        "secondary_study_accession": "SRP399678",
+                        "single_end": true,
+                        "study_accession": "PRJNA884373",
+                        "study_alias": "GSE214215",
+                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
+                        "submission_accession": "SRA1507236",
+                        "tax_id": "6239"
+                    }
+                ],
                 "versions": [
                     "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
                     "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
@@ -44,6 +354,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-06T20:43:31.440219"
+        "timestamp": "2024-01-07T13:51:43.062641"
     }
 }
\ No newline at end of file

From 7cc221dc8f8e3761f6c1c28fd0a8f0f56b8fc65d Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 7 Jan 2024 14:16:51 +0000
Subject: [PATCH 624/852] Fix snapshot for sra_skip_fastq_download

---
 workflows/sra/tests/sra_skip_fastq_download.nf.test | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index 363e246c..a08c9afe 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -43,9 +43,9 @@ nextflow_workflow {
 
             with(workflow.out.sra_metadata) {
                 assert get(0).get('experiment_accession') == 'ERX1234253'
-                assert get(1).get('experiment_accession') == 'SRX17709227'
-                assert get(2).get('experiment_accession') == 'SRX17709228'
-                assert get(3).get('experiment_accession') == 'SRX9315476'
+                assert get(1).get('experiment_accession') == 'SRX9315476'
+                assert get(2).get('experiment_accession') == 'SRX17709227'
+                assert get(3).get('experiment_accession') == 'SRX17709228'
             }
         }
     }

From f08543d165ad646e477dbea03655bf90bf076695 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 7 Jan 2024 14:26:06 +0000
Subject: [PATCH 625/852] Replace results with outputDir

---
 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test   | 2 +-
 workflows/sra/tests/sra_force_sratools_download.nf.test      | 2 +-
 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test     | 2 +-
 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test      | 2 +-
 workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test | 2 +-
 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test  | 2 +-
 workflows/sra/tests/sra_skip_fastq_download.nf.test          | 2 +-
 7 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index 356128c6..6f6cc260 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "results"
+                outdir = "$outputDir"
                 nf_core_pipeline = "rnaseq"
                 ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5"
                 sample_mapping_fields = "run_accession,library_layout"
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index 3180d720..f535223c 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "results"
+                outdir = "$outputDir"
                 force_sratools_download = true
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index 1bcbbf72..af74f32c 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "results"
+                outdir = "$outputDir"
                 nf_core_pipeline = "atacseq"
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index c8be765b..e7367134 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "results"
+                outdir = "$outputDir"
                 nf_core_pipeline = "rnaseq"
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index 17ec98da..8d44a6a6 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "results"
+                outdir = "$outputDir"
                 nf_core_pipeline = "taxprofiler"
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index 09f2a9d1..592ac0e1 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "results"
+                outdir = "$outputDir"
                 nf_core_pipeline = "viralrecon"
             }
         }
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index a08c9afe..857ee78b 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "results"
+                outdir = "$outputDir"
                 skip_fastq_download = true
             }
         }

From b0d4905d86d838827a59ec1a959e4888d78311c2 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 7 Jan 2024 14:35:55 +0000
Subject: [PATCH 626/852] Reorder samples in first column of samplesheet and
 mappings

---
 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test   | 4 ++--
 workflows/sra/tests/sra_force_sratools_download.nf.test      | 4 ++--
 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test     | 4 ++--
 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test      | 4 ++--
 workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test | 4 ++--
 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test  | 4 ++--
 workflows/sra/tests/sra_skip_fastq_download.nf.test          | 4 ++--
 7 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index 6f6cc260..7ac84d16 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -29,13 +29,13 @@ nextflow_workflow {
 
             with(workflow.out.samplesheet) {
                 assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
                 assert path(get(0)).text.contains('Illumina HiSeq 4000')
             }
 
             with(workflow.out.mappings) {
                 assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
                 assert path(get(0)).text.contains('Illumina HiSeq 4000')
             }
 
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index f535223c..ed72d48c 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -27,13 +27,13 @@ nextflow_workflow {
 
             with(workflow.out.samplesheet) {
                 assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
                 assert path(get(0)).text.contains('Illumina HiSeq 4000')
             }
 
             with(workflow.out.mappings) {
                 assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
                 assert path(get(0)).text.contains('Illumina HiSeq 4000')
             }
 
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index af74f32c..7b316778 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -27,13 +27,13 @@ nextflow_workflow {
 
             with(workflow.out.samplesheet) {
                 assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
                 assert path(get(0)).text.contains('Illumina HiSeq 4000')
             }
 
             with(workflow.out.mappings) {
                 assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
                 assert path(get(0)).text.contains('Illumina HiSeq 4000')
             }
 
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index e7367134..53fcdc91 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -27,13 +27,13 @@ nextflow_workflow {
 
             with(workflow.out.samplesheet) {
                 assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
                 assert path(get(0)).text.contains('Illumina HiSeq 4000')
             }
 
             with(workflow.out.mappings) {
                 assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
                 assert path(get(0)).text.contains('Illumina HiSeq 4000')
             }
 
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index 8d44a6a6..71605edf 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -27,13 +27,13 @@ nextflow_workflow {
 
             with(workflow.out.samplesheet) {
                 assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
                 assert path(get(0)).text.contains('Illumina HiSeq 4000')
             }
 
             with(workflow.out.mappings) {
                 assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
                 assert path(get(0)).text.contains('Illumina HiSeq 4000')
             }
 
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index 592ac0e1..3678d9dc 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -27,13 +27,13 @@ nextflow_workflow {
 
             with(workflow.out.samplesheet) {
                 assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
                 assert path(get(0)).text.contains('Illumina HiSeq 4000')
             }
 
             with(workflow.out.mappings) {
                 assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
                 assert path(get(0)).text.contains('Illumina HiSeq 4000')
             }
 
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index 857ee78b..73208ae4 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -27,13 +27,13 @@ nextflow_workflow {
 
             with(workflow.out.samplesheet) {
                 assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
                 assert path(get(0)).text.contains('Illumina HiSeq 4000')
             }
 
             with(workflow.out.mappings) {
                 assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"']
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
                 assert path(get(0)).text.contains('Illumina HiSeq 4000')
             }
 

From b7cfca7d9f5f812a12d5084fcb956533c47b7ad4 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 7 Jan 2024 15:47:19 +0000
Subject: [PATCH 627/852] Regenerate snapshots and remove metadata test

---
 workflows/sra/tests/main.nf.test              | 21 ++++++++++++++----
 workflows/sra/tests/main.nf.test.snap         |  2 +-
 .../sra_custom_ena_metadata_fields.nf.test    | 11 ++--------
 ...ra_custom_ena_metadata_fields.nf.test.snap | 10 ++++-----
 .../tests/sra_force_sratools_download.nf.test |  7 ------
 .../sra_force_sratools_download.nf.test.snap  | 22 +++++++++----------
 .../sra_nf_core_pipeline_atacseq.nf.test      |  7 ------
 .../sra_nf_core_pipeline_atacseq.nf.test.snap | 10 ++++-----
 .../tests/sra_nf_core_pipeline_rnaseq.nf.test |  7 ------
 .../sra_nf_core_pipeline_rnaseq.nf.test.snap  | 10 ++++-----
 .../sra_nf_core_pipeline_taxprofiler.nf.test  |  7 ------
 ..._nf_core_pipeline_taxprofiler.nf.test.snap | 10 ++++-----
 .../sra_nf_core_pipeline_viralrecon.nf.test   |  7 ------
 ...a_nf_core_pipeline_viralrecon.nf.test.snap | 10 ++++-----
 .../sra/tests/sra_skip_fastq_download.nf.test |  7 ------
 .../sra_skip_fastq_download.nf.test.snap      | 10 ++++-----
 16 files changed, 61 insertions(+), 97 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 072c2ebb..a57187b1 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -22,10 +22,23 @@ nextflow_workflow {
         }
 
         then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(workflow.out).match() }
-            )
+            assert workflow.success
+
+            with(workflow.out.samplesheet) {
+                assert path(get(0)).readLines().size() == 5
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
+                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+            }
+
+            with(workflow.out.mappings) {
+                assert path(get(0)).readLines().size() == 5
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
+                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+            }
+
+            with(workflow.out.sample_mappings) {
+                assert path(get(0)[0]).md5 == "3bc981f0de28023083cdf13691d249d5"
+            }
         }
     }
 }
diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
index f525d55d..a7b49740 100644
--- a/workflows/sra/tests/main.nf.test.snap
+++ b/workflows/sra/tests/main.nf.test.snap
@@ -358,6 +358,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-07T13:27:35.094044"
+        "timestamp": "2024-01-07T15:01:05.175326"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index 7ac84d16..008cc258 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -30,25 +30,18 @@ nextflow_workflow {
             with(workflow.out.samplesheet) {
                 assert path(get(0)).readLines().size() == 5
                 assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
-                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+                assert path(get(0)).text.contains('SINGLE')
             }
 
             with(workflow.out.mappings) {
                 assert path(get(0)).readLines().size() == 5
                 assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
-                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+                assert path(get(0)).text.contains('SINGLE')
             }
 
             with(workflow.out.sample_mappings) {
                 assert path(get(0)[0]).md5 == "3bc981f0de28023083cdf13691d249d5"
             }
-
-            with(workflow.out.sra_metadata) {
-                assert get(0).get('experiment_accession') == 'ERX1234253'
-                assert get(1).get('experiment_accession') == 'SRX17709227'
-                assert get(2).get('experiment_accession') == 'SRX17709228'
-                assert get(3).get('experiment_accession') == 'SRX9315476'
-            }
         }
     }
 }
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
index f182f555..b508d313 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
@@ -3,10 +3,10 @@
         "content": [
             {
                 "0": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,7cc8031f595157c6ac13ba5067e4bcfb"
                 ],
                 "1": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,7ee50def039a942e0ac8ca63292c8368"
                 ],
                 "2": [
                     [
@@ -76,7 +76,7 @@
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,7ee50def039a942e0ac8ca63292c8368"
                 ],
                 "sample_mappings": [
                     [
@@ -85,7 +85,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,7cc8031f595157c6ac13ba5067e4bcfb"
                 ],
                 "sra_metadata": [
                     {
@@ -150,6 +150,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-07T13:22:50.246795"
+        "timestamp": "2024-01-07T14:50:20.141785"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index ed72d48c..bfb7dfba 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -40,13 +40,6 @@ nextflow_workflow {
             with(workflow.out.sample_mappings) {
                 assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c"
             }
-
-            with(workflow.out.sra_metadata) {
-                assert get(0).get('experiment_accession') == 'ERX1234253'
-                assert get(1).get('experiment_accession') == 'SRX17709227'
-                assert get(2).get('experiment_accession') == 'SRX17709228'
-                assert get(3).get('experiment_accession') == 'SRX9315476'
-            }
         }
     }
 }
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
index 2dcf052c..b0879235 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
@@ -3,10 +3,10 @@
         "content": [
             {
                 "0": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,0f2c0516990774b5d7d76a7ddf763f55"
                 ],
                 "1": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "2": [
                     [
@@ -20,7 +20,7 @@
                         "experiment_accession": "ERX1234253",
                         "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
                         "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,98515d664854f1c96f55ac836fb671b9",
                         "fastq_2": "",
                         "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
                         "fastq_bytes": "18077",
@@ -98,7 +98,7 @@
                         "experiment_accession": "SRX17709227",
                         "experiment_alias": "GSM6601460_r1",
                         "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
-                        "fastq_1": "results/fastq/SRX17709227_SRR21711856_1.fastq.gz",
+                        "fastq_1": "SRX17709227_SRR21711856_1.fastq.gz:md5,5f8db5a1966e244aad03f5bd9ca45b3d",
                         "fastq_2": "",
                         "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
                         "fastq_bytes": "447377777",
@@ -137,7 +137,7 @@
                         "experiment_accession": "SRX17709228",
                         "experiment_alias": "GSM6601461_r1",
                         "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
-                        "fastq_1": "results/fastq/SRX17709228_SRR21711855_1.fastq.gz",
+                        "fastq_1": "SRX17709228_SRR21711855_1.fastq.gz:md5,bb3026b15647a3fc82a62ecb58641924",
                         "fastq_2": "",
                         "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
                         "fastq_bytes": "529798447",
@@ -179,7 +179,7 @@
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "sample_mappings": [
                     [
@@ -188,7 +188,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,0f2c0516990774b5d7d76a7ddf763f55"
                 ],
                 "sra_metadata": [
                     {
@@ -196,7 +196,7 @@
                         "experiment_accession": "ERX1234253",
                         "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
                         "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,98515d664854f1c96f55ac836fb671b9",
                         "fastq_2": "",
                         "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
                         "fastq_bytes": "18077",
@@ -274,7 +274,7 @@
                         "experiment_accession": "SRX17709227",
                         "experiment_alias": "GSM6601460_r1",
                         "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
-                        "fastq_1": "results/fastq/SRX17709227_SRR21711856_1.fastq.gz",
+                        "fastq_1": "SRX17709227_SRR21711856_1.fastq.gz:md5,5f8db5a1966e244aad03f5bd9ca45b3d",
                         "fastq_2": "",
                         "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
                         "fastq_bytes": "447377777",
@@ -313,7 +313,7 @@
                         "experiment_accession": "SRX17709228",
                         "experiment_alias": "GSM6601461_r1",
                         "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
-                        "fastq_1": "results/fastq/SRX17709228_SRR21711855_1.fastq.gz",
+                        "fastq_1": "SRX17709228_SRR21711855_1.fastq.gz:md5,bb3026b15647a3fc82a62ecb58641924",
                         "fastq_2": "",
                         "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
                         "fastq_bytes": "529798447",
@@ -356,6 +356,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-07T13:36:22.094035"
+        "timestamp": "2024-01-07T15:09:34.563421"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index 7b316778..770915a3 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -40,13 +40,6 @@ nextflow_workflow {
             with(workflow.out.sample_mappings) {
                 assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c"
             }
-
-            with(workflow.out.sra_metadata) {
-                assert get(0).get('experiment_accession') == 'ERX1234253'
-                assert get(1).get('experiment_accession') == 'SRX17709227'
-                assert get(2).get('experiment_accession') == 'SRX17709228'
-                assert get(3).get('experiment_accession') == 'SRX9315476'
-            }
         }
     }
 }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
index 5dd675d3..9d162743 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
@@ -3,10 +3,10 @@
         "content": [
             {
                 "0": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,8f985e9dd993b9c826ea095bd377d34a"
                 ],
                 "1": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "2": [
                     [
@@ -180,7 +180,7 @@
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "sample_mappings": [
                     [
@@ -189,7 +189,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,8f985e9dd993b9c826ea095bd377d34a"
                 ],
                 "sra_metadata": [
                     {
@@ -358,6 +358,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-07T13:38:47.906835"
+        "timestamp": "2024-01-07T15:13:47.475783"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index 53fcdc91..cbf42a53 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -40,13 +40,6 @@ nextflow_workflow {
             with(workflow.out.sample_mappings) {
                 assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c"
             }
-
-            with(workflow.out.sra_metadata) {
-                assert get(0).get('experiment_accession') == 'ERX1234253'
-                assert get(1).get('experiment_accession') == 'SRX17709227'
-                assert get(2).get('experiment_accession') == 'SRX17709228'
-                assert get(3).get('experiment_accession') == 'SRX9315476'
-            }
         }
     }
 }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
index b831fe54..93c66f55 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
@@ -3,10 +3,10 @@
         "content": [
             {
                 "0": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,c0f7d7b70e884c78f90630c695703d7b"
                 ],
                 "1": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "2": [
                     [
@@ -180,7 +180,7 @@
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "sample_mappings": [
                     [
@@ -189,7 +189,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,c0f7d7b70e884c78f90630c695703d7b"
                 ],
                 "sra_metadata": [
                     {
@@ -358,6 +358,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-07T13:42:36.795022"
+        "timestamp": "2024-01-07T15:17:19.511222"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index 71605edf..db0400c1 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -40,13 +40,6 @@ nextflow_workflow {
             with(workflow.out.sample_mappings) {
                 assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c"
             }
-
-            with(workflow.out.sra_metadata) {
-                assert get(0).get('experiment_accession') == 'ERX1234253'
-                assert get(1).get('experiment_accession') == 'SRX17709227'
-                assert get(2).get('experiment_accession') == 'SRX17709228'
-                assert get(3).get('experiment_accession') == 'SRX9315476'
-            }
         }
     }
 }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
index d7463e04..27e12abd 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
@@ -3,10 +3,10 @@
         "content": [
             {
                 "0": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,fe3c7ba9e7b7debe07291d6125f9edc7"
                 ],
                 "1": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "2": [
                     [
@@ -180,7 +180,7 @@
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "sample_mappings": [
                     [
@@ -189,7 +189,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,fe3c7ba9e7b7debe07291d6125f9edc7"
                 ],
                 "sra_metadata": [
                     {
@@ -358,6 +358,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-07T13:46:25.989024"
+        "timestamp": "2024-01-07T15:21:54.519934"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index 3678d9dc..e13f83b3 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -40,13 +40,6 @@ nextflow_workflow {
             with(workflow.out.sample_mappings) {
                 assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c"
             }
-
-            with(workflow.out.sra_metadata) {
-                assert get(0).get('experiment_accession') == 'ERX1234253'
-                assert get(1).get('experiment_accession') == 'SRX17709227'
-                assert get(2).get('experiment_accession') == 'SRX17709228'
-                assert get(3).get('experiment_accession') == 'SRX9315476'
-            }
         }
     }
 }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
index a8f29a95..60708a54 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
@@ -3,10 +3,10 @@
         "content": [
             {
                 "0": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,99a3fd9fe3c7cad8184b1bbeadd89c45"
                 ],
                 "1": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "2": [
                     [
@@ -180,7 +180,7 @@
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "sample_mappings": [
                     [
@@ -189,7 +189,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,99a3fd9fe3c7cad8184b1bbeadd89c45"
                 ],
                 "sra_metadata": [
                     {
@@ -358,6 +358,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-07T13:31:16.501443"
+        "timestamp": "2024-01-07T15:04:57.029889"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index 73208ae4..f5805367 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -40,13 +40,6 @@ nextflow_workflow {
             with(workflow.out.sample_mappings) {
                 assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c"
             }
-
-            with(workflow.out.sra_metadata) {
-                assert get(0).get('experiment_accession') == 'ERX1234253'
-                assert get(1).get('experiment_accession') == 'SRX9315476'
-                assert get(2).get('experiment_accession') == 'SRX17709227'
-                assert get(3).get('experiment_accession') == 'SRX17709228'
-            }
         }
     }
 }
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
index 22e9fefc..252392d7 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
@@ -3,10 +3,10 @@
         "content": [
             {
                 "0": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,eb18025bb1cb97a4fe399ca16757d2db"
                 ],
                 "1": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "2": [
                     [
@@ -178,7 +178,7 @@
                     "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
                 ],
                 "mappings": [
-                    "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a"
+                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
                 ],
                 "sample_mappings": [
                     [
@@ -187,7 +187,7 @@
                     ]
                 ],
                 "samplesheet": [
-                    "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609"
+                    "samplesheet.csv:md5,eb18025bb1cb97a4fe399ca16757d2db"
                 ],
                 "sra_metadata": [
                     {
@@ -354,6 +354,6 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-07T13:51:43.062641"
+        "timestamp": "2024-01-07T15:11:52.542678"
     }
 }
\ No newline at end of file

From f705af88bcb6fe2b8cda1de9a619ded8c2f0609e Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 7 Jan 2024 22:37:54 +0000
Subject: [PATCH 628/852] Remove all workflow snapshots

---
 workflows/sra/tests/main.nf.test.snap         | 363 ------------------
 ...ra_custom_ena_metadata_fields.nf.test.snap | 155 --------
 .../sra_force_sratools_download.nf.test.snap  | 361 -----------------
 .../sra_nf_core_pipeline_atacseq.nf.test.snap | 363 ------------------
 .../sra_nf_core_pipeline_rnaseq.nf.test.snap  | 363 ------------------
 ..._nf_core_pipeline_taxprofiler.nf.test.snap | 363 ------------------
 ...a_nf_core_pipeline_viralrecon.nf.test.snap | 363 ------------------
 .../sra_skip_fastq_download.nf.test.snap      | 359 -----------------
 8 files changed, 2690 deletions(-)
 delete mode 100644 workflows/sra/tests/main.nf.test.snap
 delete mode 100644 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
 delete mode 100644 workflows/sra/tests/sra_force_sratools_download.nf.test.snap
 delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
 delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
 delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
 delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
 delete mode 100644 workflows/sra/tests/sra_skip_fastq_download.nf.test.snap

diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
deleted file mode 100644
index a7b49740..00000000
--- a/workflows/sra/tests/main.nf.test.snap
+++ /dev/null
@@ -1,363 +0,0 @@
-{
-    "Parameters: default": {
-        "content": [
-            {
-                "0": [
-                    "samplesheet.csv:md5,d252b222b8ef94670117780d43498b86"
-                ],
-                "1": [
-                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
-                ],
-                "2": [
-                    [
-                        "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
-                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
-                    ]
-                ],
-                "3": [
-                    {
-                        "base_count": "35658",
-                        "experiment_accession": "ERX1234253",
-                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_bytes": "18077",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "10317.BLANK.93.3E.r22",
-                        "library_selection": "PCR",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "AMPLICON",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "read_count": "283",
-                        "run_accession": "ERR1160846",
-                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
-                        "sample_accession": "SAMEA3687214",
-                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
-                        "sample_description": "American Gut control",
-                        "sample_title": "10317.BLANK.93.3E.r22",
-                        "scientific_name": "metagenome",
-                        "secondary_sample_accession": "ERS994363",
-                        "secondary_study_accession": "ERP012803",
-                        "single_end": true,
-                        "study_accession": "PRJEB11419",
-                        "study_alias": "qiita_sid_10317",
-                        "study_title": "American Gut Project",
-                        "submission_accession": "ERA541392",
-                        "tax_id": "256318"
-                    },
-                    {
-                        "base_count": "431758",
-                        "experiment_accession": "SRX9315476",
-                        "experiment_alias": "F11-N1-05",
-                        "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
-                        "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381",
-                        "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb",
-                        "fastq_aspera": "",
-                        "fastq_bytes": "",
-                        "fastq_ftp": "",
-                        "fastq_galaxy": "",
-                        "fastq_md5": "",
-                        "id": "SRX9315476_SRR12848126",
-                        "instrument_model": "Illumina HiSeq 3000",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "PAIRED",
-                        "library_name": "F11-N1-05",
-                        "library_selection": "RANDOM PCR",
-                        "library_source": "GENOMIC",
-                        "library_strategy": "Synthetic-Long-Read",
-                        "md5_1": "",
-                        "md5_2": "",
-                        "read_count": "2954",
-                        "run_accession": "SRR12848126",
-                        "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam",
-                        "sample_accession": "SAMN16455283",
-                        "sample_alias": "F11-N1-05",
-                        "sample_description": "F11-N1-05",
-                        "sample_title": "Longshanks_F11-N1-05",
-                        "scientific_name": "Mus musculus domesticus",
-                        "secondary_sample_accession": "SRS7540262",
-                        "secondary_study_accession": "SRP287769",
-                        "single_end": false,
-                        "study_accession": "PRJNA670070",
-                        "study_alias": "PRJNA670070",
-                        "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
-                        "submission_accession": "SRA1145417",
-                        "tax_id": "10092"
-                    },
-                    {
-                        "base_count": "573417800",
-                        "experiment_accession": "SRX17709227",
-                        "experiment_alias": "GSM6601460_r1",
-                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
-                        "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                        "fastq_bytes": "447377777",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
-                        "id": "SRX17709227_SRR21711856",
-                        "instrument_model": "Illumina HiSeq 4000",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "GSM6601460",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "7cd1402155befc87be338132d1f31f64",
-                        "md5_2": "",
-                        "read_count": "11468356",
-                        "run_accession": "SRR21711856",
-                        "run_alias": "GSM6601460_r1",
-                        "sample_accession": "SAMN31021823",
-                        "sample_alias": "GSM6601460",
-                        "sample_description": "sham-treated worms in day 5",
-                        "sample_title": "sham-treated worms in day 5",
-                        "scientific_name": "Caenorhabditis elegans",
-                        "secondary_sample_accession": "SRS15239723",
-                        "secondary_study_accession": "SRP399678",
-                        "single_end": true,
-                        "study_accession": "PRJNA884373",
-                        "study_alias": "GSE214215",
-                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
-                        "submission_accession": "SRA1507236",
-                        "tax_id": "6239"
-                    },
-                    {
-                        "base_count": "677912850",
-                        "experiment_accession": "SRX17709228",
-                        "experiment_alias": "GSM6601461_r1",
-                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
-                        "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                        "fastq_bytes": "529798447",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
-                        "id": "SRX17709228_SRR21711855",
-                        "instrument_model": "Illumina HiSeq 4000",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "GSM6601461",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
-                        "md5_2": "",
-                        "read_count": "13558257",
-                        "run_accession": "SRR21711855",
-                        "run_alias": "GSM6601461_r1",
-                        "sample_accession": "SAMN31021822",
-                        "sample_alias": "GSM6601461",
-                        "sample_description": "PM2.5-treated worms in day 5",
-                        "sample_title": "PM2.5-treated worms in day 5",
-                        "scientific_name": "Caenorhabditis elegans",
-                        "secondary_sample_accession": "SRS15239724",
-                        "secondary_study_accession": "SRP399678",
-                        "single_end": true,
-                        "study_accession": "PRJNA884373",
-                        "study_alias": "GSE214215",
-                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
-                        "submission_accession": "SRA1507236",
-                        "tax_id": "6239"
-                    }
-                ],
-                "4": [
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
-                    "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
-                ],
-                "mappings": [
-                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
-                ],
-                "sample_mappings": [
-                    [
-                        "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
-                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
-                    ]
-                ],
-                "samplesheet": [
-                    "samplesheet.csv:md5,d252b222b8ef94670117780d43498b86"
-                ],
-                "sra_metadata": [
-                    {
-                        "base_count": "35658",
-                        "experiment_accession": "ERX1234253",
-                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_bytes": "18077",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "10317.BLANK.93.3E.r22",
-                        "library_selection": "PCR",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "AMPLICON",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "read_count": "283",
-                        "run_accession": "ERR1160846",
-                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
-                        "sample_accession": "SAMEA3687214",
-                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
-                        "sample_description": "American Gut control",
-                        "sample_title": "10317.BLANK.93.3E.r22",
-                        "scientific_name": "metagenome",
-                        "secondary_sample_accession": "ERS994363",
-                        "secondary_study_accession": "ERP012803",
-                        "single_end": true,
-                        "study_accession": "PRJEB11419",
-                        "study_alias": "qiita_sid_10317",
-                        "study_title": "American Gut Project",
-                        "submission_accession": "ERA541392",
-                        "tax_id": "256318"
-                    },
-                    {
-                        "base_count": "431758",
-                        "experiment_accession": "SRX9315476",
-                        "experiment_alias": "F11-N1-05",
-                        "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
-                        "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381",
-                        "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb",
-                        "fastq_aspera": "",
-                        "fastq_bytes": "",
-                        "fastq_ftp": "",
-                        "fastq_galaxy": "",
-                        "fastq_md5": "",
-                        "id": "SRX9315476_SRR12848126",
-                        "instrument_model": "Illumina HiSeq 3000",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "PAIRED",
-                        "library_name": "F11-N1-05",
-                        "library_selection": "RANDOM PCR",
-                        "library_source": "GENOMIC",
-                        "library_strategy": "Synthetic-Long-Read",
-                        "md5_1": "",
-                        "md5_2": "",
-                        "read_count": "2954",
-                        "run_accession": "SRR12848126",
-                        "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam",
-                        "sample_accession": "SAMN16455283",
-                        "sample_alias": "F11-N1-05",
-                        "sample_description": "F11-N1-05",
-                        "sample_title": "Longshanks_F11-N1-05",
-                        "scientific_name": "Mus musculus domesticus",
-                        "secondary_sample_accession": "SRS7540262",
-                        "secondary_study_accession": "SRP287769",
-                        "single_end": false,
-                        "study_accession": "PRJNA670070",
-                        "study_alias": "PRJNA670070",
-                        "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
-                        "submission_accession": "SRA1145417",
-                        "tax_id": "10092"
-                    },
-                    {
-                        "base_count": "573417800",
-                        "experiment_accession": "SRX17709227",
-                        "experiment_alias": "GSM6601460_r1",
-                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
-                        "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                        "fastq_bytes": "447377777",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
-                        "id": "SRX17709227_SRR21711856",
-                        "instrument_model": "Illumina HiSeq 4000",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "GSM6601460",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "7cd1402155befc87be338132d1f31f64",
-                        "md5_2": "",
-                        "read_count": "11468356",
-                        "run_accession": "SRR21711856",
-                        "run_alias": "GSM6601460_r1",
-                        "sample_accession": "SAMN31021823",
-                        "sample_alias": "GSM6601460",
-                        "sample_description": "sham-treated worms in day 5",
-                        "sample_title": "sham-treated worms in day 5",
-                        "scientific_name": "Caenorhabditis elegans",
-                        "secondary_sample_accession": "SRS15239723",
-                        "secondary_study_accession": "SRP399678",
-                        "single_end": true,
-                        "study_accession": "PRJNA884373",
-                        "study_alias": "GSE214215",
-                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
-                        "submission_accession": "SRA1507236",
-                        "tax_id": "6239"
-                    },
-                    {
-                        "base_count": "677912850",
-                        "experiment_accession": "SRX17709228",
-                        "experiment_alias": "GSM6601461_r1",
-                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
-                        "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                        "fastq_bytes": "529798447",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
-                        "id": "SRX17709228_SRR21711855",
-                        "instrument_model": "Illumina HiSeq 4000",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "GSM6601461",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
-                        "md5_2": "",
-                        "read_count": "13558257",
-                        "run_accession": "SRR21711855",
-                        "run_alias": "GSM6601461_r1",
-                        "sample_accession": "SAMN31021822",
-                        "sample_alias": "GSM6601461",
-                        "sample_description": "PM2.5-treated worms in day 5",
-                        "sample_title": "PM2.5-treated worms in day 5",
-                        "scientific_name": "Caenorhabditis elegans",
-                        "secondary_sample_accession": "SRS15239724",
-                        "secondary_study_accession": "SRP399678",
-                        "single_end": true,
-                        "study_accession": "PRJNA884373",
-                        "study_alias": "GSE214215",
-                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
-                        "submission_accession": "SRA1507236",
-                        "tax_id": "6239"
-                    }
-                ],
-                "versions": [
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
-                    "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
-                ]
-            }
-        ],
-        "timestamp": "2024-01-07T15:01:05.175326"
-    }
-}
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
deleted file mode 100644
index b508d313..00000000
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
+++ /dev/null
@@ -1,155 +0,0 @@
-{
-    "Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...": {
-        "content": [
-            {
-                "0": [
-                    "samplesheet.csv:md5,7cc8031f595157c6ac13ba5067e4bcfb"
-                ],
-                "1": [
-                    "id_mappings.csv:md5,7ee50def039a942e0ac8ca63292c8368"
-                ],
-                "2": [
-                    [
-                        "multiqc_config.yml:md5,3bc981f0de28023083cdf13691d249d5",
-                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
-                    ]
-                ],
-                "3": [
-                    {
-                        "experiment_accession": "ERX1234253",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
-                        "fastq_2": "",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "library_layout": "SINGLE",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "run_accession": "ERR1160846",
-                        "single_end": true
-                    },
-                    {
-                        "experiment_accession": "SRX17709227",
-                        "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2",
-                        "fastq_2": "",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
-                        "id": "SRX17709227_SRR21711856",
-                        "library_layout": "SINGLE",
-                        "md5_1": "7cd1402155befc87be338132d1f31f64",
-                        "md5_2": "",
-                        "run_accession": "SRR21711856",
-                        "single_end": true
-                    },
-                    {
-                        "experiment_accession": "SRX17709228",
-                        "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a",
-                        "fastq_2": "",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
-                        "id": "SRX17709228_SRR21711855",
-                        "library_layout": "SINGLE",
-                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
-                        "md5_2": "",
-                        "run_accession": "SRR21711855",
-                        "single_end": true
-                    },
-                    {
-                        "experiment_accession": "SRX9315476",
-                        "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381",
-                        "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb",
-                        "fastq_ftp": "",
-                        "fastq_md5": "",
-                        "id": "SRX9315476_SRR12848126",
-                        "library_layout": "PAIRED",
-                        "md5_1": "",
-                        "md5_2": "",
-                        "run_accession": "SRR12848126",
-                        "single_end": false
-                    }
-                ],
-                "4": [
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
-                    "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
-                ],
-                "mappings": [
-                    "id_mappings.csv:md5,7ee50def039a942e0ac8ca63292c8368"
-                ],
-                "sample_mappings": [
-                    [
-                        "multiqc_config.yml:md5,3bc981f0de28023083cdf13691d249d5",
-                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
-                    ]
-                ],
-                "samplesheet": [
-                    "samplesheet.csv:md5,7cc8031f595157c6ac13ba5067e4bcfb"
-                ],
-                "sra_metadata": [
-                    {
-                        "experiment_accession": "ERX1234253",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
-                        "fastq_2": "",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "library_layout": "SINGLE",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "run_accession": "ERR1160846",
-                        "single_end": true
-                    },
-                    {
-                        "experiment_accession": "SRX17709227",
-                        "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2",
-                        "fastq_2": "",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
-                        "id": "SRX17709227_SRR21711856",
-                        "library_layout": "SINGLE",
-                        "md5_1": "7cd1402155befc87be338132d1f31f64",
-                        "md5_2": "",
-                        "run_accession": "SRR21711856",
-                        "single_end": true
-                    },
-                    {
-                        "experiment_accession": "SRX17709228",
-                        "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a",
-                        "fastq_2": "",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
-                        "id": "SRX17709228_SRR21711855",
-                        "library_layout": "SINGLE",
-                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
-                        "md5_2": "",
-                        "run_accession": "SRR21711855",
-                        "single_end": true
-                    },
-                    {
-                        "experiment_accession": "SRX9315476",
-                        "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381",
-                        "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb",
-                        "fastq_ftp": "",
-                        "fastq_md5": "",
-                        "id": "SRX9315476_SRR12848126",
-                        "library_layout": "PAIRED",
-                        "md5_1": "",
-                        "md5_2": "",
-                        "run_accession": "SRR12848126",
-                        "single_end": false
-                    }
-                ],
-                "versions": [
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
-                    "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
-                ]
-            }
-        ],
-        "timestamp": "2024-01-07T14:50:20.141785"
-    }
-}
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
deleted file mode 100644
index b0879235..00000000
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap
+++ /dev/null
@@ -1,361 +0,0 @@
-{
-    "Parameters: --force_sratools_download": {
-        "content": [
-            {
-                "0": [
-                    "samplesheet.csv:md5,0f2c0516990774b5d7d76a7ddf763f55"
-                ],
-                "1": [
-                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
-                ],
-                "2": [
-                    [
-                        "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
-                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
-                    ]
-                ],
-                "3": [
-                    {
-                        "base_count": "35658",
-                        "experiment_accession": "ERX1234253",
-                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,98515d664854f1c96f55ac836fb671b9",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_bytes": "18077",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "10317.BLANK.93.3E.r22",
-                        "library_selection": "PCR",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "AMPLICON",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "read_count": "283",
-                        "run_accession": "ERR1160846",
-                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
-                        "sample_accession": "SAMEA3687214",
-                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
-                        "sample_description": "American Gut control",
-                        "sample_title": "10317.BLANK.93.3E.r22",
-                        "scientific_name": "metagenome",
-                        "secondary_sample_accession": "ERS994363",
-                        "secondary_study_accession": "ERP012803",
-                        "single_end": true,
-                        "study_accession": "PRJEB11419",
-                        "study_alias": "qiita_sid_10317",
-                        "study_title": "American Gut Project",
-                        "submission_accession": "ERA541392",
-                        "tax_id": "256318"
-                    },
-                    {
-                        "base_count": "431758",
-                        "experiment_accession": "SRX9315476",
-                        "experiment_alias": "F11-N1-05",
-                        "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
-                        "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381",
-                        "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb",
-                        "fastq_aspera": "",
-                        "fastq_bytes": "",
-                        "fastq_ftp": "",
-                        "fastq_galaxy": "",
-                        "fastq_md5": "",
-                        "id": "SRX9315476_SRR12848126",
-                        "instrument_model": "Illumina HiSeq 3000",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "PAIRED",
-                        "library_name": "F11-N1-05",
-                        "library_selection": "RANDOM PCR",
-                        "library_source": "GENOMIC",
-                        "library_strategy": "Synthetic-Long-Read",
-                        "md5_1": "",
-                        "md5_2": "",
-                        "read_count": "2954",
-                        "run_accession": "SRR12848126",
-                        "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam",
-                        "sample_accession": "SAMN16455283",
-                        "sample_alias": "F11-N1-05",
-                        "sample_description": "F11-N1-05",
-                        "sample_title": "Longshanks_F11-N1-05",
-                        "scientific_name": "Mus musculus domesticus",
-                        "secondary_sample_accession": "SRS7540262",
-                        "secondary_study_accession": "SRP287769",
-                        "single_end": false,
-                        "study_accession": "PRJNA670070",
-                        "study_alias": "PRJNA670070",
-                        "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
-                        "submission_accession": "SRA1145417",
-                        "tax_id": "10092"
-                    },
-                    {
-                        "base_count": "573417800",
-                        "experiment_accession": "SRX17709227",
-                        "experiment_alias": "GSM6601460_r1",
-                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
-                        "fastq_1": "SRX17709227_SRR21711856_1.fastq.gz:md5,5f8db5a1966e244aad03f5bd9ca45b3d",
-                        "fastq_2": "",
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-                    "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
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-                ]
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-        "timestamp": "2024-01-07T15:09:34.563421"
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-}
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
deleted file mode 100644
index 9d162743..00000000
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
+++ /dev/null
@@ -1,363 +0,0 @@
-{
-    "Parameters: --nf_core_pipeline atacseq": {
-        "content": [
-            {
-                "0": [
-                    "samplesheet.csv:md5,8f985e9dd993b9c826ea095bd377d34a"
-                ],
-                "1": [
-                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
-                ],
-                "2": [
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-                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
-                    ]
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-                "3": [
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-                        "experiment_accession": "ERX1234253",
-                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
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-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
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-                        "instrument_platform": "ILLUMINA",
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-                        "library_selection": "PCR",
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-                        "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb",
-                        "fastq_aspera": "",
-                        "fastq_bytes": "",
-                        "fastq_ftp": "",
-                        "fastq_galaxy": "",
-                        "fastq_md5": "",
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-                        "instrument_model": "Illumina HiSeq 3000",
-                        "instrument_platform": "ILLUMINA",
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-                        "md5_1": "",
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-                        "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
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-                        "tax_id": "10092"
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-                        "base_count": "573417800",
-                        "experiment_accession": "SRX17709227",
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-                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
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-                        "fastq_bytes": "447377777",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
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-                        "instrument_model": "Illumina HiSeq 4000",
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-                        "read_count": "11468356",
-                        "run_accession": "SRR21711856",
-                        "run_alias": "GSM6601460_r1",
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-        "timestamp": "2024-01-07T15:13:47.475783"
-    }
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\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
deleted file mode 100644
index 93c66f55..00000000
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
+++ /dev/null
@@ -1,363 +0,0 @@
-{
-    "Parameters: --nf_core_pipeline rnaseq": {
-        "content": [
-            {
-                "0": [
-                    "samplesheet.csv:md5,c0f7d7b70e884c78f90630c695703d7b"
-                ],
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-                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
-                ],
-                "2": [
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-                        "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
-                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
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-                "3": [
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-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_bytes": "18077",
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-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
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-                        "instrument_platform": "ILLUMINA",
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-                        "library_selection": "PCR",
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-                        "sample_description": "American Gut control",
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-                        "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb",
-                        "fastq_aspera": "",
-                        "fastq_bytes": "",
-                        "fastq_ftp": "",
-                        "fastq_galaxy": "",
-                        "fastq_md5": "",
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-                        "instrument_model": "Illumina HiSeq 3000",
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-                        "read_count": "2954",
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-                        "tax_id": "10092"
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-                        "experiment_accession": "SRX17709227",
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-                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
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-                        "sample_title": "PM2.5-treated worms in day 5",
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-                        "submission_accession": "SRA1507236",
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-                        "md5_2": "",
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-                        "run_accession": "SRR21711856",
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-                        "sample_accession": "SAMN31021823",
-                        "sample_alias": "GSM6601460",
-                        "sample_description": "sham-treated worms in day 5",
-                        "sample_title": "sham-treated worms in day 5",
-                        "scientific_name": "Caenorhabditis elegans",
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-                        "secondary_study_accession": "SRP399678",
-                        "single_end": true,
-                        "study_accession": "PRJNA884373",
-                        "study_alias": "GSE214215",
-                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
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-                        "experiment_alias": "GSM6601461_r1",
-                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
-                        "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a",
-                        "fastq_2": "",
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-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
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-                        "read_count": "13558257",
-                        "run_accession": "SRR21711855",
-                        "run_alias": "GSM6601461_r1",
-                        "sample_accession": "SAMN31021822",
-                        "sample_alias": "GSM6601461",
-                        "sample_description": "PM2.5-treated worms in day 5",
-                        "sample_title": "PM2.5-treated worms in day 5",
-                        "scientific_name": "Caenorhabditis elegans",
-                        "secondary_sample_accession": "SRS15239724",
-                        "secondary_study_accession": "SRP399678",
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-                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
-                        "submission_accession": "SRA1507236",
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-                    }
-                ],
-                "versions": [
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
-                    "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
-                ]
-            }
-        ],
-        "timestamp": "2024-01-07T15:17:19.511222"
-    }
-}
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
deleted file mode 100644
index 27e12abd..00000000
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
+++ /dev/null
@@ -1,363 +0,0 @@
-{
-    "Parameters: --nf_core_pipeline taxprofiler": {
-        "content": [
-            {
-                "0": [
-                    "samplesheet.csv:md5,fe3c7ba9e7b7debe07291d6125f9edc7"
-                ],
-                "1": [
-                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
-                ],
-                "2": [
-                    [
-                        "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
-                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
-                    ]
-                ],
-                "3": [
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-                        "experiment_accession": "ERX1234253",
-                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_bytes": "18077",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
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-                        "library_selection": "PCR",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "AMPLICON",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
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-                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
-                        "sample_accession": "SAMEA3687214",
-                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
-                        "sample_description": "American Gut control",
-                        "sample_title": "10317.BLANK.93.3E.r22",
-                        "scientific_name": "metagenome",
-                        "secondary_sample_accession": "ERS994363",
-                        "secondary_study_accession": "ERP012803",
-                        "single_end": true,
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-                        "study_title": "American Gut Project",
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-                        "tax_id": "256318"
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-                        "base_count": "431758",
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-                        "experiment_alias": "F11-N1-05",
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-                        "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb",
-                        "fastq_aspera": "",
-                        "fastq_bytes": "",
-                        "fastq_ftp": "",
-                        "fastq_galaxy": "",
-                        "fastq_md5": "",
-                        "id": "SRX9315476_SRR12848126",
-                        "instrument_model": "Illumina HiSeq 3000",
-                        "instrument_platform": "ILLUMINA",
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-                        "library_selection": "RANDOM PCR",
-                        "library_source": "GENOMIC",
-                        "library_strategy": "Synthetic-Long-Read",
-                        "md5_1": "",
-                        "md5_2": "",
-                        "read_count": "2954",
-                        "run_accession": "SRR12848126",
-                        "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam",
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-                        "secondary_sample_accession": "SRS7540262",
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-                        "single_end": false,
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-                        "study_alias": "PRJNA670070",
-                        "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
-                        "submission_accession": "SRA1145417",
-                        "tax_id": "10092"
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-                        "base_count": "573417800",
-                        "experiment_accession": "SRX17709227",
-                        "experiment_alias": "GSM6601460_r1",
-                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
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-                        "read_count": "11468356",
-                        "run_accession": "SRR21711856",
-                        "run_alias": "GSM6601460_r1",
-                        "sample_accession": "SAMN31021823",
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-                        "sample_title": "sham-treated worms in day 5",
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-                        "read_count": "13558257",
-                        "run_accession": "SRR21711855",
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-                        "sample_description": "PM2.5-treated worms in day 5",
-                        "sample_title": "PM2.5-treated worms in day 5",
-                        "scientific_name": "Caenorhabditis elegans",
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-                        "submission_accession": "SRA1507236",
-                        "tax_id": "6239"
-                    }
-                ],
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-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
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-                "sample_mappings": [
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-                "samplesheet": [
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-                        "experiment_accession": "ERX1234253",
-                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
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-                        "sample_description": "PM2.5-treated worms in day 5",
-                        "sample_title": "PM2.5-treated worms in day 5",
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-        ],
-        "timestamp": "2024-01-07T15:21:54.519934"
-    }
-}
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
deleted file mode 100644
index 60708a54..00000000
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
+++ /dev/null
@@ -1,363 +0,0 @@
-{
-    "Parameters: --nf_core_pipeline viralrecon": {
-        "content": [
-            {
-                "0": [
-                    "samplesheet.csv:md5,99a3fd9fe3c7cad8184b1bbeadd89c45"
-                ],
-                "1": [
-                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
-                ],
-                "2": [
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-                        "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
-                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
-                    ]
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-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
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-                        "library_layout": "PAIRED",
-                        "library_name": "F11-N1-05",
-                        "library_selection": "RANDOM PCR",
-                        "library_source": "GENOMIC",
-                        "library_strategy": "Synthetic-Long-Read",
-                        "md5_1": "",
-                        "md5_2": "",
-                        "read_count": "2954",
-                        "run_accession": "SRR12848126",
-                        "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam",
-                        "sample_accession": "SAMN16455283",
-                        "sample_alias": "F11-N1-05",
-                        "sample_description": "F11-N1-05",
-                        "sample_title": "Longshanks_F11-N1-05",
-                        "scientific_name": "Mus musculus domesticus",
-                        "secondary_sample_accession": "SRS7540262",
-                        "secondary_study_accession": "SRP287769",
-                        "single_end": false,
-                        "study_accession": "PRJNA670070",
-                        "study_alias": "PRJNA670070",
-                        "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
-                        "submission_accession": "SRA1145417",
-                        "tax_id": "10092"
-                    },
-                    {
-                        "base_count": "573417800",
-                        "experiment_accession": "SRX17709227",
-                        "experiment_alias": "GSM6601460_r1",
-                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
-                        "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                        "fastq_bytes": "447377777",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
-                        "id": "SRX17709227_SRR21711856",
-                        "instrument_model": "Illumina HiSeq 4000",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "GSM6601460",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "7cd1402155befc87be338132d1f31f64",
-                        "md5_2": "",
-                        "read_count": "11468356",
-                        "run_accession": "SRR21711856",
-                        "run_alias": "GSM6601460_r1",
-                        "sample_accession": "SAMN31021823",
-                        "sample_alias": "GSM6601460",
-                        "sample_description": "sham-treated worms in day 5",
-                        "sample_title": "sham-treated worms in day 5",
-                        "scientific_name": "Caenorhabditis elegans",
-                        "secondary_sample_accession": "SRS15239723",
-                        "secondary_study_accession": "SRP399678",
-                        "single_end": true,
-                        "study_accession": "PRJNA884373",
-                        "study_alias": "GSE214215",
-                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
-                        "submission_accession": "SRA1507236",
-                        "tax_id": "6239"
-                    },
-                    {
-                        "base_count": "677912850",
-                        "experiment_accession": "SRX17709228",
-                        "experiment_alias": "GSM6601461_r1",
-                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
-                        "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                        "fastq_bytes": "529798447",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
-                        "id": "SRX17709228_SRR21711855",
-                        "instrument_model": "Illumina HiSeq 4000",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "GSM6601461",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
-                        "md5_2": "",
-                        "read_count": "13558257",
-                        "run_accession": "SRR21711855",
-                        "run_alias": "GSM6601461_r1",
-                        "sample_accession": "SAMN31021822",
-                        "sample_alias": "GSM6601461",
-                        "sample_description": "PM2.5-treated worms in day 5",
-                        "sample_title": "PM2.5-treated worms in day 5",
-                        "scientific_name": "Caenorhabditis elegans",
-                        "secondary_sample_accession": "SRS15239724",
-                        "secondary_study_accession": "SRP399678",
-                        "single_end": true,
-                        "study_accession": "PRJNA884373",
-                        "study_alias": "GSE214215",
-                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
-                        "submission_accession": "SRA1507236",
-                        "tax_id": "6239"
-                    }
-                ],
-                "versions": [
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8",
-                    "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
-                ]
-            }
-        ],
-        "timestamp": "2024-01-07T15:04:57.029889"
-    }
-}
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
deleted file mode 100644
index 252392d7..00000000
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
+++ /dev/null
@@ -1,359 +0,0 @@
-{
-    "Parameters: --skip_fastq_download": {
-        "content": [
-            {
-                "0": [
-                    "samplesheet.csv:md5,eb18025bb1cb97a4fe399ca16757d2db"
-                ],
-                "1": [
-                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
-                ],
-                "2": [
-                    [
-                        "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
-                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
-                    ]
-                ],
-                "3": [
-                    {
-                        "base_count": "35658",
-                        "experiment_accession": "ERX1234253",
-                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_bytes": "18077",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "10317.BLANK.93.3E.r22",
-                        "library_selection": "PCR",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "AMPLICON",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "read_count": "283",
-                        "run_accession": "ERR1160846",
-                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
-                        "sample_accession": "SAMEA3687214",
-                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
-                        "sample_description": "American Gut control",
-                        "sample_title": "10317.BLANK.93.3E.r22",
-                        "scientific_name": "metagenome",
-                        "secondary_sample_accession": "ERS994363",
-                        "secondary_study_accession": "ERP012803",
-                        "single_end": true,
-                        "study_accession": "PRJEB11419",
-                        "study_alias": "qiita_sid_10317",
-                        "study_title": "American Gut Project",
-                        "submission_accession": "ERA541392",
-                        "tax_id": "256318"
-                    },
-                    {
-                        "base_count": "431758",
-                        "experiment_accession": "SRX9315476",
-                        "experiment_alias": "F11-N1-05",
-                        "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
-                        "fastq_1": "",
-                        "fastq_2": "",
-                        "fastq_aspera": "",
-                        "fastq_bytes": "",
-                        "fastq_ftp": "",
-                        "fastq_galaxy": "",
-                        "fastq_md5": "",
-                        "id": "SRX9315476_SRR12848126",
-                        "instrument_model": "Illumina HiSeq 3000",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "PAIRED",
-                        "library_name": "F11-N1-05",
-                        "library_selection": "RANDOM PCR",
-                        "library_source": "GENOMIC",
-                        "library_strategy": "Synthetic-Long-Read",
-                        "md5_1": "",
-                        "md5_2": "",
-                        "read_count": "2954",
-                        "run_accession": "SRR12848126",
-                        "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam",
-                        "sample_accession": "SAMN16455283",
-                        "sample_alias": "F11-N1-05",
-                        "sample_description": "F11-N1-05",
-                        "sample_title": "Longshanks_F11-N1-05",
-                        "scientific_name": "Mus musculus domesticus",
-                        "secondary_sample_accession": "SRS7540262",
-                        "secondary_study_accession": "SRP287769",
-                        "single_end": false,
-                        "study_accession": "PRJNA670070",
-                        "study_alias": "PRJNA670070",
-                        "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
-                        "submission_accession": "SRA1145417",
-                        "tax_id": "10092"
-                    },
-                    {
-                        "base_count": "573417800",
-                        "experiment_accession": "SRX17709227",
-                        "experiment_alias": "GSM6601460_r1",
-                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
-                        "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                        "fastq_bytes": "447377777",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
-                        "id": "SRX17709227_SRR21711856",
-                        "instrument_model": "Illumina HiSeq 4000",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "GSM6601460",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "7cd1402155befc87be338132d1f31f64",
-                        "md5_2": "",
-                        "read_count": "11468356",
-                        "run_accession": "SRR21711856",
-                        "run_alias": "GSM6601460_r1",
-                        "sample_accession": "SAMN31021823",
-                        "sample_alias": "GSM6601460",
-                        "sample_description": "sham-treated worms in day 5",
-                        "sample_title": "sham-treated worms in day 5",
-                        "scientific_name": "Caenorhabditis elegans",
-                        "secondary_sample_accession": "SRS15239723",
-                        "secondary_study_accession": "SRP399678",
-                        "single_end": true,
-                        "study_accession": "PRJNA884373",
-                        "study_alias": "GSE214215",
-                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
-                        "submission_accession": "SRA1507236",
-                        "tax_id": "6239"
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-                        "base_count": "677912850",
-                        "experiment_accession": "SRX17709228",
-                        "experiment_alias": "GSM6601461_r1",
-                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
-                        "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                        "fastq_bytes": "529798447",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
-                        "id": "SRX17709228_SRR21711855",
-                        "instrument_model": "Illumina HiSeq 4000",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "GSM6601461",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
-                        "md5_2": "",
-                        "read_count": "13558257",
-                        "run_accession": "SRR21711855",
-                        "run_alias": "GSM6601461_r1",
-                        "sample_accession": "SAMN31021822",
-                        "sample_alias": "GSM6601461",
-                        "sample_description": "PM2.5-treated worms in day 5",
-                        "sample_title": "PM2.5-treated worms in day 5",
-                        "scientific_name": "Caenorhabditis elegans",
-                        "secondary_sample_accession": "SRS15239724",
-                        "secondary_study_accession": "SRP399678",
-                        "single_end": true,
-                        "study_accession": "PRJNA884373",
-                        "study_alias": "GSE214215",
-                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
-                        "submission_accession": "SRA1507236",
-                        "tax_id": "6239"
-                    }
-                ],
-                "4": [
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
-                ],
-                "mappings": [
-                    "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296"
-                ],
-                "sample_mappings": [
-                    [
-                        "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c",
-                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
-                    ]
-                ],
-                "samplesheet": [
-                    "samplesheet.csv:md5,eb18025bb1cb97a4fe399ca16757d2db"
-                ],
-                "sra_metadata": [
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-                        "base_count": "35658",
-                        "experiment_accession": "ERX1234253",
-                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_bytes": "18077",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
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-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "10317.BLANK.93.3E.r22",
-                        "library_selection": "PCR",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "AMPLICON",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "read_count": "283",
-                        "run_accession": "ERR1160846",
-                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
-                        "sample_accession": "SAMEA3687214",
-                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
-                        "sample_description": "American Gut control",
-                        "sample_title": "10317.BLANK.93.3E.r22",
-                        "scientific_name": "metagenome",
-                        "secondary_sample_accession": "ERS994363",
-                        "secondary_study_accession": "ERP012803",
-                        "single_end": true,
-                        "study_accession": "PRJEB11419",
-                        "study_alias": "qiita_sid_10317",
-                        "study_title": "American Gut Project",
-                        "submission_accession": "ERA541392",
-                        "tax_id": "256318"
-                    },
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-                        "base_count": "431758",
-                        "experiment_accession": "SRX9315476",
-                        "experiment_alias": "F11-N1-05",
-                        "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
-                        "fastq_1": "",
-                        "fastq_2": "",
-                        "fastq_aspera": "",
-                        "fastq_bytes": "",
-                        "fastq_ftp": "",
-                        "fastq_galaxy": "",
-                        "fastq_md5": "",
-                        "id": "SRX9315476_SRR12848126",
-                        "instrument_model": "Illumina HiSeq 3000",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "PAIRED",
-                        "library_name": "F11-N1-05",
-                        "library_selection": "RANDOM PCR",
-                        "library_source": "GENOMIC",
-                        "library_strategy": "Synthetic-Long-Read",
-                        "md5_1": "",
-                        "md5_2": "",
-                        "read_count": "2954",
-                        "run_accession": "SRR12848126",
-                        "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam",
-                        "sample_accession": "SAMN16455283",
-                        "sample_alias": "F11-N1-05",
-                        "sample_description": "F11-N1-05",
-                        "sample_title": "Longshanks_F11-N1-05",
-                        "scientific_name": "Mus musculus domesticus",
-                        "secondary_sample_accession": "SRS7540262",
-                        "secondary_study_accession": "SRP287769",
-                        "single_end": false,
-                        "study_accession": "PRJNA670070",
-                        "study_alias": "PRJNA670070",
-                        "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species",
-                        "submission_accession": "SRA1145417",
-                        "tax_id": "10092"
-                    },
-                    {
-                        "base_count": "573417800",
-                        "experiment_accession": "SRX17709227",
-                        "experiment_alias": "GSM6601460_r1",
-                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
-                        "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                        "fastq_bytes": "447377777",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz",
-                        "fastq_md5": "7cd1402155befc87be338132d1f31f64",
-                        "id": "SRX17709227_SRR21711856",
-                        "instrument_model": "Illumina HiSeq 4000",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "GSM6601460",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "7cd1402155befc87be338132d1f31f64",
-                        "md5_2": "",
-                        "read_count": "11468356",
-                        "run_accession": "SRR21711856",
-                        "run_alias": "GSM6601460_r1",
-                        "sample_accession": "SAMN31021823",
-                        "sample_alias": "GSM6601460",
-                        "sample_description": "sham-treated worms in day 5",
-                        "sample_title": "sham-treated worms in day 5",
-                        "scientific_name": "Caenorhabditis elegans",
-                        "secondary_sample_accession": "SRS15239723",
-                        "secondary_study_accession": "SRP399678",
-                        "single_end": true,
-                        "study_accession": "PRJNA884373",
-                        "study_alias": "GSE214215",
-                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
-                        "submission_accession": "SRA1507236",
-                        "tax_id": "6239"
-                    },
-                    {
-                        "base_count": "677912850",
-                        "experiment_accession": "SRX17709228",
-                        "experiment_alias": "GSM6601461_r1",
-                        "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq",
-                        "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                        "fastq_bytes": "529798447",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz",
-                        "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83",
-                        "id": "SRX17709228_SRR21711855",
-                        "instrument_model": "Illumina HiSeq 4000",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "GSM6601461",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83",
-                        "md5_2": "",
-                        "read_count": "13558257",
-                        "run_accession": "SRR21711855",
-                        "run_alias": "GSM6601461_r1",
-                        "sample_accession": "SAMN31021822",
-                        "sample_alias": "GSM6601461",
-                        "sample_description": "PM2.5-treated worms in day 5",
-                        "sample_title": "PM2.5-treated worms in day 5",
-                        "scientific_name": "Caenorhabditis elegans",
-                        "secondary_sample_accession": "SRS15239724",
-                        "secondary_study_accession": "SRP399678",
-                        "single_end": true,
-                        "study_accession": "PRJNA884373",
-                        "study_alias": "GSE214215",
-                        "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans",
-                        "submission_accession": "SRA1507236",
-                        "tax_id": "6239"
-                    }
-                ],
-                "versions": [
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
-                ]
-            }
-        ],
-        "timestamp": "2024-01-07T15:11:52.542678"
-    }
-}
\ No newline at end of file

From 6a0120d07b5866f4674e0cf18ce650085dec5ef0 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 7 Jan 2024 22:53:04 +0000
Subject: [PATCH 629/852] Tidy up tests and configuration

---
 conf/test.config       |  4 ++--
 nf-test.config         | 14 ++++----------
 tests/main.nf.test     |  2 +-
 tests/nextflow.config  |  0
 tests/sra_ids_test.csv |  3 ---
 5 files changed, 7 insertions(+), 16 deletions(-)
 create mode 100644 tests/nextflow.config
 delete mode 100644 tests/sra_ids_test.csv

diff --git a/conf/test.config b/conf/test.config
index 9bfd2adc..7b8941aa 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -20,7 +20,7 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input = "${projectDir}/tests/sra_ids_test.csv"
+    input = "https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv"
 
-    validationSchemaIgnoreParams = 'test_data_base,merge_samplesheet_ids,fastq_ftp_ids,test_data'
+    validationSchemaIgnoreParams = 'test_data_base,fastq_ftp_ids,test_data'
 }
diff --git a/nf-test.config b/nf-test.config
index 76aab204..5721f19d 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -1,16 +1,10 @@
 config {
-    // location for all nf-tests
+    // Location of nf-tests
     testsDir "."
 
-    // nf-test directory including temporary files for each test
+    // nf-test directory used to create temporary files for each test
     workDir "nf-test"
 
-    // location of library folder that is added automatically to the classpath
-    libDir "lib/"
-
-    // location of an optional nextflow.config file specific for executing tests
-    configFile "nextflow.config"
-
-    // run all test with the defined docker profile from the main nextflow.config
-    profile ""
+    // Location of an optional nextflow.config file specific for executing pipeline tests
+    configFile "tests/nextflow.config"
 }
diff --git a/tests/main.nf.test b/tests/main.nf.test
index ac05aea9..6f992505 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -14,7 +14,7 @@ nextflow_pipeline {
                 max_memory = '6.GB'
                 max_time   = '6.h'
                 input      = "$projectDir/tests/sra_ids_test.csv"
-                validationSchemaIgnoreParams = 'test_data_base,merge_samplesheet_ids,fastq_ftp_ids,test_data'
+                validationSchemaIgnoreParams = 'test_data_base,fastq_ftp_ids,test_data'
             }
         }
 
diff --git a/tests/nextflow.config b/tests/nextflow.config
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/sra_ids_test.csv b/tests/sra_ids_test.csv
deleted file mode 100644
index d9a20c22..00000000
--- a/tests/sra_ids_test.csv
+++ /dev/null
@@ -1,3 +0,0 @@
-ERR1160846
-GSE214215
-SRR12848126

From f6510d596e7a7d85f75eb4cccc853ed468f2ef6b Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 7 Jan 2024 22:53:35 +0000
Subject: [PATCH 630/852] Use smaller test data to speed up test runtimes

---
 workflows/sra/tests/main.nf.test                 | 16 ++++++++--------
 .../tests/sra_custom_ena_metadata_fields.nf.test | 12 ++++++------
 .../tests/sra_force_sratools_download.nf.test    | 16 ++++++++--------
 .../tests/sra_nf_core_pipeline_atacseq.nf.test   | 16 ++++++++--------
 .../tests/sra_nf_core_pipeline_rnaseq.nf.test    | 16 ++++++++--------
 .../sra_nf_core_pipeline_taxprofiler.nf.test     | 16 ++++++++--------
 .../sra_nf_core_pipeline_viralrecon.nf.test      | 16 ++++++++--------
 .../sra/tests/sra_skip_fastq_download.nf.test    | 16 ++++++++--------
 8 files changed, 62 insertions(+), 62 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index a57187b1..e3c3025e 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -13,7 +13,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126')
+                input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035")
                 """
             }
             params {
@@ -25,19 +25,19 @@ nextflow_workflow {
             assert workflow.success
 
             with(workflow.out.samplesheet) {
-                assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
-                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+                assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                assert path(get(0)).text.contains('Illumina HiSeq 2500')
             }
 
             with(workflow.out.mappings) {
-                assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
-                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+                assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                assert path(get(0)).text.contains('Illumina HiSeq 2500')
             }
 
             with(workflow.out.sample_mappings) {
-                assert path(get(0)[0]).md5 == "3bc981f0de28023083cdf13691d249d5"
+                assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
             }
         }
     }
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index 008cc258..b8750959 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -13,7 +13,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126')
+                input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035")
                 """
             }
             params {
@@ -28,19 +28,19 @@ nextflow_workflow {
             assert workflow.success
 
             with(workflow.out.samplesheet) {
-                assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
+                assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
                 assert path(get(0)).text.contains('SINGLE')
             }
 
             with(workflow.out.mappings) {
-                assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
+                assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
                 assert path(get(0)).text.contains('SINGLE')
             }
 
             with(workflow.out.sample_mappings) {
-                assert path(get(0)[0]).md5 == "3bc981f0de28023083cdf13691d249d5"
+                assert path(get(0)[0]).md5 == "3b70bc9658eab4ba2f4ec98cb749ac9d"
             }
         }
     }
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index bfb7dfba..5109af7e 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -13,7 +13,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126')
+                input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035")
                 """
             }
             params {
@@ -26,19 +26,19 @@ nextflow_workflow {
             assert workflow.success
 
             with(workflow.out.samplesheet) {
-                assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
-                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+                assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                assert path(get(0)).text.contains('Illumina HiSeq 2500')
             }
 
             with(workflow.out.mappings) {
-                assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
-                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+                assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                assert path(get(0)).text.contains('Illumina HiSeq 2500')
             }
 
             with(workflow.out.sample_mappings) {
-                assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c"
+                assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
             }
         }
     }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index 770915a3..bdd6a572 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -13,7 +13,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126')
+                input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035")
                 """
             }
             params {
@@ -26,19 +26,19 @@ nextflow_workflow {
             assert workflow.success
 
             with(workflow.out.samplesheet) {
-                assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
-                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+                assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                assert path(get(0)).text.contains('Illumina HiSeq 2500')
             }
 
             with(workflow.out.mappings) {
-                assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
-                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+                assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                assert path(get(0)).text.contains('Illumina HiSeq 2500')
             }
 
             with(workflow.out.sample_mappings) {
-                assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c"
+                assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
             }
         }
     }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index cbf42a53..5d8241ab 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -13,7 +13,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126')
+                input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035")
                 """
             }
             params {
@@ -26,19 +26,19 @@ nextflow_workflow {
             assert workflow.success
 
             with(workflow.out.samplesheet) {
-                assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
-                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+                assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                assert path(get(0)).text.contains('Illumina HiSeq 2500')
             }
 
             with(workflow.out.mappings) {
-                assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
-                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+                assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                assert path(get(0)).text.contains('Illumina HiSeq 2500')
             }
 
             with(workflow.out.sample_mappings) {
-                assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c"
+                assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
             }
         }
     }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index db0400c1..5246581e 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -13,7 +13,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126')
+                input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035")
                 """
             }
             params {
@@ -26,19 +26,19 @@ nextflow_workflow {
             assert workflow.success
 
             with(workflow.out.samplesheet) {
-                assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
-                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+                assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                assert path(get(0)).text.contains('Illumina HiSeq 2500')
             }
 
             with(workflow.out.mappings) {
-                assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
-                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+                assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                assert path(get(0)).text.contains('Illumina HiSeq 2500')
             }
 
             with(workflow.out.sample_mappings) {
-                assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c"
+                assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
             }
         }
     }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index e13f83b3..ec57b425 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -13,7 +13,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126')
+                input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035")
                 """
             }
             params {
@@ -26,19 +26,19 @@ nextflow_workflow {
             assert workflow.success
 
             with(workflow.out.samplesheet) {
-                assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
-                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+                assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                assert path(get(0)).text.contains('Illumina HiSeq 2500')
             }
 
             with(workflow.out.mappings) {
-                assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
-                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+                assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                assert path(get(0)).text.contains('Illumina HiSeq 2500')
             }
 
             with(workflow.out.sample_mappings) {
-                assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c"
+                assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
             }
         }
     }
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index f5805367..65a6bc28 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -13,7 +13,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126')
+                input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035")
                 """
             }
             params {
@@ -26,19 +26,19 @@ nextflow_workflow {
             assert workflow.success
 
             with(workflow.out.samplesheet) {
-                assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
-                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+                assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                assert path(get(0)).text.contains('Illumina HiSeq 2500')
             }
 
             with(workflow.out.mappings) {
-                assert path(get(0)).readLines().size() == 5
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"']
-                assert path(get(0)).text.contains('Illumina HiSeq 4000')
+                assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                assert path(get(0)).text.contains('Illumina HiSeq 2500')
             }
 
             with(workflow.out.sample_mappings) {
-                assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c"
+                assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
             }
         }
     }

From 8fc22ecef6d7463befc8036ee05a645e2810d4bd Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 7 Jan 2024 23:06:36 +0000
Subject: [PATCH 631/852] Update pipeline test to load test.config directly

---
 tests/main.nf.test | 13 +++----------
 1 file changed, 3 insertions(+), 10 deletions(-)

diff --git a/tests/main.nf.test b/tests/main.nf.test
index 6f992505..f9ad32e2 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -2,6 +2,7 @@ nextflow_pipeline {
 
     name "Test pipeline"
     script "../main.nf"
+    config "../conf/test.config"
     tag "pipeline"
     tag "pipeline_fetchngs"
 
@@ -9,20 +10,12 @@ nextflow_pipeline {
 
         when {
             params {
-                outdir     = "results"
-                max_cpus   = 2
-                max_memory = '6.GB'
-                max_time   = '6.h'
-                input      = "$projectDir/tests/sra_ids_test.csv"
-                validationSchemaIgnoreParams = 'test_data_base,fastq_ftp_ids,test_data'
+                outdir = "$outputDir"
             }
         }
 
         then {
-            assertAll(
-                { assert workflow.success }
-            )
+            assert workflow.success
         }
     }
-
 }

From 61b36d8437f7efae9674022dd753b758396e7c4d Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Jan 2024 13:34:40 +0000
Subject: [PATCH 632/852] Standardise nf-test env vars and add tap output
 option

---
 .github/workflows/ci.yml | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8917a345..1b4921ce 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -13,7 +13,8 @@ on:
 
 env:
   NXF_ANSI_LOG: false
-  NFTEST_VER: "0.8.3"
+  NFT_VER: "0.8.3"
+  NFT_WORKDIR: "~"
   NFT_DIFF: "icdiff"
   NFT_DIFF_ARGS: "-N --cols 200 -L expected -L observed -t"
 
@@ -83,7 +84,7 @@ jobs:
           path: |
             /usr/local/bin/nf-test
             /home/runner/.nf-test/nf-test.jar
-          key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest
+          key: ${{ runner.os }}-${{ env.NFT_VER }}-nftest
 
       - name: Install nf-test
         if: steps.cache-software.outputs.cache-hit != 'true'
@@ -96,8 +97,12 @@ jobs:
           sudo apt install icdiff
 
       - name: Run nf-test
+        uses: pcolby/tap-summary@v1
+        with:
+          path: >-
+            test.tap
         run: |
-          nf-test test --verbose --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml
+          nf-test test --verbose --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
 
       - name: Output log on failure
         if: failure()

From 25eac030c5e0c9660afa726d3928e8cbbf1ccee0 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Jan 2024 13:34:58 +0000
Subject: [PATCH 633/852] Use env var to evaluate nf-test workDir

---
 nf-test.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf-test.config b/nf-test.config
index 5721f19d..6f5e2c47 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -3,7 +3,7 @@ config {
     testsDir "."
 
     // nf-test directory used to create temporary files for each test
-    workDir "nf-test"
+    workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
 
     // Location of an optional nextflow.config file specific for executing pipeline tests
     configFile "tests/nextflow.config"

From 3255d8fc07d7df5105b5fb2e8210f3e6b9e8693a Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Jan 2024 13:35:25 +0000
Subject: [PATCH 634/852] Bump tower-launch plugin version and switch off
 default tests for GCP

---
 .github/workflows/cloud_tests_full.yml  | 39 ++++++++++++++-----------
 .github/workflows/cloud_tests_small.yml | 39 ++++++++++++++-----------
 2 files changed, 44 insertions(+), 34 deletions(-)

diff --git a/.github/workflows/cloud_tests_full.yml b/.github/workflows/cloud_tests_full.yml
index d0ed0552..522cfc4a 100644
--- a/.github/workflows/cloud_tests_full.yml
+++ b/.github/workflows/cloud_tests_full.yml
@@ -20,62 +20,67 @@ jobs:
     if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' || !github.event.inputs }}
     runs-on: ubuntu-latest
     steps:
-      - uses: seqeralabs/action-tower-launch@v1
+      - uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
           workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/fetchngs/work-${{ github.sha }}"
           run_name: "aws_fetchngs_full"
+          revision: ${{ github.sha }}
           profiles: test_full
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-                "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/fetchngs/results-${{ github.sha }}"
+                "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/fetchngs/results-${{ github.sha }}/"
             }
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
           path: tower_action_*.log
-  run-full-tests-on-gcp:
-    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' || !github.event.inputs }}
+
+  run-full-tests-on-azure:
+    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' || !github.event.inputs }}
     runs-on: ubuntu-latest
     steps:
-      - uses: seqeralabs/action-tower-launch@v1
+      - uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_CE_GCP_CPU }}
-          workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/fetchngs/work-${{ github.sha }}"
-          run_name: "gcp_fetchngs_full"
+          compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }}
+          workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/fetchngs/work-${{ github.sha }}"
+          run_name: "azure_fetchngs_full"
+          revision: ${{ github.sha }}
           profiles: test_full
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-                "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/fetchngs/results-${{ github.sha }}"
+                "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/fetchngs/results-${{ github.sha }}/"
             }
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
           path: tower_action_*.log
-  run-full-tests-on-azure:
-    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' || !github.event.inputs }}
+
+  run-full-tests-on-gcp:
+    if: ${{ github.event.inputs.platform == 'gcp' || !github.event.inputs }}
     runs-on: ubuntu-latest
     steps:
-      - uses: seqeralabs/action-tower-launch@v1
+      - uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }}
-          workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/fetchngs/work-${{ github.sha }}"
-          run_name: "azure_fetchngs_full"
+          compute_env: ${{ secrets.TOWER_CE_GCP_CPU }}
+          workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/fetchngs/work-${{ github.sha }}"
+          run_name: "gcp_fetchngs_full"
+          revision: ${{ github.sha }}
           profiles: test_full
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-                "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/fetchngs/results-${{ github.sha }}"
+                "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/fetchngs/results-${{ github.sha }}/"
             }
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
+          path: tower_action_*.log
\ No newline at end of file
diff --git a/.github/workflows/cloud_tests_small.yml b/.github/workflows/cloud_tests_small.yml
index 12b8daab..e64ab1ef 100644
--- a/.github/workflows/cloud_tests_small.yml
+++ b/.github/workflows/cloud_tests_small.yml
@@ -18,59 +18,64 @@ jobs:
     if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' }}
     runs-on: ubuntu-latest
     steps:
-      - uses: seqeralabs/action-tower-launch@v1
+      - uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
           workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/fetchngs/work-${{ github.sha }}"
           run_name: "aws_fetchngs_small"
+          revision: ${{ github.sha }}
           profiles: test
           parameters: |
             {
-                "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/fetchngs/results-test-${{ github.sha }}"
+                "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/fetchngs/results-test-${{ github.sha }}/"
             }
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
           path: tower_action_*.log
-  run-small-tests-on-gcp:
-    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' }}
+
+  run-small-tests-on-azure:
+    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' }}
     runs-on: ubuntu-latest
     steps:
-      - uses: seqeralabs/action-tower-launch@v1
+      - uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_CE_GCP_CPU }}
-          workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/fetchngs/work-${{ github.sha }}"
-          run_name: "gcp_fetchngs_small"
+          compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }}
+          workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/fetchngs/work-${{ github.sha }}"
+          run_name: "azure_fetchngs_small"
+          revision: ${{ github.sha }}
           profiles: test
           parameters: |
             {
-                "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/fetchngs/results-test-${{ github.sha }}"
+                "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/fetchngs/results-test-${{ github.sha }}/"
             }
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
           path: tower_action_*.log
-  run-small-tests-on-azure:
-    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' }}
+
+  run-small-tests-on-gcp:
+    if: ${{ github.event.inputs.platform == 'gcp' }}
     runs-on: ubuntu-latest
     steps:
-      - uses: seqeralabs/action-tower-launch@v1
+      - uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }}
-          workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/fetchngs/work-${{ github.sha }}"
-          run_name: "azure_fetchngs_small"
+          compute_env: ${{ secrets.TOWER_CE_GCP_CPU }}
+          workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/fetchngs/work-${{ github.sha }}"
+          run_name: "gcp_fetchngs_small"
+          revision: ${{ github.sha }}
           profiles: test
           parameters: |
             {
-                "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/fetchngs/results-test-${{ github.sha }}"
+                "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/fetchngs/results-test-${{ github.sha }}/"
             }
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
+          path: tower_action_*.log
\ No newline at end of file

From 86618c1a19571dbb9b7d285853e8799983dd5226 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Jan 2024 13:46:58 +0000
Subject: [PATCH 635/852] Fix prettier

---
 .github/workflows/cloud_tests_full.yml  | 2 +-
 .github/workflows/cloud_tests_small.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cloud_tests_full.yml b/.github/workflows/cloud_tests_full.yml
index 522cfc4a..2748b542 100644
--- a/.github/workflows/cloud_tests_full.yml
+++ b/.github/workflows/cloud_tests_full.yml
@@ -83,4 +83,4 @@ jobs:
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
\ No newline at end of file
+          path: tower_action_*.log
diff --git a/.github/workflows/cloud_tests_small.yml b/.github/workflows/cloud_tests_small.yml
index e64ab1ef..195eb9d4 100644
--- a/.github/workflows/cloud_tests_small.yml
+++ b/.github/workflows/cloud_tests_small.yml
@@ -78,4 +78,4 @@ jobs:
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
\ No newline at end of file
+          path: tower_action_*.log

From a5f4ec4f251e1fc016ccd7a0772e4eb6943e129c Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Jan 2024 13:47:23 +0000
Subject: [PATCH 636/852] Use SHA in paths to test data used in pipeline

---
 conf/test.config      | 2 +-
 conf/test_full.config | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/test.config b/conf/test.config
index 7b8941aa..4272648c 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -20,7 +20,7 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input = "https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv"
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/testdata/v1.12.0/sra_ids_test.csv'
 
     validationSchemaIgnoreParams = 'test_data_base,fastq_ftp_ids,test_data'
 }
diff --git a/conf/test_full.config b/conf/test_full.config
index c16fda7f..9215d510 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -15,5 +15,5 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test_full.csv'
+    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/bb634bcfef520552e8314dfa3f8a764e1d62f7dc/testdata/v1.12.0/sra_ids_test_full.csv'
 }

From d2ea5cf17cebf708c495cfe2feb7f26890b4c3d0 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Jan 2024 14:21:48 +0000
Subject: [PATCH 637/852] Be more explicit with pipeline tests

---
 tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/main.nf.test b/tests/main.nf.test
index f9ad32e2..c52e98a8 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -2,7 +2,6 @@ nextflow_pipeline {
 
     name "Test pipeline"
     script "../main.nf"
-    config "../conf/test.config"
     tag "pipeline"
     tag "pipeline_fetchngs"
 
@@ -11,6 +10,7 @@ nextflow_pipeline {
         when {
             params {
                 outdir = "$outputDir"
+                input = 'https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/testdata/v1.12.0/sra_ids_test.csv'
             }
         }
 

From 375a4e52d2081d20bad83277b32bbdaf0e29baeb Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Jan 2024 15:45:17 +0000
Subject: [PATCH 638/852] Add --nf_core_pipeline specific tests at the workflow
 level

---
 workflows/sra/tests/main.nf.test                             | 1 +
 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test   | 1 +
 workflows/sra/tests/sra_force_sratools_download.nf.test      | 1 +
 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test     | 1 +
 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test      | 1 +
 workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test | 1 +
 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test  | 1 +
 workflows/sra/tests/sra_skip_fastq_download.nf.test          | 1 +
 8 files changed, 8 insertions(+)

diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index e3c3025e..24dbf9cc 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -26,6 +26,7 @@ nextflow_workflow {
 
             with(workflow.out.samplesheet) {
                 assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
                 assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
                 assert path(get(0)).text.contains('Illumina HiSeq 2500')
             }
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index b8750959..3e88691e 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -29,6 +29,7 @@ nextflow_workflow {
 
             with(workflow.out.samplesheet) {
                 assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
                 assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
                 assert path(get(0)).text.contains('SINGLE')
             }
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index 5109af7e..3db1ae13 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -27,6 +27,7 @@ nextflow_workflow {
 
             with(workflow.out.samplesheet) {
                 assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
                 assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
                 assert path(get(0)).text.contains('Illumina HiSeq 2500')
             }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index bdd6a572..b7c89ec3 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -27,6 +27,7 @@ nextflow_workflow {
 
             with(workflow.out.samplesheet) {
                 assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"replicate"', '"run_accession"']
                 assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
                 assert path(get(0)).text.contains('Illumina HiSeq 2500')
             }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index 5d8241ab..b4ff8467 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -27,6 +27,7 @@ nextflow_workflow {
 
             with(workflow.out.samplesheet) {
                 assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"strandedness"' , '"run_accession"']
                 assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
                 assert path(get(0)).text.contains('Illumina HiSeq 2500')
             }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index 5246581e..9b76b683 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -27,6 +27,7 @@ nextflow_workflow {
 
             with(workflow.out.samplesheet) {
                 assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"fasta"', '"run_accession"']
                 assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
                 assert path(get(0)).text.contains('Illumina HiSeq 2500')
             }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index ec57b425..d2aaf569 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -27,6 +27,7 @@ nextflow_workflow {
 
             with(workflow.out.samplesheet) {
                 assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
                 assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
                 assert path(get(0)).text.contains('Illumina HiSeq 2500')
             }
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index 65a6bc28..249c0387 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -27,6 +27,7 @@ nextflow_workflow {
 
             with(workflow.out.samplesheet) {
                 assert path(get(0)).readLines().size() == 4
+                assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
                 assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
                 assert path(get(0)).text.contains('Illumina HiSeq 2500')
             }

From 5b9348c428d10b6a33bd0df66c0f8cf4319ec364 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Jan 2024 16:00:32 +0000
Subject: [PATCH 639/852] Use pdiff instead of icdiff for nf-test snapshot
 diffs

---
 .github/workflows/ci.yml | 21 ++++++++++++++++-----
 1 file changed, 16 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1b4921ce..b395350f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -15,8 +15,8 @@ env:
   NXF_ANSI_LOG: false
   NFT_VER: "0.8.3"
   NFT_WORKDIR: "~"
-  NFT_DIFF: "icdiff"
-  NFT_DIFF_ARGS: "-N --cols 200 -L expected -L observed -t"
+  NFT_DIFF: "pdiff"
+  NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
@@ -77,6 +77,16 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+          architecture: "x64"
+
+      - name: Install pdiff to see diff between nf-test snapshots
+        run: |
+          python -m pip install --upgrade pip
+          pip install pdiff
+
       - name: Cache nf-test installation
         id: cache-software
         uses: actions/cache@v3
@@ -97,12 +107,13 @@ jobs:
           sudo apt install icdiff
 
       - name: Run nf-test
-        uses: pcolby/tap-summary@v1
+        run: |
+          nf-test test --verbose --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
+
+      - uses: pcolby/tap-summary@v1
         with:
           path: >-
             test.tap
-        run: |
-          nf-test test --verbose --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
 
       - name: Output log on failure
         if: failure()

From e392e376d2fd1a062aed405ba87fbd885ebe17b7 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Jan 2024 17:25:14 +0000
Subject: [PATCH 640/852] Update workflow tests to use assertAll

---
 workflows/sra/tests/main.nf.test              | 30 ++++++++++---------
 .../sra_custom_ena_metadata_fields.nf.test    | 30 ++++++++++---------
 .../tests/sra_force_sratools_download.nf.test | 30 ++++++++++---------
 .../sra_nf_core_pipeline_atacseq.nf.test      | 30 ++++++++++---------
 .../tests/sra_nf_core_pipeline_rnaseq.nf.test | 30 ++++++++++---------
 .../sra_nf_core_pipeline_taxprofiler.nf.test  | 30 ++++++++++---------
 .../sra_nf_core_pipeline_viralrecon.nf.test   | 30 ++++++++++---------
 .../sra/tests/sra_skip_fastq_download.nf.test | 30 ++++++++++---------
 8 files changed, 128 insertions(+), 112 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 24dbf9cc..102b8796 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -24,22 +24,24 @@ nextflow_workflow {
         then {
             assert workflow.success
 
-            with(workflow.out.samplesheet) {
-                assert path(get(0)).readLines().size() == 4
-                assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                assert path(get(0)).text.contains('Illumina HiSeq 2500')
-            }
+            assertAll(
+                with(workflow.out.samplesheet) {
+                    assert path(get(0)).readLines().size() == 4
+                    assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
+                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                }
 
-            with(workflow.out.mappings) {
-                assert path(get(0)).readLines().size() == 4
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                assert path(get(0)).text.contains('Illumina HiSeq 2500')
-            }
+                with(workflow.out.mappings) {
+                    assert path(get(0)).readLines().size() == 4
+                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                }
 
-            with(workflow.out.sample_mappings) {
-                assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
-            }
+                with(workflow.out.sample_mappings) {
+                    assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
+                }
+            )
         }
     }
 }
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index 3e88691e..c5379bee 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -27,22 +27,24 @@ nextflow_workflow {
         then {
             assert workflow.success
 
-            with(workflow.out.samplesheet) {
-                assert path(get(0)).readLines().size() == 4
-                assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                assert path(get(0)).text.contains('SINGLE')
-            }
+            assertAll(
+                with(workflow.out.samplesheet) {
+                    assert path(get(0)).readLines().size() == 4
+                    assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"strandedness"' , '"run_accession"']
+                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                    assert path(get(0)).text.contains('SINGLE')
+                }
 
-            with(workflow.out.mappings) {
-                assert path(get(0)).readLines().size() == 4
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                assert path(get(0)).text.contains('SINGLE')
-            }
+                with(workflow.out.mappings) {
+                    assert path(get(0)).readLines().size() == 4
+                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                    assert path(get(0)).text.contains('SINGLE')
+                }
 
-            with(workflow.out.sample_mappings) {
-                assert path(get(0)[0]).md5 == "3b70bc9658eab4ba2f4ec98cb749ac9d"
-            }
+                with(workflow.out.sample_mappings) {
+                    assert path(get(0)[0]).md5 == "3b70bc9658eab4ba2f4ec98cb749ac9d"
+                }
+            )
         }
     }
 }
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index 3db1ae13..2a821807 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -25,22 +25,24 @@ nextflow_workflow {
         then {
             assert workflow.success
 
-            with(workflow.out.samplesheet) {
-                assert path(get(0)).readLines().size() == 4
-                assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                assert path(get(0)).text.contains('Illumina HiSeq 2500')
-            }
+            assertAll(
+                with(workflow.out.samplesheet) {
+                    assert path(get(0)).readLines().size() == 4
+                    assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
+                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                }
 
-            with(workflow.out.mappings) {
-                assert path(get(0)).readLines().size() == 4
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                assert path(get(0)).text.contains('Illumina HiSeq 2500')
-            }
+                with(workflow.out.mappings) {
+                    assert path(get(0)).readLines().size() == 4
+                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                }
 
-            with(workflow.out.sample_mappings) {
-                assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
-            }
+                with(workflow.out.sample_mappings) {
+                    assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
+                }
+            )
         }
     }
 }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index b7c89ec3..45f8f478 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -25,22 +25,24 @@ nextflow_workflow {
         then {
             assert workflow.success
 
-            with(workflow.out.samplesheet) {
-                assert path(get(0)).readLines().size() == 4
-                assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"replicate"', '"run_accession"']
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                assert path(get(0)).text.contains('Illumina HiSeq 2500')
-            }
+            assertAll(
+                with(workflow.out.samplesheet) {
+                    assert path(get(0)).readLines().size() == 4
+                    assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"replicate"', '"run_accession"']
+                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                }
 
-            with(workflow.out.mappings) {
-                assert path(get(0)).readLines().size() == 4
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                assert path(get(0)).text.contains('Illumina HiSeq 2500')
-            }
+                with(workflow.out.mappings) {
+                    assert path(get(0)).readLines().size() == 4
+                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                }
 
-            with(workflow.out.sample_mappings) {
-                assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
-            }
+                with(workflow.out.sample_mappings) {
+                    assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
+                }
+            )
         }
     }
 }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index b4ff8467..faeee87c 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -25,22 +25,24 @@ nextflow_workflow {
         then {
             assert workflow.success
 
-            with(workflow.out.samplesheet) {
-                assert path(get(0)).readLines().size() == 4
-                assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"strandedness"' , '"run_accession"']
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                assert path(get(0)).text.contains('Illumina HiSeq 2500')
-            }
+            assertAll(
+                with(workflow.out.samplesheet) {
+                    assert path(get(0)).readLines().size() == 4
+                    assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"strandedness"' , '"run_accession"']
+                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                }
 
-            with(workflow.out.mappings) {
-                assert path(get(0)).readLines().size() == 4
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                assert path(get(0)).text.contains('Illumina HiSeq 2500')
-            }
+                with(workflow.out.mappings) {
+                    assert path(get(0)).readLines().size() == 4
+                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                }
 
-            with(workflow.out.sample_mappings) {
-                assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
-            }
+                with(workflow.out.sample_mappings) {
+                    assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
+                }
+            )
         }
     }
 }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index 9b76b683..714d45d9 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -25,22 +25,24 @@ nextflow_workflow {
         then {
             assert workflow.success
 
-            with(workflow.out.samplesheet) {
-                assert path(get(0)).readLines().size() == 4
-                assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"fasta"', '"run_accession"']
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                assert path(get(0)).text.contains('Illumina HiSeq 2500')
-            }
+            assertAll(
+                with(workflow.out.samplesheet) {
+                    assert path(get(0)).readLines().size() == 4
+                    assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"fasta"', '"run_accession"']
+                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                }
 
-            with(workflow.out.mappings) {
-                assert path(get(0)).readLines().size() == 4
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                assert path(get(0)).text.contains('Illumina HiSeq 2500')
-            }
+                with(workflow.out.mappings) {
+                    assert path(get(0)).readLines().size() == 4
+                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                }
 
-            with(workflow.out.sample_mappings) {
-                assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
-            }
+                with(workflow.out.sample_mappings) {
+                    assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
+                }
+            )
         }
     }
 }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index d2aaf569..a5f68cb6 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -25,22 +25,24 @@ nextflow_workflow {
         then {
             assert workflow.success
 
-            with(workflow.out.samplesheet) {
-                assert path(get(0)).readLines().size() == 4
-                assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                assert path(get(0)).text.contains('Illumina HiSeq 2500')
-            }
+            assertAll(
+                with(workflow.out.samplesheet) {
+                    assert path(get(0)).readLines().size() == 4
+                    assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
+                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                }
 
-            with(workflow.out.mappings) {
-                assert path(get(0)).readLines().size() == 4
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                assert path(get(0)).text.contains('Illumina HiSeq 2500')
-            }
+                with(workflow.out.mappings) {
+                    assert path(get(0)).readLines().size() == 4
+                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                }
 
-            with(workflow.out.sample_mappings) {
-                assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
-            }
+                with(workflow.out.sample_mappings) {
+                    assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
+                }
+            )
         }
     }
 }
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index 249c0387..8cc3bd94 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -25,22 +25,24 @@ nextflow_workflow {
         then {
             assert workflow.success
 
-            with(workflow.out.samplesheet) {
-                assert path(get(0)).readLines().size() == 4
-                assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                assert path(get(0)).text.contains('Illumina HiSeq 2500')
-            }
+            assertAll(
+                with(workflow.out.samplesheet) {
+                    assert path(get(0)).readLines().size() == 4
+                    assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
+                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                }
 
-            with(workflow.out.mappings) {
-                assert path(get(0)).readLines().size() == 4
-                assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                assert path(get(0)).text.contains('Illumina HiSeq 2500')
-            }
+                with(workflow.out.mappings) {
+                    assert path(get(0)).readLines().size() == 4
+                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                }
 
-            with(workflow.out.sample_mappings) {
-                assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
-            }
+                with(workflow.out.sample_mappings) {
+                    assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
+                }
+            )
         }
     }
 }

From 30333c46827cb40b71e9801ca95710125d77095a Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Jan 2024 17:25:43 +0000
Subject: [PATCH 641/852] Add more explicit pipeline tests for file paths and
 samplesheet contents

---
 tests/main.nf.test | 62 ++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 62 insertions(+)

diff --git a/tests/main.nf.test b/tests/main.nf.test
index c52e98a8..d85519f4 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -11,11 +11,73 @@ nextflow_pipeline {
             params {
                 outdir = "$outputDir"
                 input = 'https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/testdata/v1.12.0/sra_ids_test.csv'
+                //input = "$projectDir/ids.csv"
             }
         }
 
         then {
             assert workflow.success
+
+            assertAll(
+                { assert new File("$outputDir/samplesheet/samplesheet.csv").readLines().size() == 15 },
+                { assert new File("$outputDir/samplesheet/samplesheet.csv").readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"'] },
+                { assert new File("$outputDir/samplesheet/samplesheet.csv").readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX024467"', '"DRX026011"', '"ERX1234253"', '"SRX10940790"', '"SRX11047067"', '"SRX17709227"', '"SRX17709228"', '"SRX6725035"', '"SRX9315476"', '"SRX9504942"', '"SRX9504942"', '"SRX9504942"', '"SRX9504942"', '"SRX9626017"'] },
+                { assert new File("$outputDir/samplesheet/samplesheet.csv").text.contains('Illumina HiSeq 2500') },                
+                { assert new File("$outputDir/custom/user-settings.mkfg").exists() },
+                { assert new File("$outputDir/fastq/DRX024467_DRR026872.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/DRX026011_DRR028935_1.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/DRX026011_DRR028935_2.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/ERX1234253_ERR1160846.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX10940790_SRR14593545_1.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX10940790_SRR14593545_2.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX11047067_SRR14709033.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX17709227_SRR21711856.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX17709228_SRR21711855.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX6725035_SRR9984183.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9315476_SRR12848126_1.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9315476_SRR12848126_2.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9504942_SRR13055517_1.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9504942_SRR13055517_2.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9504942_SRR13055518_1.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9504942_SRR13055518_2.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9504942_SRR13055519_1.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9504942_SRR13055519_2.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9504942_SRR13055520_1.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9504942_SRR13055520_2.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9626017_SRR13191702_1.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9626017_SRR13191702_2.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/md5/DRX024467_DRR026872.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/fastq/md5/DRX026011_DRR028935_1.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/fastq/md5/DRX026011_DRR028935_2.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/fastq/md5/ERX1234253_ERR1160846.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/fastq/md5/SRX17709227_SRR21711856.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/fastq/md5/SRX17709228_SRR21711855.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/fastq/md5/SRX6725035_SRR9984183.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/fastq/md5/SRX9504942_SRR13055517_1.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/fastq/md5/SRX9504942_SRR13055517_2.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/fastq/md5/SRX9504942_SRR13055518_1.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/fastq/md5/SRX9504942_SRR13055518_2.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/fastq/md5/SRX9504942_SRR13055519_1.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/fastq/md5/SRX9504942_SRR13055519_2.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/fastq/md5/SRX9504942_SRR13055520_1.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/fastq/md5/SRX9504942_SRR13055520_2.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/fastq/md5/SRX9626017_SRR13191702_1.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/fastq/md5/SRX9626017_SRR13191702_2.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/metadata/DRR026872.runinfo_ftp.tsv").exists() },
+                { assert new File("$outputDir/metadata/DRR028935.runinfo_ftp.tsv").exists() },
+                { assert new File("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv").exists() },
+                { assert new File("$outputDir/metadata/GSE214215.runinfo_ftp.tsv").exists() },
+                { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
+                { assert new File("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv").exists() },
+                { assert new File("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv").exists() },
+                { assert new File("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv").exists() },
+                { assert new File("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv").exists() },
+                { assert new File("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv").exists() },
+                { assert new File("$outputDir/pipeline_info/fetchngs_mqc_versions.yml").exists() },
+                { assert new File("$outputDir/samplesheet/id_mappings.csv").exists() },
+                { assert new File("$outputDir/samplesheet/multiqc_config.yml").exists() },
+                { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
+            )
         }
     }
 }

From a367b4b0d5ad86c916ecb6aad9c83ff93f8936b6 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Jan 2024 17:26:07 +0000
Subject: [PATCH 642/852] Remove comments

---
 tests/main.nf.test | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/main.nf.test b/tests/main.nf.test
index d85519f4..b79f1cc2 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -11,7 +11,6 @@ nextflow_pipeline {
             params {
                 outdir = "$outputDir"
                 input = 'https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/testdata/v1.12.0/sra_ids_test.csv'
-                //input = "$projectDir/ids.csv"
             }
         }
 

From b31ab040e4beea8609d9569620f77da7a8340bab Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Jan 2024 17:58:55 +0000
Subject: [PATCH 643/852] Use closures for with statements in assertAll blocks

---
 workflows/sra/tests/main.nf.test              | 34 +++++++++++--------
 .../sra_custom_ena_metadata_fields.nf.test    | 34 +++++++++++--------
 .../tests/sra_force_sratools_download.nf.test | 34 +++++++++++--------
 .../sra_nf_core_pipeline_atacseq.nf.test      | 34 +++++++++++--------
 .../tests/sra_nf_core_pipeline_rnaseq.nf.test | 34 +++++++++++--------
 .../sra_nf_core_pipeline_taxprofiler.nf.test  | 34 +++++++++++--------
 .../sra_nf_core_pipeline_viralrecon.nf.test   | 34 +++++++++++--------
 .../sra/tests/sra_skip_fastq_download.nf.test | 34 +++++++++++--------
 8 files changed, 152 insertions(+), 120 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 102b8796..902debe6 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -25,21 +25,25 @@ nextflow_workflow {
             assert workflow.success
 
             assertAll(
-                with(workflow.out.samplesheet) {
-                    assert path(get(0)).readLines().size() == 4
-                    assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
-                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
-                }
-
-                with(workflow.out.mappings) {
-                    assert path(get(0)).readLines().size() == 4
-                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
-                }
-
-                with(workflow.out.sample_mappings) {
-                    assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
+                {
+                    with(workflow.out.samplesheet) {
+                        assert path(get(0)).readLines().size() == 4
+                        assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
+                        assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                        assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                    }
+                },
+                {
+                    with(workflow.out.mappings) {
+                        assert path(get(0)).readLines().size() == 4
+                        assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                        assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                    }
+                },
+                {
+                    with(workflow.out.sample_mappings) {
+                        assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
+                    }
                 }
             )
         }
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index c5379bee..433288f9 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -28,21 +28,25 @@ nextflow_workflow {
             assert workflow.success
 
             assertAll(
-                with(workflow.out.samplesheet) {
-                    assert path(get(0)).readLines().size() == 4
-                    assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"strandedness"' , '"run_accession"']
-                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                    assert path(get(0)).text.contains('SINGLE')
-                }
-
-                with(workflow.out.mappings) {
-                    assert path(get(0)).readLines().size() == 4
-                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                    assert path(get(0)).text.contains('SINGLE')
-                }
-
-                with(workflow.out.sample_mappings) {
-                    assert path(get(0)[0]).md5 == "3b70bc9658eab4ba2f4ec98cb749ac9d"
+                {
+                    with(workflow.out.samplesheet) {
+                        assert path(get(0)).readLines().size() == 4
+                        assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"strandedness"' , '"run_accession"']
+                        assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                        assert path(get(0)).text.contains('SINGLE')
+                    }
+                },
+                {
+                    with(workflow.out.mappings) {
+                        assert path(get(0)).readLines().size() == 4
+                        assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                        assert path(get(0)).text.contains('SINGLE')
+                    }
+                },
+                {
+                    with(workflow.out.sample_mappings) {
+                        assert path(get(0)[0]).md5 == "3b70bc9658eab4ba2f4ec98cb749ac9d"
+                    }
                 }
             )
         }
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index 2a821807..2019be08 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -26,21 +26,25 @@ nextflow_workflow {
             assert workflow.success
 
             assertAll(
-                with(workflow.out.samplesheet) {
-                    assert path(get(0)).readLines().size() == 4
-                    assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
-                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
-                }
-
-                with(workflow.out.mappings) {
-                    assert path(get(0)).readLines().size() == 4
-                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
-                }
-
-                with(workflow.out.sample_mappings) {
-                    assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
+                {
+                    with(workflow.out.samplesheet) {
+                        assert path(get(0)).readLines().size() == 4
+                        assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
+                        assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                        assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                    }
+                },
+                {
+                    with(workflow.out.mappings) {
+                        assert path(get(0)).readLines().size() == 4
+                        assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                        assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                    }
+                },
+                {
+                    with(workflow.out.sample_mappings) {
+                        assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
+                    }
                 }
             )
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index 45f8f478..46e4eed8 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -26,21 +26,25 @@ nextflow_workflow {
             assert workflow.success
 
             assertAll(
-                with(workflow.out.samplesheet) {
-                    assert path(get(0)).readLines().size() == 4
-                    assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"replicate"', '"run_accession"']
-                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
-                }
-
-                with(workflow.out.mappings) {
-                    assert path(get(0)).readLines().size() == 4
-                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
-                }
-
-                with(workflow.out.sample_mappings) {
-                    assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
+                {
+                    with(workflow.out.samplesheet) {
+                        assert path(get(0)).readLines().size() == 4
+                        assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"replicate"', '"run_accession"']
+                        assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                        assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                    }
+                },
+                {
+                    with(workflow.out.mappings) {
+                        assert path(get(0)).readLines().size() == 4
+                        assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                        assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                    }
+                },
+                {
+                    with(workflow.out.sample_mappings) {
+                        assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
+                    }
                 }
             )
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index faeee87c..f24d2648 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -26,21 +26,25 @@ nextflow_workflow {
             assert workflow.success
 
             assertAll(
-                with(workflow.out.samplesheet) {
-                    assert path(get(0)).readLines().size() == 4
-                    assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"strandedness"' , '"run_accession"']
-                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
-                }
-
-                with(workflow.out.mappings) {
-                    assert path(get(0)).readLines().size() == 4
-                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
-                }
-
-                with(workflow.out.sample_mappings) {
-                    assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
+                {
+                    with(workflow.out.samplesheet) {
+                        assert path(get(0)).readLines().size() == 4
+                        assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"strandedness"' , '"run_accession"']
+                        assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                        assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                    }
+                },
+                {
+                    with(workflow.out.mappings) {
+                        assert path(get(0)).readLines().size() == 4
+                        assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                        assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                    }
+                },
+                {
+                    with(workflow.out.sample_mappings) {
+                        assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
+                    }
                 }
             )
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index 714d45d9..447e8c6e 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -26,21 +26,25 @@ nextflow_workflow {
             assert workflow.success
 
             assertAll(
-                with(workflow.out.samplesheet) {
-                    assert path(get(0)).readLines().size() == 4
-                    assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"fasta"', '"run_accession"']
-                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
-                }
-
-                with(workflow.out.mappings) {
-                    assert path(get(0)).readLines().size() == 4
-                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
-                }
-
-                with(workflow.out.sample_mappings) {
-                    assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
+                {
+                    with(workflow.out.samplesheet) {
+                        assert path(get(0)).readLines().size() == 4
+                        assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"fasta"', '"run_accession"']
+                        assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                        assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                    }
+                },
+                {
+                    with(workflow.out.mappings) {
+                        assert path(get(0)).readLines().size() == 4
+                        assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                        assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                    }
+                },
+                {
+                    with(workflow.out.sample_mappings) {
+                        assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
+                    }
                 }
             )
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index a5f68cb6..9b27c0a5 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -26,21 +26,25 @@ nextflow_workflow {
             assert workflow.success
 
             assertAll(
-                with(workflow.out.samplesheet) {
-                    assert path(get(0)).readLines().size() == 4
-                    assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
-                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
-                }
-
-                with(workflow.out.mappings) {
-                    assert path(get(0)).readLines().size() == 4
-                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
-                }
-
-                with(workflow.out.sample_mappings) {
-                    assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
+                { 
+                    with(workflow.out.samplesheet) {
+                        assert path(get(0)).readLines().size() == 4
+                        assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
+                        assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                        assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                    }
+                },
+                {
+                    with(workflow.out.mappings) {
+                        assert path(get(0)).readLines().size() == 4
+                        assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                        assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                    }
+                },
+                {
+                    with(workflow.out.sample_mappings) {
+                        assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
+                    }
                 }
             )
         }
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index 8cc3bd94..1a3ab733 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -26,21 +26,25 @@ nextflow_workflow {
             assert workflow.success
 
             assertAll(
-                with(workflow.out.samplesheet) {
-                    assert path(get(0)).readLines().size() == 4
-                    assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
-                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
-                }
-
-                with(workflow.out.mappings) {
-                    assert path(get(0)).readLines().size() == 4
-                    assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                    assert path(get(0)).text.contains('Illumina HiSeq 2500')
-                }
-
-                with(workflow.out.sample_mappings) {
-                    assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
+                { 
+                    with(workflow.out.samplesheet) {
+                        assert path(get(0)).readLines().size() == 4
+                        assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
+                        assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                        assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                    } 
+                },
+                { 
+                    with(workflow.out.mappings) {
+                        assert path(get(0)).readLines().size() == 4
+                        assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                        assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                    } 
+                },
+                { 
+                    with(workflow.out.sample_mappings) {
+                        assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
+                    } 
                 }
             )
         }

From c135899c0a741650457d2b78495f6231fe7219e0 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Jan 2024 18:00:14 +0000
Subject: [PATCH 644/852] Fix ECLint

---
 tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/main.nf.test b/tests/main.nf.test
index b79f1cc2..21c6ac8b 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -21,7 +21,7 @@ nextflow_pipeline {
                 { assert new File("$outputDir/samplesheet/samplesheet.csv").readLines().size() == 15 },
                 { assert new File("$outputDir/samplesheet/samplesheet.csv").readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"'] },
                 { assert new File("$outputDir/samplesheet/samplesheet.csv").readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX024467"', '"DRX026011"', '"ERX1234253"', '"SRX10940790"', '"SRX11047067"', '"SRX17709227"', '"SRX17709228"', '"SRX6725035"', '"SRX9315476"', '"SRX9504942"', '"SRX9504942"', '"SRX9504942"', '"SRX9504942"', '"SRX9626017"'] },
-                { assert new File("$outputDir/samplesheet/samplesheet.csv").text.contains('Illumina HiSeq 2500') },                
+                { assert new File("$outputDir/samplesheet/samplesheet.csv").text.contains('Illumina HiSeq 2500') },
                 { assert new File("$outputDir/custom/user-settings.mkfg").exists() },
                 { assert new File("$outputDir/fastq/DRX024467_DRR026872.fastq.gz").exists() },
                 { assert new File("$outputDir/fastq/DRX026011_DRR028935_1.fastq.gz").exists() },

From 20769af129780bb304db51f1d38543702ed2b44a Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Jan 2024 18:08:36 +0000
Subject: [PATCH 645/852] Update all nf-core modules and subworkflows

---
 modules.json                                  |  28 +-
 .../sratoolsncbisettings/environment.yml      |   7 +
 .../custom/sratoolsncbisettings/main.nf       |   2 +-
 .../custom/sratoolsncbisettings/meta.yml      |   4 +-
 .../sratoolsncbisettings/nextflow.config      |   0
 .../sratools/fasterqdump/environment.yml      |   8 +
 modules/nf-core/sratools/fasterqdump/main.nf  |  12 +-
 modules/nf-core/sratools/fasterqdump/meta.yml |  14 +-
 .../sratools/fasterqdump/nextflow.config      |  10 -
 .../fasterqdump/sratools-fasterqdump.diff     |  36 --
 .../sratools/fasterqdump/tests/main.nf.test   |   4 +-
 .../fasterqdump/tests/main.nf.test.snap       |   4 +-
 .../nf-core/sratools/prefetch/environment.yml |   7 +
 modules/nf-core/sratools/prefetch/main.nf     |  13 +-
 modules/nf-core/sratools/prefetch/meta.yml    |  16 +-
 .../nf-core/sratools/prefetch/nextflow.config |   8 -
 modules/nf-core/untar/environment.yml         |   9 +
 modules/nf-core/untar/main.nf                 |   2 +-
 modules/nf-core/untar/meta.yml                |   5 +
 modules/nf-core/untar/tests/main.nf.test      |  77 +++
 modules/nf-core/untar/tests/main.nf.test.snap | 513 ++++++++++++++++++
 modules/nf-core/untar/tests/tags.yml          |   2 +
 .../meta.yml                                  |  13 +-
 .../nextflow.config                           |   3 -
 .../nf-core/nextflowpipelineutils/main.nf     | 126 -----
 .../nf-core/nextflowpipelineutils/meta.yml    |  34 --
 .../tests/main.functions.nf.test              |  71 ---
 .../tests/main.functions.nf.test.snap         |  12 -
 .../tests/main.workflow.nf.test               | 104 ----
 .../tests/main.workflow.nf.test.snap          |  44 --
 .../tests/nextflow.config                     |   9 -
 .../nf-core/nfcore_pipeline_utils/main.nf     | 311 -----------
 .../nf-core/nfcore_pipeline_utils/meta.yml    |  17 -
 .../tests/main.function.nf.test               | 120 ----
 .../tests/main.function.nf.test.snap          |  78 ---
 .../tests/main.workflow.nf.test               |  33 --
 .../tests/nextflow.config                     |   9 -
 .../nf-core/nfvalidation_plugin_utils/main.nf |  62 ---
 .../nfvalidation_plugin_utils/meta.yml        |  49 --
 .../tests/main.nf.test                        | 199 -------
 .../tests/main.nf.test.snap                   |  26 -
 .../tests/nextflow_schema.json                |  96 ----
 42 files changed, 690 insertions(+), 1507 deletions(-)
 create mode 100644 modules/nf-core/custom/sratoolsncbisettings/environment.yml
 delete mode 100644 modules/nf-core/custom/sratoolsncbisettings/nextflow.config
 create mode 100644 modules/nf-core/sratools/fasterqdump/environment.yml
 delete mode 100644 modules/nf-core/sratools/fasterqdump/nextflow.config
 delete mode 100644 modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff
 create mode 100644 modules/nf-core/sratools/prefetch/environment.yml
 delete mode 100644 modules/nf-core/sratools/prefetch/nextflow.config
 create mode 100644 modules/nf-core/untar/environment.yml
 create mode 100644 modules/nf-core/untar/tests/main.nf.test
 create mode 100644 modules/nf-core/untar/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/untar/tests/tags.yml
 delete mode 100644 subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config
 delete mode 100644 subworkflows/nf-core/nextflowpipelineutils/main.nf
 delete mode 100644 subworkflows/nf-core/nextflowpipelineutils/meta.yml
 delete mode 100644 subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test
 delete mode 100644 subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test.snap
 delete mode 100644 subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test
 delete mode 100644 subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test.snap
 delete mode 100644 subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config
 delete mode 100644 subworkflows/nf-core/nfcore_pipeline_utils/main.nf
 delete mode 100644 subworkflows/nf-core/nfcore_pipeline_utils/meta.yml
 delete mode 100644 subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test
 delete mode 100644 subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test.snap
 delete mode 100644 subworkflows/nf-core/nfcore_pipeline_utils/tests/main.workflow.nf.test
 delete mode 100644 subworkflows/nf-core/nfcore_pipeline_utils/tests/nextflow.config
 delete mode 100644 subworkflows/nf-core/nfvalidation_plugin_utils/main.nf
 delete mode 100644 subworkflows/nf-core/nfvalidation_plugin_utils/meta.yml
 delete mode 100644 subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test
 delete mode 100644 subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test.snap
 delete mode 100644 subworkflows/nf-core/nfvalidation_plugin_utils/tests/nextflow_schema.json

diff --git a/modules.json b/modules.json
index 81312b77..59b7e9c4 100644
--- a/modules.json
+++ b/modules.json
@@ -7,23 +7,22 @@
                 "nf-core": {
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
-                        "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5",
-                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"],
-                        "patch": "modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff"
+                        "git_sha": "b1d2002587ed81dcd0f4b4ffa79fcdbda59b4e80",
+                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/prefetch": {
                         "branch": "master",
-                        "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5",
+                        "git_sha": "b1d2002587ed81dcd0f4b4ffa79fcdbda59b4e80",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     }
                 }
@@ -32,22 +31,7 @@
                 "nf-core": {
                     "fastq_download_prefetch_fasterqdump_sratools": {
                         "branch": "master",
-                        "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5",
-                        "installed_by": ["subworkflows"]
-                    },
-                    "nextflowpipelineutils": {
-                        "branch": "master",
-                        "git_sha": "1405b3d5078f108f86a2c122846ed2797b4ec8bf",
-                        "installed_by": ["subworkflows"]
-                    },
-                    "nfcore_pipeline_utils": {
-                        "branch": "master",
-                        "git_sha": "b1f3d31bbf14fe83959cc03f98db96c6b4f73b37",
-                        "installed_by": ["subworkflows"]
-                    },
-                    "nfvalidation_plugin_utils": {
-                        "branch": "master",
-                        "git_sha": "a8223a72def6cc46f4652a348feba21845ce68c6",
+                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/custom/sratoolsncbisettings/environment.yml b/modules/nf-core/custom/sratoolsncbisettings/environment.yml
new file mode 100644
index 00000000..5ea32741
--- /dev/null
+++ b/modules/nf-core/custom/sratoolsncbisettings/environment.yml
@@ -0,0 +1,7 @@
+name: sratoolsncbisettings
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::sra-tools=2.11.0
diff --git a/modules/nf-core/custom/sratoolsncbisettings/main.nf b/modules/nf-core/custom/sratoolsncbisettings/main.nf
index 5deb8892..bad6f9cf 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/main.nf
+++ b/modules/nf-core/custom/sratoolsncbisettings/main.nf
@@ -2,7 +2,7 @@ process CUSTOM_SRATOOLSNCBISETTINGS {
     tag 'ncbi-settings'
     label 'process_low'
 
-    conda "bioconda::sra-tools=2.11.0"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' :
         'biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
diff --git a/modules/nf-core/custom/sratoolsncbisettings/meta.yml b/modules/nf-core/custom/sratoolsncbisettings/meta.yml
index 01e98856..8637dd19 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/meta.yml
+++ b/modules/nf-core/custom/sratoolsncbisettings/meta.yml
@@ -13,7 +13,6 @@ tools:
       documentation: https://github.com/ncbi/sra-tools/wiki
       tool_dev_url: https://github.com/ncbi/sra-tools
       licence: "['Public Domain']"
-
 output:
   - versions:
       type: file
@@ -23,6 +22,7 @@ output:
       type: file
       description: An NCBI user settings file.
       pattern: "*.mkfg"
-
 authors:
   - "@Midnighter"
+maintainers:
+  - "@Midnighter"
diff --git a/modules/nf-core/custom/sratoolsncbisettings/nextflow.config b/modules/nf-core/custom/sratoolsncbisettings/nextflow.config
deleted file mode 100644
index e69de29b..00000000
diff --git a/modules/nf-core/sratools/fasterqdump/environment.yml b/modules/nf-core/sratools/fasterqdump/environment.yml
new file mode 100644
index 00000000..4011b691
--- /dev/null
+++ b/modules/nf-core/sratools/fasterqdump/environment.yml
@@ -0,0 +1,8 @@
+name: sratools_fasterqdump
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::sra-tools=3.0.8
+  - conda-forge::pigz=2.6
diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf
index 2c5cc8f6..f86d15b7 100644
--- a/modules/nf-core/sratools/fasterqdump/main.nf
+++ b/modules/nf-core/sratools/fasterqdump/main.nf
@@ -2,7 +2,7 @@ process SRATOOLS_FASTERQDUMP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::sra-tools=3.0.8 conda-forge::pigz=2.6"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:2f4a4c900edd6801ff0068c2b3048b4459d119eb-0' :
         'biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:2f4a4c900edd6801ff0068c2b3048b4459d119eb-0' }"
@@ -24,7 +24,15 @@ process SRATOOLS_FASTERQDUMP {
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def outfile = meta.single_end ? "${prefix}.fastq" : prefix
-    def key_file = certificate ? "--perm ${certificate}" : ''
+    def key_file = ''
+
+    if (certificate.toString().endsWith('.jwt')){
+        key_file += " --perm ${certificate}"
+        }
+    else if (certificate.toString().endsWith('.ngc')){
+        key_file += " --ngc ${certificate}"
+    }
+
     """
     export NCBI_SETTINGS="\$PWD/${ncbi_settings}"
 
diff --git a/modules/nf-core/sratools/fasterqdump/meta.yml b/modules/nf-core/sratools/fasterqdump/meta.yml
index 629bdca5..b5e0175a 100644
--- a/modules/nf-core/sratools/fasterqdump/meta.yml
+++ b/modules/nf-core/sratools/fasterqdump/meta.yml
@@ -11,13 +11,12 @@ tools:
       documentation: https://github.com/ncbi/sra-tools/wiki
       tool_dev_url: https://github.com/ncbi/sra-tools
       licence: ["Public Domain"]
-
 input:
   - meta:
       type: map
       description: >
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
+        Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
+
   - sra:
       type: directory
       description: Directory containing ETL data for the given SRA.
@@ -26,18 +25,20 @@ input:
       type: file
       description: >
         An NCBI user settings file.
+
       pattern: "*.mkfg"
   - certificate:
       type: file
       description: >
         Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit
+
       pattern: "*.cart"
 output:
   - meta:
       type: map
       description: >
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
+        Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
+
   - versions:
       type: file
       description: File containing software versions
@@ -46,6 +47,7 @@ output:
       type: file
       description: Extracted FASTQ file or files if the sequencing reads are paired-end.
       pattern: "*.fastq.gz"
-
 authors:
   - "@Midnighter"
+maintainers:
+  - "@Midnighter"
diff --git a/modules/nf-core/sratools/fasterqdump/nextflow.config b/modules/nf-core/sratools/fasterqdump/nextflow.config
deleted file mode 100644
index f98b140d..00000000
--- a/modules/nf-core/sratools/fasterqdump/nextflow.config
+++ /dev/null
@@ -1,10 +0,0 @@
-process {
-    withName: SRATOOLS_FASTERQDUMP {
-        ext.args = '--split-files --include-technical'
-        publishDir = [
-            path: { "${params.outdir}/fastq" },
-            mode: params.publish_dir_mode,
-            pattern: "*.fastq.gz"
-        ]
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff b/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff
deleted file mode 100644
index 5275d3e4..00000000
--- a/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff
+++ /dev/null
@@ -1,36 +0,0 @@
-Changes in module 'nf-core/sratools/fasterqdump'
---- /dev/null
-+++ modules/nf-core/sratools/fasterqdump/nextflow.config
-@@ -0,0 +1,10 @@
-+process {
-+    withName: SRATOOLS_FASTERQDUMP {
-+        ext.args = '--split-files --include-technical'
-+        publishDir = [
-+            path: { "${params.outdir}/fastq" },
-+            mode: params.publish_dir_mode,
-+            pattern: "*.fastq.gz"
-+        ]
-+    }
-+}
---- modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
-+++ modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
-@@ -8,7 +8,7 @@
-                             "id": "test_single_end",
-                             "single_end": true
-                         },
--                        "test_single_end.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82"
-+                        "test_single_end_1.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82"
-                     ]
-                 ],
-                 "1": [
-@@ -20,7 +20,7 @@
-                             "id": "test_single_end",
-                             "single_end": true
-                         },
--                        "test_single_end.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82"
-+                        "test_single_end_1.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82"
-                     ]
-                 ],
-                 "versions": [
-
-************************************************************
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
index ee4c5844..e194b52a 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
@@ -22,7 +22,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = UNTAR.out.untar.collect{ meta, files -> files }.map{ files -> [ [ id:'test_single_end', single_end:true ], files]}
+                input[0] = UNTAR.out.untar.map{ meta, files -> [ [ id:'test_single_end', single_end:true ], files]}
                 input[1] = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true)
                 input[2] = []
                 """
@@ -53,7 +53,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = UNTAR.out.untar.collect{ meta, files -> files }.map{ files -> [ [ id:'test_paired_end', single_end:false ], files]}
+                input[0] = UNTAR.out.untar.map{ meta, files -> [ [ id:'test_paired_end', single_end:false ], files]}
                 input[1] = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true)
                 input[2] = []
                 """
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
index 77fd6c79..d3bf90f7 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
@@ -8,7 +8,7 @@
                             "id": "test_single_end",
                             "single_end": true
                         },
-                        "test_single_end_1.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82"
+                        "test_single_end.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82"
                     ]
                 ],
                 "1": [
@@ -20,7 +20,7 @@
                             "id": "test_single_end",
                             "single_end": true
                         },
-                        "test_single_end_1.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82"
+                        "test_single_end.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82"
                     ]
                 ],
                 "versions": [
diff --git a/modules/nf-core/sratools/prefetch/environment.yml b/modules/nf-core/sratools/prefetch/environment.yml
new file mode 100644
index 00000000..cfc7d9a8
--- /dev/null
+++ b/modules/nf-core/sratools/prefetch/environment.yml
@@ -0,0 +1,7 @@
+name: sratools_prefetch
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::sra-tools=3.0.8
diff --git a/modules/nf-core/sratools/prefetch/main.nf b/modules/nf-core/sratools/prefetch/main.nf
index fb226962..f12dc68d 100644
--- a/modules/nf-core/sratools/prefetch/main.nf
+++ b/modules/nf-core/sratools/prefetch/main.nf
@@ -2,7 +2,7 @@ process SRATOOLS_PREFETCH {
     tag "$id"
     label 'process_low'
 
-    conda "bioconda::sra-tools=3.0.8"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/sra-tools:3.0.8--h9f5acd7_0' :
         'biocontainers/sra-tools:3.0.8--h9f5acd7_0' }"
@@ -21,7 +21,16 @@ process SRATOOLS_PREFETCH {
 
     shell:
     args = task.ext.args ?: ''
-    args += certificate ? " --perm ${certificate}" : ''
+
+    if (certificate){
+        if (certificate.toString().endsWith('.jwt')){
+            args += " --perm ${certificate}"
+            }
+        else if (certificate.toString().endsWith('.ngc')){
+            args += " --ngc ${certificate}"
+        }
+    }
+
     args2 = task.ext.args2 ?: '5 1 100'  // <num retries> <base delay in seconds> <max delay in seconds>
     template 'retry_with_backoff.sh'
 }
diff --git a/modules/nf-core/sratools/prefetch/meta.yml b/modules/nf-core/sratools/prefetch/meta.yml
index 9817b0b2..ff54229f 100644
--- a/modules/nf-core/sratools/prefetch/meta.yml
+++ b/modules/nf-core/sratools/prefetch/meta.yml
@@ -11,42 +11,46 @@ tools:
       documentation: https://github.com/ncbi/sra-tools/wiki
       tool_dev_url: https://github.com/ncbi/sra-tools
       licence: ["Public Domain"]
-
 input:
   - meta:
       type: map
       description: >
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
+        Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
+
   - id:
       type: string
       description: >
         A string denoting an SRA id.
+
   - ncbi_settings:
       type: file
       description: >
         An NCBI user settings file.
+
       pattern: "*.mkfg"
   - certificate:
       type: file
       description: >
         Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit
+
       pattern: "*.cart"
 output:
   - meta:
       type: map
       description: >
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
+        Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
+
   - sra:
       type: directory
       description: >
         Directory containing the ETL data for the given SRA id.
+
       pattern: "*/*.sra"
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-
 authors:
   - "@Midnighter"
+maintainers:
+  - "@Midnighter"
diff --git a/modules/nf-core/sratools/prefetch/nextflow.config b/modules/nf-core/sratools/prefetch/nextflow.config
deleted file mode 100644
index a2ca8848..00000000
--- a/modules/nf-core/sratools/prefetch/nextflow.config
+++ /dev/null
@@ -1,8 +0,0 @@
-process {
-    withName: SRATOOLS_PREFETCH {
-        publishDir = [
-            path: { "${params.outdir}/sra" },
-            enabled: false
-        ]
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml
new file mode 100644
index 00000000..d6917da3
--- /dev/null
+++ b/modules/nf-core/untar/environment.yml
@@ -0,0 +1,9 @@
+name: untar
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::sed=4.7
+  - conda-forge::grep=3.11
+  - conda-forge::tar=1.34
diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf
index 61461c39..8a75bb95 100644
--- a/modules/nf-core/untar/main.nf
+++ b/modules/nf-core/untar/main.nf
@@ -2,7 +2,7 @@ process UNTAR {
     tag "$archive"
     label 'process_single'
 
-    conda "conda-forge::sed=4.7 conda-forge::grep=3.11 conda-forge::tar=1.34"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
         'nf-core/ubuntu:20.04' }"
diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml
index db241a6e..a9a2110f 100644
--- a/modules/nf-core/untar/meta.yml
+++ b/modules/nf-core/untar/meta.yml
@@ -39,3 +39,8 @@ authors:
   - "@drpatelh"
   - "@matthdsm"
   - "@jfy133"
+maintainers:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@matthdsm"
+  - "@jfy133"
diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test
new file mode 100644
index 00000000..d40db13d
--- /dev/null
+++ b/modules/nf-core/untar/tests/main.nf.test
@@ -0,0 +1,77 @@
+nextflow_process {
+
+    name "Test Process UNTAR"
+    script "../main.nf"
+    process "UNTAR"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "untar"
+
+    test("test_untar") {
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out.untar).match("test_untar") },
+            )
+        }
+
+    }
+
+    test("test_untar_different_output_path") {
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [ [], file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out.untar).match("test_untar_different_output_path") },
+            )
+        }
+
+    }
+
+    test("test_untar_onlyfiles") {
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [ [], file(params.test_data['generic']['tar']['tar_gz'], checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out.untar).match("test_untar_onlyfiles") },
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap
new file mode 100644
index 00000000..146c8678
--- /dev/null
+++ b/modules/nf-core/untar/tests/main.nf.test.snap
@@ -0,0 +1,513 @@
+{
+    "test_untar_different_output_path": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    [
+                        [
+                            [
+                                [
+                                    [
+                                        [
+                                            "s_1_1101.bcl:md5,ad01889e2ff43e2f194224e20bdb600c",
+                                            "s_1_1101.stats:md5,4bbbf103454b37fbc3138fadf1b4446b"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,565384bbe67a694dfd690bae6d1d30c2",
+                                            "s_1_1101.stats:md5,55e5abd8f129ff38ef169873547abdb8"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,650fa58a630a9148835ba79e323d4237",
+                                            "s_1_1101.stats:md5,77403669ca1b05340c390dff64425c1e"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,54471c9e97299cd141e202e204637702",
+                                            "s_1_1101.stats:md5,67b14c9a89b7f8556674a7524d5cfb2d"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,74e4f929fc7476c380fd9d741ddb6700",
+                                            "s_1_1101.stats:md5,5730a4c35463eaa12a06b6758710b98c"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,c785f472f4350c120c02c888c8189590",
+                                            "s_1_1101.stats:md5,fee4ec63895ea81007e06ee6a36ba5e0"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,b7ea50bb25f08d43c301741d77050a9b",
+                                            "s_1_1101.stats:md5,fa7c68f3122c74d14364e6f7b011af70"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,9d5087dc4bcae39d66486363d4f68ecf",
+                                            "s_1_1101.stats:md5,23cdceee4d82c4b8e7c60018b9276ace"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,581e0c5ee94e8f2de14b2b1d8e777530",
+                                            "s_1_1101.stats:md5,9a3536d573c97f66bb56b49463612607"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,296fc026bb34c67bbe2b44845fe0d1de",
+                                            "s_1_1101.stats:md5,a7f57a7770fb9c5ae2a0fb1ef403ec4f"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,2a3ca15531556c36d10d132a9e051de8",
+                                            "s_1_1101.stats:md5,2d0bcdb0a1b51d3d79e415db2ab2d3b1"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,1150d46a2ccd4ac58aee0585d3e4ffd7",
+                                            "s_1_1101.stats:md5,2e97550bd5b5864ffd0565bb7a3f6d40"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,0b85c4b3da0de95e7b862d849c5333ae",
+                                            "s_1_1101.stats:md5,6eab9746fbeb783b0cd70398f44e0c1a"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,e0e9c91f4698804d7a6d1058ef68b34f",
+                                            "s_1_1101.stats:md5,790022cdc7878a02b2ebd166e1ddf0a7"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,38cd0ad4de359e651c8ac0d5777ea625",
+                                            "s_1_1101.stats:md5,a1b1d5ea5371d326abb029774483c5e6"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,b0ddc05c4012ccba24e712a1cfec748f",
+                                            "s_1_1101.stats:md5,af3d232f839d720f76f40ba06caa2987"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,af32fcc5dc3b836cf7a5ba3db85a75dd",
+                                            "s_1_1101.stats:md5,f93f2c09bd4e486c74a5f6e2040f7296"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,54b7428e037ca87816107647d4a3d9db",
+                                            "s_1_1101.stats:md5,e5ac77a72cd7bed5e9bf03cccda0e48c"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,fc8b4eacd493bf3d0b20bc23998dc7ff",
+                                            "s_1_1101.stats:md5,190315e159e2f4bc4c057ded7470dc52"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,9484ecffda489927fce424ac6a44fa9d",
+                                            "s_1_1101.stats:md5,0825feeb457ecc9efcf6f8526ba32311"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,eec59e21036e31c95ce1e847bfb0a9c4",
+                                            "s_1_1101.stats:md5,9acc13f63c98e5a8445e7be70d49222b"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,a9fb24476f87cba4fba68e2b3c3f2c07",
+                                            "s_1_1101.stats:md5,dc0aa7db9790733291c3e6480ca2a0fc"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,ed950b3e82c500927c2e236c9df005c6",
+                                            "s_1_1101.stats:md5,dccb71ec47d1f9d33a192da6d5660a45"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,b3e992025e995ca56b5ea2820144ef47",
+                                            "s_1_1101.stats:md5,a6a829bf2cffb26ac5d9dc3012057699"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,89edc726a5a4e0b4ff8ca3899ed0232b",
+                                            "s_1_1101.stats:md5,5b9b4fd8110577a59b82d0c419519d29"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,4dc696149169f232c451225f563cb5cd",
+                                            "s_1_1101.stats:md5,d3514a71ea3adc60e2943c6b8f6e2598"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,35b992d0318afb7c825ceaa31b0755e6",
+                                            "s_1_1101.stats:md5,2826093acc175c16c3795de7c4ca8f07"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,7bc927f56a362e49c00b5d76ee048901",
+                                            "s_1_1101.stats:md5,e47d862b795fd6b88a31d7d482ab22f6"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,84742233ff2a651626fe9036f27f7cb2",
+                                            "s_1_1101.stats:md5,b78fad11d3c50bc76b722cdc03e3028b"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,3935341c86263a7938e8c49620ef39f8",
+                                            "s_1_1101.stats:md5,cc6585b2daac5354073d150874da9704"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,3627f4fd548bf6e64aaf08fba3a342be",
+                                            "s_1_1101.stats:md5,120ae4831ae004ff7d16728aef36e82f"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,07631014bc35124149fabd80ef19f933",
+                                            "s_1_1101.stats:md5,eadd63d91f47cc6db6b6f0a967a23927"
+                                        ],
+                                        [
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+                                            "s_1_1101.stats:md5,ca89a9def67611a9151c6ce685b7cce1"
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+                                        [
+                                            "s_1_1101.bcl:md5,eb5f71d4741d2f40618756bc72eaf8b4",
+                                            "s_1_1101.stats:md5,90f48501e735e5915b843478e23d1ae2"
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+                                        [
+                                            "s_1_1101.bcl:md5,9bf270fe3f6add1a591ebc24fff10078",
+                                            "s_1_1101.stats:md5,a4e429671d4098034293c638aa655e16"
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+                                        [
+                                            "s_1_1101.bcl:md5,219bedcbd24bae54fe4cf05dae05282c",
+                                            "s_1_1101.stats:md5,dd97525b65b68207137d51fcf19132c7"
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+                                            "s_1_1101.bcl:md5,5163bc00a68fd57ae50cae0b76350892",
+                                            "s_1_1101.stats:md5,b606a5368eff1f012f3ea5d11ccdf2e0"
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+                                        [
+                                            "s_1_1101.bcl:md5,fc429195a5af59a59e0cc4c48e6c05ea",
+                                            "s_1_1101.stats:md5,d809aa19698053f90d639da4dcad8008"
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+                                        [
+                                            "s_1_1101.bcl:md5,383340219a1dd77076a092a64a71a7e4",
+                                            "s_1_1101.stats:md5,b204a5cf256378679ffc906c15cc1bae"
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+                                            "s_1_1101.bcl:md5,0c369540d3e24696cf1f9c55bab69315",
+                                            "s_1_1101.stats:md5,a2bc69a4031a22ce9621dcc623a0bf4b"
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+                                        [
+                                            "s_1_1101.bcl:md5,3127abc8016ba8eb954f8f8015dff387",
+                                            "s_1_1101.stats:md5,5deafff31150b7bf757f814e49a53bc2"
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+                                        [
+                                            "s_1_1101.bcl:md5,045f40c82de676bafec3d59f91376a7a",
+                                            "s_1_1101.stats:md5,890700edc20687c090ef52248c7884b1"
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+                                        [
+                                            "s_1_1101.bcl:md5,78af269aa2b39a1d765703f0a4739a86",
+                                            "s_1_1101.stats:md5,303cf457aa1543a8208544f694cbc531"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,0ab8c781959b783b62888e9274364a46",
+                                            "s_1_1101.stats:md5,2605b0e8322f83aa4d0dae5da4ec7a7a"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,d0cf823ffe352e8b3f75d589544ab617",
+                                            "s_1_1101.stats:md5,efa3c0e01e3db71e12fd961cb2d03739"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,db4ca4ab7a01e03c246f9160c3758d82",
+                                            "s_1_1101.stats:md5,f61550d9e4a90df6b860e68f41f82f60"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,1af39a2c7e5ff20ece91cb8160b51d17",
+                                            "s_1_1101.stats:md5,d0e20879afcaf6dfcd88c73f1c5c78cf"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,4cf7123bb0fffcd79266df03aef01665",
+                                            "s_1_1101.stats:md5,29bff4075109a121b087116b58d7e927"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,aa9980428cb60cd6320f4b48f4dd0d74",
+                                            "s_1_1101.stats:md5,6b0e20bde93133117a8d1a6df3d6f37b"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,0f6e440374e15b9b491d52fb83a8adfe",
+                                            "s_1_1101.stats:md5,55cb5eb0ecdabd23dca39ab8c4607598"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,2c645d7bdaddaa403f6e304d36df9e4b",
+                                            "s_1_1101.stats:md5,53acf33d21f832779b400c2447386ce4"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,3bbf0863b423b770c879203644420206",
+                                            "s_1_1101.stats:md5,579bdc7293cac8c3d7407249cacf4c25"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,6658a08409e81d29cfeb2d096b491985",
+                                            "s_1_1101.stats:md5,bb559ffbea46d612f9933cefa84c4c03"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,1700d9a13d3d4f7643af2943ef838acb",
+                                            "s_1_1101.stats:md5,f01cb6050ebfb15da1e0399ebd791eb4"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,1ac7aa9ffae25eb103f755f33e4a39c6",
+                                            "s_1_1101.stats:md5,0b9d45d7929ccf336d5e5b95373ed3c2"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,812a97af2e983a53226e18c75190b06c",
+                                            "s_1_1101.stats:md5,d2410c7b0e506dab2972e77e2398de1e"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,c981e8e4dcc434956c2b86159da268bc",
+                                            "s_1_1101.stats:md5,e9c826e85361ce673f1f248786c9a611"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,88e09e99a0a4ef3357b203a41b22f77c",
+                                            "s_1_1101.stats:md5,ef06f2e5ad667bbd383f9ed6a05b7b42"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,461c8b146fc8a7938be38689978ecd09",
+                                            "s_1_1101.stats:md5,65115693935da66f9791b27136e22fb0"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,c7b827df5ce20e0f21916fe60860ca3f",
+                                            "s_1_1101.stats:md5,87be73613aeb507847f94d3cac5bb30a"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,7c4cc3dc9c8a1b0f15917b282dfb40ce",
+                                            "s_1_1101.stats:md5,bdd9181fa89debbfafe7b6ea3e064065"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,19f4debaf91e118aca8934517179ac33",
+                                            "s_1_1101.stats:md5,1143082719e136241d21b14a6b19b8a2"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,38aa256ad2d697d84b0b2c0e876a3eba",
+                                            "s_1_1101.stats:md5,64dd82f03df23f7f437eede2671ed4fe"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,b7929970378949571fed922c1b8cab32",
+                                            "s_1_1101.stats:md5,3d6d7985a41629fe196e4342d7fe36aa"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,fb2ed0bf6e89d79624ee78754e773491",
+                                            "s_1_1101.stats:md5,f34940810ff255aee79953496a12716d"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,4f8a8311f5f9c3a7629c1a973a7b280e",
+                                            "s_1_1101.stats:md5,4fd7cd28c09f4e152e7c2ad1ab541cd2"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,9eb46c903d0344e25af51f88cc311d60",
+                                            "s_1_1101.stats:md5,df3abd5f620d9e7f99496098d9fd3f7f"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,3ecbc17f3660e2014b58d7fe70ae62d5",
+                                            "s_1_1101.stats:md5,8e89a13c85a6d6ab3ccd251b66d1f165"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,5d59cc2499a77791233a64f73fe82894",
+                                            "s_1_1101.stats:md5,32ec99cd400f4b80cb26e2fa8e07ece0"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,1c052da47b9ae8554388f0fa3aade482",
+                                            "s_1_1101.stats:md5,d23f438772673688aa7bc92421dc6dce"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,1a52bd4f23130c0c96bc967ccd448a2b",
+                                            "s_1_1101.stats:md5,9b597e3388d59ef1f61aba30ac90ea79"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,8a1e84b79cf3f80794c20e3a0cc84688",
+                                            "s_1_1101.stats:md5,9561f7b6ef4b1849afc72b2bb49792bd"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,75c00111051f3fa95d04286823cb9109",
+                                            "s_1_1101.stats:md5,1fe786cdf8181767deafbd60b3c76610"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,529255d8deee0873ed5565e6d1a2ebda",
+                                            "s_1_1101.stats:md5,3fa7f467e97a75880f32d17b7429d316"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,ea4d960e3d9355d2149da71b88a21df4",
+                                            "s_1_1101.stats:md5,2540fe65586e8e800c1ddd8cddd1e8cd"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,0dfe1fd92a2dce2f23119aa483429744",
+                                            "s_1_1101.stats:md5,78257b2169fb9f0cf40966e06e847e86"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,f692ddc9aa3ab849271d07c666d0b3b9",
+                                            "s_1_1101.stats:md5,aa2ec6a3e3a9c116e34fe74a21e6459e"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,29cc4c239eae7c871c9a1adf92ebdb98",
+                                            "s_1_1101.stats:md5,263184813090acd740a5bf25304aed3a"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,e005af6a84925e326afbfe264241f047",
+                                            "s_1_1101.stats:md5,b6fb20868eebaffcc19daa694a449795"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,02f1a699b1ba9967accccf99a7af3d24",
+                                            "s_1_1101.stats:md5,4f007efacecaf26dc0e0231aede28754"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,df308c72a2dcc655cd95e98f5457187a",
+                                            "s_1_1101.stats:md5,130c4b07f4c14030bab012824cbe34da"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,f3ce10d8d2406b72355023bfa8c96822",
+                                            "s_1_1101.stats:md5,2638f4db393ed5b699ec2ce59ff0ec19"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,cc2f6d675ad1593ff96f734b172d249e",
+                                            "s_1_1101.stats:md5,f5b13f1e1ababc9e1a7a73b0b993cbf1"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,7938a0b21448305a951b023b1845b3a7",
+                                            "s_1_1101.stats:md5,fcd57511adabfc3ba1ac045165330006"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,44879bc6a38df1fee8def61868115041",
+                                            "s_1_1101.stats:md5,517e20e4b58a8023a37f9af62e0e2036"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,8749611e62406a7d2f34c610a55e56af",
+                                            "s_1_1101.stats:md5,8ccf24b3676ef84f2e513be8f2a9f3d1"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,a9846a037611cda3721958088f714c0e",
+                                            "s_1_1101.stats:md5,6438fa5a1892f328cab1605a95d80a3b"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,d6c4a2a726496476eb826532f974ed5f",
+                                            "s_1_1101.stats:md5,8c2c65b5e8b00dbf61ada65252aeb266"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,be3dde6cae7dd85855a6bf295ebfacfe",
+                                            "s_1_1101.stats:md5,93bc13f3b0749b2b8d8bcb0b1199f4f0"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,7c64514735a6cf1565b60647edd17d20",
+                                            "s_1_1101.stats:md5,4a0aa6c49b24f876415e5878cef7f805"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,3983b4043bc9df4b505202a5134ccf03",
+                                            "s_1_1101.stats:md5,1c9d9a8558adc1279ca27c96bc1b9758"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,a0b8d77f116ec95975f9253dcb768136",
+                                            "s_1_1101.stats:md5,c3992b786756e7ec42f65ef4b13b50d4"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,43c95ba35d06bb7c57fbd16f3d1cfd6c",
+                                            "s_1_1101.stats:md5,3cb69d04698c39f97f962e5bf1eea7f0"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,3dbeea0cad7052f19f53ff6f19dd4d90",
+                                            "s_1_1101.stats:md5,58bbc8254f0f5f4a244531e8e9c12a04"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,da56d088996376c898d855b6cd0a7dfc",
+                                            "s_1_1101.stats:md5,9f2d78af6908ce1576b89cdc059844ff"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,7b641a5565f095e9a6ffcad9e4305033",
+                                            "s_1_1101.stats:md5,3ada06c59b4fb41b83ab6abd0979e9fc"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,a3843d397a01d51657825bb652c191e5",
+                                            "s_1_1101.stats:md5,19341e52a4bfc7d9d48e9d2acc68c519"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,048e3ebfc8efeb8012def6b741c9060d",
+                                            "s_1_1101.stats:md5,88bd38deca1e87d700effab1fd099565"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,b340db0e07e829dd5da22371916a1a9e",
+                                            "s_1_1101.stats:md5,e44cfaddcc4ffb968e5b1a2f41ac48a5"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,e6011ec6eabbc2b8792deb283c621ce0",
+                                            "s_1_1101.stats:md5,090875dcd1a431af24bc631333f089c4"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,a08f216e3352345031ed100ec4245082",
+                                            "s_1_1101.stats:md5,97b949ef4b96219e1369f673cf5f8a6c"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,b43337c76fb037dfcf5f8f7bcb3618e5",
+                                            "s_1_1101.stats:md5,ddef585805e79951f69d23ab7354f69b"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,8c61fd004104397b360855e058bbf1bf",
+                                            "s_1_1101.stats:md5,0f8d253816d594dcfea3ccf48c826401"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,594d06310d328b188aa0b3edfff22cb2",
+                                            "s_1_1101.stats:md5,3160bf271b39aeb7590e4fd2984710ba"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,4c9eada67c9d55437211d83e111961d5",
+                                            "s_1_1101.stats:md5,2901b46ab16ec4863d30e4c84ec29c97"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,e03971ae5282f0accc0c1b7374d9ef1b",
+                                            "s_1_1101.stats:md5,60d2a19ce59bf70a21a28555484cead8"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,e1c6f7a06e63d149895d3e48e63df155",
+                                            "s_1_1101.stats:md5,44beb10af847ea3dddaf06dda7031126"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,960a99bf29a8f9d936e9b8582d46c9c6",
+                                            "s_1_1101.stats:md5,544cd1a7aaaa841914b40ece43399334"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,5706679f349fd4a6b6313bc2c41c7a42",
+                                            "s_1_1101.stats:md5,627eea844b26dae033848c2f9f69177b"
+                                        ],
+                                        [
+                                            "s_1_1101.bcl:md5,21da5abc4b0402bbac14b5ab998b0b4f",
+                                            "s_1_1101.stats:md5,515bd140b095ad90473ca7a9a69877ab"
+                                        ],
+                                        "s_1_1101.control:md5,08a72e2198ae95150718e8adf011d105",
+                                        "s_1_1101.filter:md5,3a72bc73b323c8cb0ac5bfeb62d98989"
+                                    ]
+                                ],
+                                [
+                                    "s_1_1101.locs:md5,0827ea802e5257cc5b20e757a33d4c98"
+                                ],
+                                "RTAConfiguration.xml:md5,c7d6e257bc374f142dc64b9d2281d4c9",
+                                "config.xml:md5,9a4cc7ec01fefa2f1ce9bcb45bbad6e9"
+                            ]
+                        ],
+                        [
+                            "ControlMetricsOut.bin:md5,6d77b38d0793a6e1ce1e85706e488953",
+                            "CorrectedIntMetricsOut.bin:md5,2bbf84d3be72734addaa2fe794711434",
+                            "ErrorMetricsOut.bin:md5,38c88def138e9bb832539911affdb286",
+                            "ExtractionMetricsOut.bin:md5,7497c3178837eea8f09350b5cd252e99",
+                            "IndexMetricsOut.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "QMetricsOut.bin:md5,7e9f198d53ebdfbb699a5f94cf1ed51c",
+                            "TileMetricsOut.bin:md5,83891751ec1c91a425a524b476b6ca3c"
+                        ],
+                        "RunInfo.xml:md5,03038959f4dd181c86bc97ae71fe270a"
+                    ]
+                ]
+            ]
+        ],
+        "timestamp": "2023-10-18T11:56:39.562418"
+    },
+    "test_untar_onlyfiles": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    [
+                        "hello.txt:md5,e59ff97941044f85df5297e1c302d260"
+                    ]
+                ]
+            ]
+        ],
+        "timestamp": "2023-10-18T11:56:46.878844"
+    },
+    "test_untar": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    [
+                        "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9",
+                        "opts.k2d:md5,a033d00cf6759407010b21700938f543",
+                        "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c"
+                    ]
+                ]
+            ]
+        ],
+        "timestamp": "2023-10-18T11:56:08.16574"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/untar/tests/tags.yml b/modules/nf-core/untar/tests/tags.yml
new file mode 100644
index 00000000..feb6f15c
--- /dev/null
+++ b/modules/nf-core/untar/tests/tags.yml
@@ -0,0 +1,2 @@
+untar:
+  - modules/nf-core/untar/**
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml
index 6a36b225..1b968acc 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml
@@ -16,24 +16,26 @@ input:
   - meta:
       type: map
       description: >
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
+        Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
+
   - id:
       type: string
       description: >
         SRA run identifier.
+
   - certificate:
       type: file
       description: >
         Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit
+
       pattern: "*.cart"
 # TODO Update when we decide on a standard for subworkflow docs
 output:
   - meta:
       type: map
       description: >
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
+        Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
+
   - reads:
       type: file
       description: Extracted FASTQ file or files if the sequencing reads are paired-end.
@@ -45,3 +47,6 @@ output:
 authors:
   - "@Midnighter"
   - "@drpatelh"
+maintainers:
+  - "@Midnighter"
+  - "@drpatelh"
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config
deleted file mode 100644
index 996c1888..00000000
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config
+++ /dev/null
@@ -1,3 +0,0 @@
-includeConfig '../../../modules/nf-core/sratools/prefetch/nextflow.config'
-includeConfig '../../../modules/nf-core/sratools/fasterqdump/nextflow.config'
-includeConfig '../../../modules/nf-core/custom/sratoolsncbisettings/nextflow.config'
\ No newline at end of file
diff --git a/subworkflows/nf-core/nextflowpipelineutils/main.nf b/subworkflows/nf-core/nextflowpipelineutils/main.nf
deleted file mode 100644
index 5cb9af8c..00000000
--- a/subworkflows/nf-core/nextflowpipelineutils/main.nf
+++ /dev/null
@@ -1,126 +0,0 @@
-//
-// Subworkflow with functionality that may be useful for any Nextflow pipeline
-//
-
-import org.yaml.snakeyaml.Yaml
-import groovy.json.JsonOutput
-
-/*
-========================================================================================
-    SUBWORKFLOW DEFINITION
-========================================================================================
-*/
-
-workflow NEXTFLOW_PIPELINE_UTILS {
-
-    take:
-    print_version        // bool
-    dump_parameters      // bool
-    output_directory     // path: base directory used to publish pipeline results
-    check_conda_channels // bool
-
-    main:
-
-    //
-    // Print workflow version and exit on --version
-    //
-    if (print_version) {
-        log.info "${workflow.manifest.name} ${getWorkflowVersion()}"
-        System.exit(0)
-    }
-
-    //
-    // Dump pipeline parameters to a JSON file
-    //
-    if (dump_parameters && output_directory) {
-        dumpParametersToJSON(output_directory)
-    }
-
-    //
-    // When running with Conda, warn if channels have not been set-up appropriately
-    //
-    if (check_conda_channels) {
-        checkCondaChannels()
-    }
-
-    emit:
-        out = true
-}
-
-/*
-========================================================================================
-    FUNCTIONS
-========================================================================================
-*/
-
-//
-// Generate version string
-//
-def getWorkflowVersion() {
-    String version_string = ""
-    if (workflow.manifest.version) {
-        def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
-        version_string += "${prefix_v}${workflow.manifest.version}"
-    }
-
-    if (workflow.commitId) {
-        def git_shortsha = workflow.commitId.substring(0, 7)
-        version_string += "-g${git_shortsha}"
-    }
-
-    return version_string
-}
-
-//
-// Dump pipeline parameters to a JSON file
-//
-def dumpParametersToJSON(output_directory) {
-    def output_d = new File("${output_directory}/pipeline_info/")
-    if (!output_d.exists()) {
-        output_d.mkdirs()
-    }
-
-    def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
-    def output_pf  = new File(output_d, "params_${timestamp}.json")
-    def jsonStr    = JsonOutput.toJson(params)
-    output_pf.text = JsonOutput.prettyPrint(jsonStr)
-}
-
-//
-// When running with -profile conda, warn if channels have not been set-up appropriately
-//
-def checkCondaChannels() {
-    Yaml parser = new Yaml()
-    def channels = []
-    try {
-        def config = parser.load("conda config --show channels".execute().text)
-        channels = config.channels
-    } catch(NullPointerException | IOException e) {
-        log.warn "Could not verify conda channel configuration."
-        return
-    }
-
-    // Check that all channels are present
-    // This channel list is ordered by required channel priority.
-    def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
-    def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
-
-    // Check that they are in the right order
-    def channel_priority_violation = false
-    def n = required_channels_in_order.size()
-    for (int i = 0; i < n - 1; i++) {
-        channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
-    }
-
-    if (channels_missing | channel_priority_violation) {
-        log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-            "  There is a problem with your Conda configuration!\n\n" +
-            "  You will need to set-up the conda-forge and bioconda channels correctly.\n" +
-            "  Please refer to https://bioconda.github.io/\n" +
-            "  The observed channel order is \n" +
-            "  ${channels}\n" +
-            "  but the following channel order is required:\n" +
-            "  ${required_channels_in_order}\n" +
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-    }
-}
diff --git a/subworkflows/nf-core/nextflowpipelineutils/meta.yml b/subworkflows/nf-core/nextflowpipelineutils/meta.yml
deleted file mode 100644
index f56b827b..00000000
--- a/subworkflows/nf-core/nextflowpipelineutils/meta.yml
+++ /dev/null
@@ -1,34 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "nextflow_pipeline_utils"
-description: Subworkflow with functionality that may be useful for any Nextflow pipeline
-keywords:
-  - utility
-  - pipeline
-  - initialise
-  - version
-components: []
-input:
-  - print_version:
-      type: boolean
-      description: |
-        Print the version of the pipeline and exit
-  - dump_parameters:
-      type: boolean
-      description: |
-        Dump the parameters of the pipeline to a JSON file
-  - output_directory:
-      type: directory
-      description: Path to output dir to write JSON file to.
-      pattern: "results/"
-  - check_conda_channel:
-      type: boolean
-      description: |
-        Check if the conda channel priority is correct.
-output:
-  - out:
-      type: boolean
-      description: |
-        Dummy output for making using in process chaining.
-authors:
-  - "@adamrtalbot"
-  - "@drpatelh"
diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test b/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test
deleted file mode 100644
index 1a1577eb..00000000
--- a/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test
+++ /dev/null
@@ -1,71 +0,0 @@
-
-nextflow_function {
-
-    name "Test Functions"
-    script "subworkflows/nf-core/nextflowpipelineutils/main.nf"
-    config "subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config"
-    tag 'subworkflows'
-    tag 'nextflowpipelineutils'
-    tag 'subworkflows/nextflowpipelineutils'
-
-    test("Test Function getWorkflowVersion") {
-
-        function "getWorkflowVersion"
-
-        when {
-            function {
-                """
-                // no inputs
-                """
-            }
-        }
-
-        then {
-            assert function.success
-            assert snapshot(function.result).match()
-        }
-
-    }
-
-
-    test("Test Function dumpParametersToJSON") {
-
-        function "dumpParametersToJSON"
-
-        when {
-            function {
-                """
-                // define inputs of the function here. Example:
-                input[0] = "$outputDir"
-                """.stripIndent()
-            }
-        }
-
-        then {
-            assert function.success
-            assert function.result =~ /publish_dir_mode/
-            assert function.result =~ /copy/
-        }
-
-    }
-	
-    test("Test Function checkCondaChannels") {
-
-        function "checkCondaChannels"
-
-        when {
-            function {
-                """
-                // no inputs
-                """
-            }
-        }
-
-        then {
-            assert function.success
-            assert snapshot(function.result).match()
-        }
-
-    }
-
-}
\ No newline at end of file
diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test.snap b/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test.snap
deleted file mode 100644
index 939dbbad..00000000
--- a/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test.snap
+++ /dev/null
@@ -1,12 +0,0 @@
-{
-    "Test Function getWorkflowVersion": {
-        "content": [
-            "v9.9.9"
-        ],
-        "timestamp": "2023-10-15T13:43:55.128868"
-    },
-    "Test Function checkCondaChannels": {
-        "content": null,
-        "timestamp": "2023-10-12T17:09:24.933468"
-    }
-}
\ No newline at end of file
diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test b/subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test
deleted file mode 100644
index 3cf7f034..00000000
--- a/subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test
+++ /dev/null
@@ -1,104 +0,0 @@
-nextflow_workflow {
-
-    name "Test Workflow NEXTFLOW_PIPELINE_UTILS"
-    script "../main.nf"
-    config "subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config"
-    workflow "NEXTFLOW_PIPELINE_UTILS"
-    tag 'subworkflows'
-    tag 'nextflowpipelineutils'
-    tag 'subworkflows/nextflowpipelineutils'
-
-    test("Should run no inputs") {
-
-        when {
-            params {
-                outdir = "tests/results"
-            }
-            workflow {
-                """
-                input[0] = false
-                input[1] = false
-                input[2] = null
-                input[3] = false
-                """
-            }
-        }
-
-        then {
-            assert workflow.success
-            assert snapshot(workflow.out).match()
-        }
-
-    }
-
-    test("Should print version") {
-
-        when {
-            params {
-                outdir = "tests/results"
-            }
-            workflow {
-                """
-                input[0] = true
-                input[1] = false
-                input[2] = null
-                input[3] = false
-                """
-            }
-        }
-
-        then {
-            assert workflow.success
-            assert workflow.stdout.contains("nextflow_workflow v9.9.9")
-        }
-
-    }
-
-
-    test("Should dump params") {
-
-        when {
-            params {
-                outdir = "$outputDir"
-            }
-            workflow {
-                """
-                input[0] = false
-                input[1] = true
-                input[2] = params.outdir
-                input[3] = false
-                """
-            }
-        }
-
-        then {
-            assert workflow.success
-            assert snapshot(workflow.out).match()
-        }
-
-    }
-
-    test("Should not create params JSON if no output directory") {
-
-        when {
-            params {
-                outdir = "$outputDir"
-            }
-            workflow {
-                """
-                input[0] = false
-                input[1] = true
-                input[2] = null
-                input[3] = false
-                """
-            }
-        }
-
-        then {
-            assert workflow.success
-            assert snapshot(workflow.out, path(params.outdir).list()).match()
-        }
-
-    }
-
-}
diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test.snap
deleted file mode 100644
index 08040fd4..00000000
--- a/subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test.snap
+++ /dev/null
@@ -1,44 +0,0 @@
-{
-    "Should not create params JSON if no output directory": {
-        "content": [
-            {
-                "0": [
-                    true
-                ],
-                "out": [
-                    true
-                ]
-            },
-            [
-                
-            ]
-        ],
-        "timestamp": "2023-10-13T11:55:54.576748"
-    },
-    "Should dump params": {
-        "content": [
-            {
-                "0": [
-                    true
-                ],
-                "out": [
-                    true
-                ]
-            }
-        ],
-        "timestamp": "2023-10-13T11:55:52.711329"
-    },
-    "Should run no inputs": {
-        "content": [
-            {
-                "0": [
-                    true
-                ],
-                "out": [
-                    true
-                ]
-            }
-        ],
-        "timestamp": "2023-10-13T11:55:49.048315"
-    }
-}
\ No newline at end of file
diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config b/subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config
deleted file mode 100644
index 53574ffe..00000000
--- a/subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-manifest {
-    name            = 'nextflow_workflow'
-    author          = """nf-core"""
-    homePage        = 'https://127.0.0.1'
-    description     = """Dummy pipeline"""
-    nextflowVersion  = '!>=23.04.0'
-    version         = '9.9.9'
-    doi             = 'https://doi.org/10.5281/zenodo.5070524'
-}
\ No newline at end of file
diff --git a/subworkflows/nf-core/nfcore_pipeline_utils/main.nf b/subworkflows/nf-core/nfcore_pipeline_utils/main.nf
deleted file mode 100644
index b3b136dc..00000000
--- a/subworkflows/nf-core/nfcore_pipeline_utils/main.nf
+++ /dev/null
@@ -1,311 +0,0 @@
-//
-// Subworkflow with utility functions specific to the nf-core pipeline template
-//
-
-/*
-========================================================================================
-    SUBWORKFLOW DEFINITION
-========================================================================================
-*/
-
-workflow NFCORE_PIPELINE_UTILS {
-
-    main:
-    checkConfigProvided()
-
-    emit:
-    success = true
-
-}
-
-/*
-========================================================================================
-    FUNCTIONS
-========================================================================================
-*/
-
-//
-//  Warn if a -profile or Nextflow config has not been provided to run the pipeline
-//
-def checkConfigProvided() {
-    if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
-        log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
-            "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
-            "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
-            "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
-            "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
-            "Please refer to the quick start section and usage docs for the pipeline.\n "
-    }
-}
-
-//
-// Citation string for pipeline
-//
-def workflowCitation() {
-    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-        "* The pipeline\n" +
-        "  ${workflow.manifest.doi}\n\n" +
-        "* The nf-core framework\n" +
-        "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
-        "* Software dependencies\n" +
-        "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
-}
-
-//
-// nf-core logo
-//
-def nfCoreLogo(workflow_version) {
-    Map colors = logColours()
-    String.format(
-        """\n
-        ${dashedLine()}
-                                                ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
-        ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
-        ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
-        ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
-                                                ${colors.green}`._,._,\'${colors.reset}
-        ${colors.purple}  ${workflow.manifest.name} ${workflow_version}${colors.reset}
-        ${dashedLine()}
-        """.stripIndent()
-    )
-}
-
-//
-// Return dashed line
-//
-def dashedLine() {
-    Map colors = logColours()
-    return "-${colors.dim}----------------------------------------------------${colors.reset}-"
-}
-
-//
-// ANSII colours used for terminal logging
-//
-def logColours() {
-    Map colorcodes = [:]
-
-    // Reset / Meta
-    colorcodes['reset']      = params.monochrome_logs ? '' : "\033[0m"
-    colorcodes['bold']       = params.monochrome_logs ? '' : "\033[1m"
-    colorcodes['dim']        = params.monochrome_logs ? '' : "\033[2m"
-    colorcodes['underlined'] = params.monochrome_logs ? '' : "\033[4m"
-    colorcodes['blink']      = params.monochrome_logs ? '' : "\033[5m"
-    colorcodes['reverse']    = params.monochrome_logs ? '' : "\033[7m"
-    colorcodes['hidden']     = params.monochrome_logs ? '' : "\033[8m"
-
-    // Regular Colors
-    colorcodes['black']      = params.monochrome_logs ? '' : "\033[0;30m"
-    colorcodes['red']        = params.monochrome_logs ? '' : "\033[0;31m"
-    colorcodes['green']      = params.monochrome_logs ? '' : "\033[0;32m"
-    colorcodes['yellow']     = params.monochrome_logs ? '' : "\033[0;33m"
-    colorcodes['blue']       = params.monochrome_logs ? '' : "\033[0;34m"
-    colorcodes['purple']     = params.monochrome_logs ? '' : "\033[0;35m"
-    colorcodes['cyan']       = params.monochrome_logs ? '' : "\033[0;36m"
-    colorcodes['white']      = params.monochrome_logs ? '' : "\033[0;37m"
-
-    // Bold
-    colorcodes['bblack']     = params.monochrome_logs ? '' : "\033[1;30m"
-    colorcodes['bred']       = params.monochrome_logs ? '' : "\033[1;31m"
-    colorcodes['bgreen']     = params.monochrome_logs ? '' : "\033[1;32m"
-    colorcodes['byellow']    = params.monochrome_logs ? '' : "\033[1;33m"
-    colorcodes['bblue']      = params.monochrome_logs ? '' : "\033[1;34m"
-    colorcodes['bpurple']    = params.monochrome_logs ? '' : "\033[1;35m"
-    colorcodes['bcyan']      = params.monochrome_logs ? '' : "\033[1;36m"
-    colorcodes['bwhite']     = params.monochrome_logs ? '' : "\033[1;37m"
-
-    // Underline
-    colorcodes['ublack']     = params.monochrome_logs ? '' : "\033[4;30m"
-    colorcodes['ured']       = params.monochrome_logs ? '' : "\033[4;31m"
-    colorcodes['ugreen']     = params.monochrome_logs ? '' : "\033[4;32m"
-    colorcodes['uyellow']    = params.monochrome_logs ? '' : "\033[4;33m"
-    colorcodes['ublue']      = params.monochrome_logs ? '' : "\033[4;34m"
-    colorcodes['upurple']    = params.monochrome_logs ? '' : "\033[4;35m"
-    colorcodes['ucyan']      = params.monochrome_logs ? '' : "\033[4;36m"
-    colorcodes['uwhite']     = params.monochrome_logs ? '' : "\033[4;37m"
-
-    // High Intensity
-    colorcodes['iblack']     = params.monochrome_logs ? '' : "\033[0;90m"
-    colorcodes['ired']       = params.monochrome_logs ? '' : "\033[0;91m"
-    colorcodes['igreen']     = params.monochrome_logs ? '' : "\033[0;92m"
-    colorcodes['iyellow']    = params.monochrome_logs ? '' : "\033[0;93m"
-    colorcodes['iblue']      = params.monochrome_logs ? '' : "\033[0;94m"
-    colorcodes['ipurple']    = params.monochrome_logs ? '' : "\033[0;95m"
-    colorcodes['icyan']      = params.monochrome_logs ? '' : "\033[0;96m"
-    colorcodes['iwhite']     = params.monochrome_logs ? '' : "\033[0;97m"
-
-    // Bold High Intensity
-    colorcodes['biblack']    = params.monochrome_logs ? '' : "\033[1;90m"
-    colorcodes['bired']      = params.monochrome_logs ? '' : "\033[1;91m"
-    colorcodes['bigreen']    = params.monochrome_logs ? '' : "\033[1;92m"
-    colorcodes['biyellow']   = params.monochrome_logs ? '' : "\033[1;93m"
-    colorcodes['biblue']     = params.monochrome_logs ? '' : "\033[1;94m"
-    colorcodes['bipurple']   = params.monochrome_logs ? '' : "\033[1;95m"
-    colorcodes['bicyan']     = params.monochrome_logs ? '' : "\033[1;96m"
-    colorcodes['biwhite']    = params.monochrome_logs ? '' : "\033[1;97m"
-
-    return colorcodes
-}
-
-//
-// Construct and send completion email
-//
-def completionEmail(summary_params) {
-
-    // Set up the e-mail variables
-    def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
-    if (!workflow.success) {
-        subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
-    }
-
-    def summary = [:]
-    for (group in summary_params.keySet()) {
-        summary << summary_params[group]
-    }
-
-    def misc_fields = [:]
-    misc_fields['Date Started']              = workflow.start
-    misc_fields['Date Completed']            = workflow.complete
-    misc_fields['Pipeline script file path'] = workflow.scriptFile
-    misc_fields['Pipeline script hash ID']   = workflow.scriptId
-    if (workflow.repository) misc_fields['Pipeline repository Git URL']    = workflow.repository
-    if (workflow.commitId)   misc_fields['Pipeline repository Git Commit'] = workflow.commitId
-    if (workflow.revision)   misc_fields['Pipeline Git branch/tag']        = workflow.revision
-    misc_fields['Nextflow Version']           = workflow.nextflow.version
-    misc_fields['Nextflow Build']             = workflow.nextflow.build
-    misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
-
-    def email_fields = [:]
-    email_fields['version']      = NfcoreTemplate.version(workflow)
-    email_fields['runName']      = workflow.runName
-    email_fields['success']      = workflow.success
-    email_fields['dateComplete'] = workflow.complete
-    email_fields['duration']     = workflow.duration
-    email_fields['exitStatus']   = workflow.exitStatus
-    email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
-    email_fields['errorReport']  = (workflow.errorReport ?: 'None')
-    email_fields['commandLine']  = workflow.commandLine
-    email_fields['projectDir']   = workflow.projectDir
-    email_fields['summary']      = summary << misc_fields
-
-    // Check if we are only sending emails on failure
-    def email_address = params.email
-    if (!params.email && params.email_on_fail && !workflow.success) {
-        email_address = params.email_on_fail
-    }
-
-    // Render the TXT template
-    def engine       = new groovy.text.GStringTemplateEngine()
-    def tf           = new File("${workflow.projectDir}/assets/email_template.txt")
-    def txt_template = engine.createTemplate(tf).make(email_fields)
-    def email_txt    = txt_template.toString()
-
-    // Render the HTML template
-    def hf            = new File("${workflow.projectDir}/assets/email_template.html")
-    def html_template = engine.createTemplate(hf).make(email_fields)
-    def email_html    = html_template.toString()
-
-    // Render the sendmail template
-    def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}" ]
-    def sf                     = new File("${workflow.projectDir}/assets/sendmail_template.txt")
-    def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
-    def sendmail_html          = sendmail_template.toString()
-
-    // Send the HTML e-mail
-    Map colors = logColours()
-    if (email_address) {
-        try {
-            if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
-            // Try to send HTML e-mail using sendmail
-            [ 'sendmail', '-t' ].execute() << sendmail_html
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
-        } catch (all) {
-            // Catch failures and try with plaintext
-            def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
-            mail_cmd.execute() << email_html
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
-        }
-    }
-
-    // Write summary e-mail HTML to a file
-    def output_d = new File("${params.outdir}/pipeline_info/")
-    if (!output_d.exists()) {
-        output_d.mkdirs()
-    }
-    def output_hf = new File(output_d, "pipeline_report.html")
-    output_hf.withWriter { w -> w << email_html }
-    def output_tf = new File(output_d, "pipeline_report.txt")
-    output_tf.withWriter { w -> w << email_txt }
-}
-
-//
-// Print pipeline summary on completion
-//
-def completionSummary() {
-    Map colors = logColours()
-    if (workflow.success) {
-        if (workflow.stats.ignoredCount == 0) {
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
-        } else {
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
-        }
-    } else {
-        log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
-    }
-}
-
-//
-// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack
-//
-def imNotification(summary_params) {
-    def hook_url = params.hook_url
-
-    def summary = [:]
-    for (group in summary_params.keySet()) {
-        summary << summary_params[group]
-    }
-
-    def misc_fields = [:]
-    misc_fields['start']                                = workflow.start
-    misc_fields['complete']                             = workflow.complete
-    misc_fields['scriptfile']                           = workflow.scriptFile
-    misc_fields['scriptid']                             = workflow.scriptId
-    if (workflow.repository) misc_fields['repository']  = workflow.repository
-    if (workflow.commitId)   misc_fields['commitid']    = workflow.commitId
-    if (workflow.revision)   misc_fields['revision']    = workflow.revision
-    misc_fields['nxf_version']                          = workflow.nextflow.version
-    misc_fields['nxf_build']                            = workflow.nextflow.build
-    misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
-
-    def msg_fields = [:]
-    msg_fields['version']      = NfcoreTemplate.version(workflow)
-    msg_fields['runName']      = workflow.runName
-    msg_fields['success']      = workflow.success
-    msg_fields['dateComplete'] = workflow.complete
-    msg_fields['duration']     = workflow.duration
-    msg_fields['exitStatus']   = workflow.exitStatus
-    msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
-    msg_fields['errorReport']  = (workflow.errorReport ?: 'None')
-    msg_fields['commandLine']  = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "")
-    msg_fields['projectDir']   = workflow.projectDir
-    msg_fields['summary']      = summary << misc_fields
-
-    // Render the JSON template
-    def engine       = new groovy.text.GStringTemplateEngine()
-    // Different JSON depending on the service provider
-    // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format
-    def json_path     = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json"
-    def hf            = new File("${workflow.projectDir}/assets/${json_path}")
-    def json_template = engine.createTemplate(hf).make(msg_fields)
-    def json_message  = json_template.toString()
-
-    // POST
-    def post = new URL(hook_url).openConnection();
-    post.setRequestMethod("POST")
-    post.setDoOutput(true)
-    post.setRequestProperty("Content-Type", "application/json")
-    post.getOutputStream().write(json_message.getBytes("UTF-8"));
-    def postRC = post.getResponseCode();
-    if (! postRC.equals(200)) {
-        log.warn(post.getErrorStream().getText());
-    }
-}
diff --git a/subworkflows/nf-core/nfcore_pipeline_utils/meta.yml b/subworkflows/nf-core/nfcore_pipeline_utils/meta.yml
deleted file mode 100644
index 5721b7e3..00000000
--- a/subworkflows/nf-core/nfcore_pipeline_utils/meta.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "NFCORE_PIPELINE_UTILS"
-description: Subworkflow with utility functions specific to the nf-core pipeline template
-keywords:
-  - utility
-  - pipeline
-  - initialise
-  - version
-components: []
-input: []
-output:
-  - success:
-      type: boolean
-      description: |
-        Dummy output to indicate success
-authors:
-  - "@adamrtalbot"
diff --git a/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test b/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test
deleted file mode 100644
index 265ece39..00000000
--- a/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test
+++ /dev/null
@@ -1,120 +0,0 @@
-
-nextflow_function {
-
-    name "Test Functions"
-    script "../main.nf"
-    config "subworkflows/nf-core/nfcore_pipeline_utils/tests/nextflow.config"
-	
-    test("Test Function checkConfigProvided") {
-
-        function "checkConfigProvided"
-
-        when {
-            function {
-                """
-                // define inputs of the function here. Example:
-                // input[0] = 1
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert function.success                  },
-                { assert snapshot(function.result).match() }
-            )
-        }
-
-    }
-
-    test("Test Function workflowCitation") {
-
-        function "workflowCitation"
-
-        when {
-            function {
-                """
-                // define inputs of the function here. Example:
-                // input[0] = 1
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert function.success                  },
-                { assert snapshot(function.result).match() }
-            )
-        }
-
-    }
-
-    test("Test Function nfCoreLogo") {
-
-        function "nfCoreLogo"
-
-        when {
-            function {
-                """
-                input[0] = "9.9.9"
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert function.success                  },
-                { assert snapshot(function.result).match() }
-            )
-        }
-
-    }
-
-	
-
-    test("Test Function dashedLine") {
-
-        function "dashedLine"
-
-        when {
-            function {
-                """
-                // define inputs of the function here. Example:
-                // input[0] = 1
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert function.success                  },
-                { assert snapshot(function.result).match() }
-            )
-        }
-
-    }
-
-	
-
-    test("Test Function logColours") {
-
-        function "logColours"
-
-        when {
-            function {
-                """
-                // define inputs of the function here. Example:
-                // input[0] = 1
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert function.success                  },
-                { assert snapshot(function.result).match() }
-            )
-        }
-
-    }
-}
\ No newline at end of file
diff --git a/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test.snap b/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test.snap
deleted file mode 100644
index 3ea51f68..00000000
--- a/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test.snap
+++ /dev/null
@@ -1,78 +0,0 @@
-{
-    "Test Function logColours": {
-        "content": [
-            {
-                "reset": "\u001b[0m",
-                "bold": "\u001b[1m",
-                "dim": "\u001b[2m",
-                "underlined": "\u001b[4m",
-                "blink": "\u001b[5m",
-                "reverse": "\u001b[7m",
-                "hidden": "\u001b[8m",
-                "black": "\u001b[0;30m",
-                "red": "\u001b[0;31m",
-                "green": "\u001b[0;32m",
-                "yellow": "\u001b[0;33m",
-                "blue": "\u001b[0;34m",
-                "purple": "\u001b[0;35m",
-                "cyan": "\u001b[0;36m",
-                "white": "\u001b[0;37m",
-                "bblack": "\u001b[1;30m",
-                "bred": "\u001b[1;31m",
-                "bgreen": "\u001b[1;32m",
-                "byellow": "\u001b[1;33m",
-                "bblue": "\u001b[1;34m",
-                "bpurple": "\u001b[1;35m",
-                "bcyan": "\u001b[1;36m",
-                "bwhite": "\u001b[1;37m",
-                "ublack": "\u001b[4;30m",
-                "ured": "\u001b[4;31m",
-                "ugreen": "\u001b[4;32m",
-                "uyellow": "\u001b[4;33m",
-                "ublue": "\u001b[4;34m",
-                "upurple": "\u001b[4;35m",
-                "ucyan": "\u001b[4;36m",
-                "uwhite": "\u001b[4;37m",
-                "iblack": "\u001b[0;90m",
-                "ired": "\u001b[0;91m",
-                "igreen": "\u001b[0;92m",
-                "iyellow": "\u001b[0;93m",
-                "iblue": "\u001b[0;94m",
-                "ipurple": "\u001b[0;95m",
-                "icyan": "\u001b[0;96m",
-                "iwhite": "\u001b[0;97m",
-                "biblack": "\u001b[1;90m",
-                "bired": "\u001b[1;91m",
-                "bigreen": "\u001b[1;92m",
-                "biyellow": "\u001b[1;93m",
-                "biblue": "\u001b[1;94m",
-                "bipurple": "\u001b[1;95m",
-                "bicyan": "\u001b[1;96m",
-                "biwhite": "\u001b[1;97m"
-            }
-        ],
-        "timestamp": "2023-10-16T14:27:09.843064"
-    },
-    "Test Function checkConfigProvided": {
-        "content": null,
-        "timestamp": "2023-10-16T14:27:01.415849"
-    },
-    "Test Function nfCoreLogo": {
-        "content": [
-            "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n                                        \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m        ___     __   __   __   ___     \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \u001b[0;33m}  {\u001b[0m\n\u001b[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \u001b[0;32m\\`-._,-`-,\u001b[0m\n                                        \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m  nextflow_workflow 9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n"
-        ],
-        "timestamp": "2023-10-16T14:27:51.566211"
-    },
-    "Test Function workflowCitation": {
-        "content": [
-            "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n  https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n  https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n  https://github.com/nextflow_workflow/blob/master/CITATIONS.md"
-        ],
-        "timestamp": "2023-10-16T14:27:03.505737"
-    },
-    "Test Function dashedLine": {
-        "content": [
-            "-\u001b[2m----------------------------------------------------\u001b[0m-"
-        ],
-        "timestamp": "2023-10-16T14:27:07.721916"
-    }
-}
\ No newline at end of file
diff --git a/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.workflow.nf.test b/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.workflow.nf.test
deleted file mode 100644
index ad7c73a8..00000000
--- a/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.workflow.nf.test
+++ /dev/null
@@ -1,33 +0,0 @@
-nextflow_workflow {
-
-    name "Test Workflow NFCORE_PIPELINE_UTILS"
-    script "../main.nf"
-    config "subworkflows/nf-core/nfcore_pipeline_utils/tests/nextflow.config"
-    workflow "NFCORE_PIPELINE_UTILS"
-    tag "subworkflows"
-    tag "subworkflows_nfcore"
-    tag "nfcorepipelineutils"
-    tag "subworkflows/nfcorepipelineutils"
-
-    test("Should run without failures") {
-
-        when {
-            params {
-                // define parameters here. Example:
-                // outdir = "tests/results"
-            }
-            workflow {
-                """
-                // define inputs of the workflow here. Example:
-                // input[0] = file("test-file.txt")
-                """
-            }
-        }
-
-        then {
-            assert workflow.success
-        }
-
-    }
-
-}
diff --git a/subworkflows/nf-core/nfcore_pipeline_utils/tests/nextflow.config b/subworkflows/nf-core/nfcore_pipeline_utils/tests/nextflow.config
deleted file mode 100644
index 53574ffe..00000000
--- a/subworkflows/nf-core/nfcore_pipeline_utils/tests/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-manifest {
-    name            = 'nextflow_workflow'
-    author          = """nf-core"""
-    homePage        = 'https://127.0.0.1'
-    description     = """Dummy pipeline"""
-    nextflowVersion  = '!>=23.04.0'
-    version         = '9.9.9'
-    doi             = 'https://doi.org/10.5281/zenodo.5070524'
-}
\ No newline at end of file
diff --git a/subworkflows/nf-core/nfvalidation_plugin_utils/main.nf b/subworkflows/nf-core/nfvalidation_plugin_utils/main.nf
deleted file mode 100644
index 22531719..00000000
--- a/subworkflows/nf-core/nfvalidation_plugin_utils/main.nf
+++ /dev/null
@@ -1,62 +0,0 @@
-//
-// Subworkflow that uses the nf-validation plugin to render help text and parameter summary
-//
-
-/*
-========================================================================================
-    IMPORT NF-VALIDATION PLUGIN
-========================================================================================
-*/
-
-include { paramsHelp; paramsSummaryLog; paramsSummaryMap; validateParameters } from 'plugin/nf-validation'
-
-/*
-========================================================================================
-    SUBWORKFLOW DEFINITION
-========================================================================================
-*/
-
-workflow NF_VALIDATION_PLUGIN_UTILS {
-
-    take:
-        print_help        // bool
-        workflow_command   // string: default commmand used to run pipeline
-        pre_help_text     // string: string to be printed before help text and summary log
-        post_help_text    // string: string to be printed after help text and summary log
-        validate_params   // bool: Validate parameters
-        schema_filename    // path: JSON schema file, null to use default value
-
-    main:
-
-        log.debug "Using schema file: ${schema_filename}"
-
-        // Default values for strings
-        pre_help_text   = pre_help_text    ?: ''
-        post_help_text  = post_help_text   ?: ''
-        workflow_command = workflow_command  ?: ''
-
-        //
-        // Print help message if needed
-        //
-        if (print_help) {
-            log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text
-            System.exit(0)
-        }
-
-        //
-        // Print parameter summary to stdout
-        //
-        log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text
-
-        //
-        // Validate parameters relative to the parameter JSON schema
-        //
-        if (validate_params){
-            validateParameters(parameters_schema: schema_filename)
-        }
-
-        summary_params = paramsSummaryMap(workflow, parameters_schema: schema_filename)
-
-    emit:
-        summary_params = summary_params
-}
diff --git a/subworkflows/nf-core/nfvalidation_plugin_utils/meta.yml b/subworkflows/nf-core/nfvalidation_plugin_utils/meta.yml
deleted file mode 100644
index 6117b455..00000000
--- a/subworkflows/nf-core/nfvalidation_plugin_utils/meta.yml
+++ /dev/null
@@ -1,49 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "nfvalidationpluginutils"
-## TODO nf-core: Add a description of the subworkflow and list keywords
-description: Sort SAM/BAM/CRAM file
-keywords:
-  - sort
-  - bam
-  - sam
-  - cram
-## TODO nf-core: Add a list of the modules and/or subworkflows used in the subworkflow
-components:
-  - samtools/sort
-  - samtools/index
-## TODO nf-core: List all of the channels used as input with a description and their structure
-input:
-  - ch_bam:
-      type: file
-      description: |
-        The input channel containing the BAM/CRAM/SAM files
-        Structure: [ val(meta), path(bam) ]
-      pattern: "*.{bam/cram/sam}"
-## TODO nf-core: List all of the channels used as output with a descriptions and their structure
-output:
-  - bam:
-      type: file
-      description: |
-        Channel containing BAM files
-        Structure: [ val(meta), path(bam) ]
-      pattern: "*.bam"
-  - bai:
-      type: file
-      description: |
-        Channel containing indexed BAM (BAI) files
-        Structure: [ val(meta), path(bai) ]
-      pattern: "*.bai"
-  - csi:
-      type: file
-      description: |
-        Channel containing CSI files
-        Structure: [ val(meta), path(csi) ]
-      pattern: "*.csi"
-  - versions:
-      type: file
-      description: |
-        File containing software versions
-        Structure: [ path(versions.yml) ]
-      pattern: "versions.yml"
-authors:
-  - "@adamrtalbot"
diff --git a/subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test b/subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test
deleted file mode 100644
index 6a0efd1e..00000000
--- a/subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test
+++ /dev/null
@@ -1,199 +0,0 @@
-nextflow_workflow {
-
-    name "Test Workflow NF_VALIDATION_PLUGIN_UTILS"
-    script "../main.nf"
-    workflow "NF_VALIDATION_PLUGIN_UTILS"
-    tag "subworkflow"
-    tag "subworkflow_nfcore"
-    tag "nfvalidationpluginutils"
-    tag "subworkflows/nfvalidationpluginutils"
-
-    test("Should run nothing") {
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-
-            workflow {
-                """
-                help            = false
-                workflow_command = null
-                pre_help_text   = null
-                post_help_text  = null
-                validate_params = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assert workflow.success
-        }
-
-    }
-
-    test("Should run help") {
-
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command = null
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assert workflow.success
-            assert workflow.exitStatus == 0
-            assert workflow.stdout.any { it.contains('Input/output options') }
-            assert workflow.stdout.any { it.contains('--outdir') }
-            assert workflow.stdout.any { it.contains('--outdir') }
-        }
-
-    }
-
-    test("Should run help with command") {
-
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command  = "nextflow run noorg/doesntexist"
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assert workflow.success
-            assert workflow.exitStatus == 0
-            assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') }
-            assert workflow.stdout.any { it.contains('Input/output options') }
-            assert workflow.stdout.any { it.contains('--outdir') }
-            assert workflow.stdout.any { it.contains('--outdir') }
-        }
-
-    }
-
-    test("Should run help with extra text") {
-
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command  = "nextflow run noorg/doesntexist"
-                pre_help_text    = "pre-help-text"
-                post_help_text   = "post-help-text"
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assert workflow.success
-            assert workflow.exitStatus == 0
-            assert workflow.stdout.any { it.contains('pre-help-text') }
-            assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') }
-            assert workflow.stdout.any { it.contains('Input/output options') }
-            assert workflow.stdout.any { it.contains('--outdir') }
-            assert workflow.stdout.any { it.contains('--outdir') }
-            assert workflow.stdout.any { it.contains('post-help-text') }
-        }
-
-    }
-
-    test("Should validate params") {
-
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = false
-                workflow_command  = null
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = true
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assert workflow.failed
-            assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') }
-            assert workflow.stdout.any { it.contains('The following invalid input values have been detected:') }
-        }
-
-    }
-
-}
diff --git a/subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test.snap b/subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test.snap
deleted file mode 100644
index ae33a930..00000000
--- a/subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test.snap
+++ /dev/null
@@ -1,26 +0,0 @@
-{
-    "Should run help": {
-        "content": [
-            {
-                "stderr": [
-
-                ],
-                "errorReport": "",
-                "exitStatus": 0,
-                "failed": false,
-                "stdout": [
-
-                ],
-                "errorMessage": "",
-                "trace": {
-                    "tasksFailed": 0,
-                    "tasksCount": 0,
-                    "tasksSucceeded": 0
-                },
-                "name": "workflow",
-                "success": true
-            }
-        ],
-        "timestamp": "2023-10-13T13:18:16.933251413"
-    }
-}
diff --git a/subworkflows/nf-core/nfvalidation_plugin_utils/tests/nextflow_schema.json b/subworkflows/nf-core/nfvalidation_plugin_utils/tests/nextflow_schema.json
deleted file mode 100644
index 7626c1c9..00000000
--- a/subworkflows/nf-core/nfvalidation_plugin_utils/tests/nextflow_schema.json
+++ /dev/null
@@ -1,96 +0,0 @@
-{
-    "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
-    "title": ". pipeline parameters",
-    "description": "",
-    "type": "object",
-    "definitions": {
-        "input_output_options": {
-            "title": "Input/output options",
-            "type": "object",
-            "fa_icon": "fas fa-terminal",
-            "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["outdir"],
-            "properties": {
-                "validate_params": {
-                    "type": "boolean",
-                    "description": "Validate parameters?",
-                    "default": true,
-                    "hidden": true
-                },
-                "outdir": {
-                    "type": "string",
-                    "format": "directory-path",
-                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
-                    "fa_icon": "fas fa-folder-open"
-                },
-                "test_data_base": {
-                    "type": "string",
-                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules",
-                    "description": "Base for test data directory",
-                    "hidden": true
-                },
-                "test_data": {
-                    "type": "string",
-                    "description": "Fake test data param",
-                    "hidden": true
-                }
-            }
-        },
-        "generic_options": {
-            "title": "Generic options",
-            "type": "object",
-            "fa_icon": "fas fa-file-import",
-            "description": "Less common options for the pipeline, typically set in a config file.",
-            "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
-            "properties": {
-                "help": {
-                    "type": "boolean",
-                    "description": "Display help text.",
-                    "fa_icon": "fas fa-question-circle",
-                    "hidden": true
-                },
-                "version": {
-                    "type": "boolean",
-                    "description": "Display version and exit.",
-                    "fa_icon": "fas fa-question-circle",
-                    "hidden": true
-                },
-                "logo": {
-                    "type": "boolean",
-                    "default": true,
-                    "description": "Display nf-core logo in console output.",
-                    "fa_icon": "fas fa-image",
-                    "hidden": true
-                },
-                "singularity_pull_docker_container": {
-                    "type": "boolean",
-                    "description": "Pull Singularity container from Docker?",
-                    "hidden": true
-                },
-                "publish_dir_mode": {
-                    "type": "string",
-                    "default": "copy",
-                    "description": "Method used to save pipeline results to output directory.",
-                    "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
-                    "fa_icon": "fas fa-copy",
-                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
-                    "hidden": true
-                },
-                "monochrome_logs": {
-                    "type": "boolean",
-                    "description": "Use monochrome_logs",
-                    "hidden": true
-                }
-            }
-        }
-    },
-    "allOf": [
-        {
-            "$ref": "#/definitions/input_output_options"
-        },
-        {
-            "$ref": "#/definitions/generic_options"
-        }
-    ]
-}

From bce4b7a09ee14ff9e25e5bc94e1939f3d345bef1 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Jan 2024 18:10:44 +0000
Subject: [PATCH 646/852] Install new utils subworkflows

---
 modules.json                                  |  15 +
 .../nf-core/utils_nextflow_pipeline/main.nf   | 126 +++++++
 .../nf-core/utils_nextflow_pipeline/meta.yml  |  37 +++
 .../tests/main.functions.nf.test              |  71 ++++
 .../tests/main.functions.nf.test.snap         |  12 +
 .../tests/main.workflow.nf.test               | 104 ++++++
 .../tests/main.workflow.nf.test.snap          |  44 +++
 .../tests/nextflow.config                     |   9 +
 .../utils_nextflow_pipeline/tests/tags.yml    |   2 +
 .../nf-core/utils_nfcore_pipeline/main.nf     | 311 ++++++++++++++++++
 .../nf-core/utils_nfcore_pipeline/meta.yml    |  19 ++
 .../tests/main.function.nf.test               | 124 +++++++
 .../tests/main.function.nf.test.snap          |  78 +++++
 .../tests/main.workflow.nf.test               |  33 ++
 .../tests/nextflow.config                     |   9 +
 .../utils_nfcore_pipeline/tests/tags.yml      |   2 +
 .../nf-core/utils_nfvalidation_plugin/main.nf |  62 ++++
 .../utils_nfvalidation_plugin/meta.yml        |  46 +++
 .../tests/main.nf.test                        | 201 +++++++++++
 .../tests/main.nf.test.snap                   |  26 ++
 .../tests/nextflow_schema.json                |  96 ++++++
 .../utils_nfvalidation_plugin/tests/tags.yml  |   2 +
 22 files changed, 1429 insertions(+)
 create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/main.nf
 create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/meta.yml
 create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test
 create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test.snap
 create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
 create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test.snap
 create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
 create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
 create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/main.nf
 create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/meta.yml
 create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
 create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
 create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
 create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
 create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
 create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
 create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
 create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
 create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test.snap
 create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
 create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml

diff --git a/modules.json b/modules.json
index 59b7e9c4..d0766098 100644
--- a/modules.json
+++ b/modules.json
@@ -33,6 +33,21 @@
                         "branch": "master",
                         "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
                         "installed_by": ["subworkflows"]
+                    },
+                    "utils_nextflow_pipeline": {
+                        "branch": "master",
+                        "git_sha": "c81784b47d44464b35e04220e00051bb5be27524",
+                        "installed_by": ["subworkflows"]
+                    },
+                    "utils_nfcore_pipeline": {
+                        "branch": "master",
+                        "git_sha": "c81784b47d44464b35e04220e00051bb5be27524",
+                        "installed_by": ["subworkflows"]
+                    },
+                    "utils_nfvalidation_plugin": {
+                        "branch": "master",
+                        "git_sha": "f0f8f4dc889970251eb251b85610f7ec2eafded9",
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
new file mode 100644
index 00000000..9dbb86c7
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -0,0 +1,126 @@
+//
+// Subworkflow with functionality that may be useful for any Nextflow pipeline
+//
+
+import org.yaml.snakeyaml.Yaml
+import groovy.json.JsonOutput
+
+/*
+========================================================================================
+    SUBWORKFLOW DEFINITION
+========================================================================================
+*/
+
+workflow UTILS_NEXTFLOW_PIPELINE {
+
+    take:
+    print_version        // bool
+    dump_parameters      // bool
+    output_directory     // path: base directory used to publish pipeline results
+    check_conda_channels // bool
+
+    main:
+
+    //
+    // Print workflow version and exit on --version
+    //
+    if (print_version) {
+        log.info "${workflow.manifest.name} ${getWorkflowVersion()}"
+        System.exit(0)
+    }
+
+    //
+    // Dump pipeline parameters to a JSON file
+    //
+    if (dump_parameters && output_directory) {
+        dumpParametersToJSON(output_directory)
+    }
+
+    //
+    // When running with Conda, warn if channels have not been set-up appropriately
+    //
+    if (check_conda_channels) {
+        checkCondaChannels()
+    }
+
+    emit:
+        out = true
+}
+
+/*
+========================================================================================
+    FUNCTIONS
+========================================================================================
+*/
+
+//
+// Generate version string
+//
+def getWorkflowVersion() {
+    String version_string = ""
+    if (workflow.manifest.version) {
+        def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
+        version_string += "${prefix_v}${workflow.manifest.version}"
+    }
+
+    if (workflow.commitId) {
+        def git_shortsha = workflow.commitId.substring(0, 7)
+        version_string += "-g${git_shortsha}"
+    }
+
+    return version_string
+}
+
+//
+// Dump pipeline parameters to a JSON file
+//
+def dumpParametersToJSON(output_directory) {
+    def output_d = new File("${output_directory}/pipeline_info/")
+    if (!output_d.exists()) {
+        output_d.mkdirs()
+    }
+
+    def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+    def output_pf  = new File(output_d, "params_${timestamp}.json")
+    def jsonStr    = JsonOutput.toJson(params)
+    output_pf.text = JsonOutput.prettyPrint(jsonStr)
+}
+
+//
+// When running with -profile conda, warn if channels have not been set-up appropriately
+//
+def checkCondaChannels() {
+    Yaml parser = new Yaml()
+    def channels = []
+    try {
+        def config = parser.load("conda config --show channels".execute().text)
+        channels = config.channels
+    } catch(NullPointerException | IOException e) {
+        log.warn "Could not verify conda channel configuration."
+        return
+    }
+
+    // Check that all channels are present
+    // This channel list is ordered by required channel priority.
+    def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
+    def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
+
+    // Check that they are in the right order
+    def channel_priority_violation = false
+    def n = required_channels_in_order.size()
+    for (int i = 0; i < n - 1; i++) {
+        channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
+    }
+
+    if (channels_missing | channel_priority_violation) {
+        log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+            "  There is a problem with your Conda configuration!\n\n" +
+            "  You will need to set-up the conda-forge and bioconda channels correctly.\n" +
+            "  Please refer to https://bioconda.github.io/\n" +
+            "  The observed channel order is \n" +
+            "  ${channels}\n" +
+            "  but the following channel order is required:\n" +
+            "  ${required_channels_in_order}\n" +
+            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+    }
+}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml
new file mode 100644
index 00000000..3d2b304f
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml
@@ -0,0 +1,37 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "UTILS_NEXTFLOW_PIPELINE"
+description: Subworkflow with functionality that may be useful for any Nextflow pipeline
+keywords:
+  - utility
+  - pipeline
+  - initialise
+  - version
+components: []
+input:
+  - print_version:
+      type: boolean
+      description: |
+        Print the version of the pipeline and exit
+  - dump_parameters:
+      type: boolean
+      description: |
+        Dump the parameters of the pipeline to a JSON file
+  - output_directory:
+      type: directory
+      description: Path to output dir to write JSON file to.
+      pattern: "results/"
+  - check_conda_channel:
+      type: boolean
+      description: |
+        Check if the conda channel priority is correct.
+output:
+  - out:
+      type: boolean
+      description: |
+        Dummy output for making using in process chaining.
+authors:
+  - "@adamrtalbot"
+  - "@drpatelh"
+maintainers:
+  - "@adamrtalbot"
+  - "@drpatelh"
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test
new file mode 100644
index 00000000..05f54930
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test
@@ -0,0 +1,71 @@
+
+nextflow_function {
+
+    name "Test Functions"
+    script "subworkflows/nf-core/utils_nextflow_pipeline/main.nf"
+    config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config"
+    tag 'subworkflows'
+    tag 'utils_nextflow_pipeline'
+    tag 'subworkflows/utils_nextflow_pipeline'
+
+    test("Test Function getWorkflowVersion") {
+
+        function "getWorkflowVersion"
+
+        when {
+            function {
+                """
+                // no inputs
+                """
+            }
+        }
+
+        then {
+            assert function.success
+            assert snapshot(function.result).match()
+        }
+
+    }
+
+
+    test("Test Function dumpParametersToJSON") {
+
+        function "dumpParametersToJSON"
+
+        when {
+            function {
+                """
+                // define inputs of the function here. Example:
+                input[0] = "$outputDir"
+                """.stripIndent()
+            }
+        }
+
+        then {
+            assert function.success
+            assert function.result =~ /publish_dir_mode/
+            assert function.result =~ /copy/
+        }
+
+    }
+	
+    test("Test Function checkCondaChannels") {
+
+        function "checkCondaChannels"
+
+        when {
+            function {
+                """
+                // no inputs
+                """
+            }
+        }
+
+        then {
+            assert function.success
+            assert snapshot(function.result).match()
+        }
+
+    }
+
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test.snap
new file mode 100644
index 00000000..939dbbad
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test.snap
@@ -0,0 +1,12 @@
+{
+    "Test Function getWorkflowVersion": {
+        "content": [
+            "v9.9.9"
+        ],
+        "timestamp": "2023-10-15T13:43:55.128868"
+    },
+    "Test Function checkCondaChannels": {
+        "content": null,
+        "timestamp": "2023-10-12T17:09:24.933468"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
new file mode 100644
index 00000000..583f6a84
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -0,0 +1,104 @@
+nextflow_workflow {
+
+    name "Test Workflow UTILS_NEXTFLOW_PIPELINE"
+    script "../main.nf"
+    config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config"
+    workflow "UTILS_NEXTFLOW_PIPELINE"
+    tag 'subworkflows'
+    tag 'utils_nextflow_pipeline'
+    tag 'subworkflows/utils_nextflow_pipeline'
+
+    test("Should run no inputs") {
+
+        when {
+            params {
+                outdir = "tests/results"
+            }
+            workflow {
+                """
+                input[0] = false
+                input[1] = false
+                input[2] = null
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(workflow.out).match()
+        }
+
+    }
+
+    test("Should print version") {
+
+        when {
+            params {
+                outdir = "tests/results"
+            }
+            workflow {
+                """
+                input[0] = true
+                input[1] = false
+                input[2] = null
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.stdout.contains("nextflow_workflow v9.9.9")
+        }
+
+    }
+
+
+    test("Should dump params") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            workflow {
+                """
+                input[0] = false
+                input[1] = true
+                input[2] = params.outdir
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(workflow.out).match()
+        }
+
+    }
+
+    test("Should not create params JSON if no output directory") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            workflow {
+                """
+                input[0] = false
+                input[1] = true
+                input[2] = null
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(workflow.out, path(params.outdir).list()).match()
+        }
+
+    }
+
+}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test.snap
new file mode 100644
index 00000000..08040fd4
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test.snap
@@ -0,0 +1,44 @@
+{
+    "Should not create params JSON if no output directory": {
+        "content": [
+            {
+                "0": [
+                    true
+                ],
+                "out": [
+                    true
+                ]
+            },
+            [
+                
+            ]
+        ],
+        "timestamp": "2023-10-13T11:55:54.576748"
+    },
+    "Should dump params": {
+        "content": [
+            {
+                "0": [
+                    true
+                ],
+                "out": [
+                    true
+                ]
+            }
+        ],
+        "timestamp": "2023-10-13T11:55:52.711329"
+    },
+    "Should run no inputs": {
+        "content": [
+            {
+                "0": [
+                    true
+                ],
+                "out": [
+                    true
+                ]
+            }
+        ],
+        "timestamp": "2023-10-13T11:55:49.048315"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
new file mode 100644
index 00000000..53574ffe
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
@@ -0,0 +1,9 @@
+manifest {
+    name            = 'nextflow_workflow'
+    author          = """nf-core"""
+    homePage        = 'https://127.0.0.1'
+    description     = """Dummy pipeline"""
+    nextflowVersion  = '!>=23.04.0'
+    version         = '9.9.9'
+    doi             = 'https://doi.org/10.5281/zenodo.5070524'
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
new file mode 100644
index 00000000..f8476112
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/utils_nextflow_pipeline:
+  - subworkflows/nf-core/utils_nextflow_pipeline/**
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
new file mode 100644
index 00000000..d88aeebe
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -0,0 +1,311 @@
+//
+// Subworkflow with utility functions specific to the nf-core pipeline template
+//
+
+/*
+========================================================================================
+    SUBWORKFLOW DEFINITION
+========================================================================================
+*/
+
+workflow UTILS_NFCORE_PIPELINE {
+
+    main:
+    checkConfigProvided()
+
+    emit:
+    success = true
+
+}
+
+/*
+========================================================================================
+    FUNCTIONS
+========================================================================================
+*/
+
+//
+//  Warn if a -profile or Nextflow config has not been provided to run the pipeline
+//
+def checkConfigProvided() {
+    if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
+        log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
+            "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
+            "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
+            "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
+            "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
+            "Please refer to the quick start section and usage docs for the pipeline.\n "
+    }
+}
+
+//
+// Citation string for pipeline
+//
+def workflowCitation() {
+    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
+        "* The pipeline\n" +
+        "  ${workflow.manifest.doi}\n\n" +
+        "* The nf-core framework\n" +
+        "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
+        "* Software dependencies\n" +
+        "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
+}
+
+//
+// nf-core logo
+//
+def nfCoreLogo(workflow_version) {
+    Map colors = logColours()
+    String.format(
+        """\n
+        ${dashedLine()}
+                                                ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
+        ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
+        ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
+        ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
+                                                ${colors.green}`._,._,\'${colors.reset}
+        ${colors.purple}  ${workflow.manifest.name} ${workflow_version}${colors.reset}
+        ${dashedLine()}
+        """.stripIndent()
+    )
+}
+
+//
+// Return dashed line
+//
+def dashedLine() {
+    Map colors = logColours()
+    return "-${colors.dim}----------------------------------------------------${colors.reset}-"
+}
+
+//
+// ANSII colours used for terminal logging
+//
+def logColours() {
+    Map colorcodes = [:]
+
+    // Reset / Meta
+    colorcodes['reset']      = params.monochrome_logs ? '' : "\033[0m"
+    colorcodes['bold']       = params.monochrome_logs ? '' : "\033[1m"
+    colorcodes['dim']        = params.monochrome_logs ? '' : "\033[2m"
+    colorcodes['underlined'] = params.monochrome_logs ? '' : "\033[4m"
+    colorcodes['blink']      = params.monochrome_logs ? '' : "\033[5m"
+    colorcodes['reverse']    = params.monochrome_logs ? '' : "\033[7m"
+    colorcodes['hidden']     = params.monochrome_logs ? '' : "\033[8m"
+
+    // Regular Colors
+    colorcodes['black']      = params.monochrome_logs ? '' : "\033[0;30m"
+    colorcodes['red']        = params.monochrome_logs ? '' : "\033[0;31m"
+    colorcodes['green']      = params.monochrome_logs ? '' : "\033[0;32m"
+    colorcodes['yellow']     = params.monochrome_logs ? '' : "\033[0;33m"
+    colorcodes['blue']       = params.monochrome_logs ? '' : "\033[0;34m"
+    colorcodes['purple']     = params.monochrome_logs ? '' : "\033[0;35m"
+    colorcodes['cyan']       = params.monochrome_logs ? '' : "\033[0;36m"
+    colorcodes['white']      = params.monochrome_logs ? '' : "\033[0;37m"
+
+    // Bold
+    colorcodes['bblack']     = params.monochrome_logs ? '' : "\033[1;30m"
+    colorcodes['bred']       = params.monochrome_logs ? '' : "\033[1;31m"
+    colorcodes['bgreen']     = params.monochrome_logs ? '' : "\033[1;32m"
+    colorcodes['byellow']    = params.monochrome_logs ? '' : "\033[1;33m"
+    colorcodes['bblue']      = params.monochrome_logs ? '' : "\033[1;34m"
+    colorcodes['bpurple']    = params.monochrome_logs ? '' : "\033[1;35m"
+    colorcodes['bcyan']      = params.monochrome_logs ? '' : "\033[1;36m"
+    colorcodes['bwhite']     = params.monochrome_logs ? '' : "\033[1;37m"
+
+    // Underline
+    colorcodes['ublack']     = params.monochrome_logs ? '' : "\033[4;30m"
+    colorcodes['ured']       = params.monochrome_logs ? '' : "\033[4;31m"
+    colorcodes['ugreen']     = params.monochrome_logs ? '' : "\033[4;32m"
+    colorcodes['uyellow']    = params.monochrome_logs ? '' : "\033[4;33m"
+    colorcodes['ublue']      = params.monochrome_logs ? '' : "\033[4;34m"
+    colorcodes['upurple']    = params.monochrome_logs ? '' : "\033[4;35m"
+    colorcodes['ucyan']      = params.monochrome_logs ? '' : "\033[4;36m"
+    colorcodes['uwhite']     = params.monochrome_logs ? '' : "\033[4;37m"
+
+    // High Intensity
+    colorcodes['iblack']     = params.monochrome_logs ? '' : "\033[0;90m"
+    colorcodes['ired']       = params.monochrome_logs ? '' : "\033[0;91m"
+    colorcodes['igreen']     = params.monochrome_logs ? '' : "\033[0;92m"
+    colorcodes['iyellow']    = params.monochrome_logs ? '' : "\033[0;93m"
+    colorcodes['iblue']      = params.monochrome_logs ? '' : "\033[0;94m"
+    colorcodes['ipurple']    = params.monochrome_logs ? '' : "\033[0;95m"
+    colorcodes['icyan']      = params.monochrome_logs ? '' : "\033[0;96m"
+    colorcodes['iwhite']     = params.monochrome_logs ? '' : "\033[0;97m"
+
+    // Bold High Intensity
+    colorcodes['biblack']    = params.monochrome_logs ? '' : "\033[1;90m"
+    colorcodes['bired']      = params.monochrome_logs ? '' : "\033[1;91m"
+    colorcodes['bigreen']    = params.monochrome_logs ? '' : "\033[1;92m"
+    colorcodes['biyellow']   = params.monochrome_logs ? '' : "\033[1;93m"
+    colorcodes['biblue']     = params.monochrome_logs ? '' : "\033[1;94m"
+    colorcodes['bipurple']   = params.monochrome_logs ? '' : "\033[1;95m"
+    colorcodes['bicyan']     = params.monochrome_logs ? '' : "\033[1;96m"
+    colorcodes['biwhite']    = params.monochrome_logs ? '' : "\033[1;97m"
+
+    return colorcodes
+}
+
+//
+// Construct and send completion email
+//
+def completionEmail(summary_params) {
+
+    // Set up the e-mail variables
+    def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
+    if (!workflow.success) {
+        subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
+    }
+
+    def summary = [:]
+    for (group in summary_params.keySet()) {
+        summary << summary_params[group]
+    }
+
+    def misc_fields = [:]
+    misc_fields['Date Started']              = workflow.start
+    misc_fields['Date Completed']            = workflow.complete
+    misc_fields['Pipeline script file path'] = workflow.scriptFile
+    misc_fields['Pipeline script hash ID']   = workflow.scriptId
+    if (workflow.repository) misc_fields['Pipeline repository Git URL']    = workflow.repository
+    if (workflow.commitId)   misc_fields['Pipeline repository Git Commit'] = workflow.commitId
+    if (workflow.revision)   misc_fields['Pipeline Git branch/tag']        = workflow.revision
+    misc_fields['Nextflow Version']           = workflow.nextflow.version
+    misc_fields['Nextflow Build']             = workflow.nextflow.build
+    misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
+
+    def email_fields = [:]
+    email_fields['version']      = NfcoreTemplate.version(workflow)
+    email_fields['runName']      = workflow.runName
+    email_fields['success']      = workflow.success
+    email_fields['dateComplete'] = workflow.complete
+    email_fields['duration']     = workflow.duration
+    email_fields['exitStatus']   = workflow.exitStatus
+    email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+    email_fields['errorReport']  = (workflow.errorReport ?: 'None')
+    email_fields['commandLine']  = workflow.commandLine
+    email_fields['projectDir']   = workflow.projectDir
+    email_fields['summary']      = summary << misc_fields
+
+    // Check if we are only sending emails on failure
+    def email_address = params.email
+    if (!params.email && params.email_on_fail && !workflow.success) {
+        email_address = params.email_on_fail
+    }
+
+    // Render the TXT template
+    def engine       = new groovy.text.GStringTemplateEngine()
+    def tf           = new File("${workflow.projectDir}/assets/email_template.txt")
+    def txt_template = engine.createTemplate(tf).make(email_fields)
+    def email_txt    = txt_template.toString()
+
+    // Render the HTML template
+    def hf            = new File("${workflow.projectDir}/assets/email_template.html")
+    def html_template = engine.createTemplate(hf).make(email_fields)
+    def email_html    = html_template.toString()
+
+    // Render the sendmail template
+    def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}" ]
+    def sf                     = new File("${workflow.projectDir}/assets/sendmail_template.txt")
+    def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
+    def sendmail_html          = sendmail_template.toString()
+
+    // Send the HTML e-mail
+    Map colors = logColours()
+    if (email_address) {
+        try {
+            if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+            // Try to send HTML e-mail using sendmail
+            [ 'sendmail', '-t' ].execute() << sendmail_html
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
+        } catch (all) {
+            // Catch failures and try with plaintext
+            def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
+            mail_cmd.execute() << email_html
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
+        }
+    }
+
+    // Write summary e-mail HTML to a file
+    def output_d = new File("${params.outdir}/pipeline_info/")
+    if (!output_d.exists()) {
+        output_d.mkdirs()
+    }
+    def output_hf = new File(output_d, "pipeline_report.html")
+    output_hf.withWriter { w -> w << email_html }
+    def output_tf = new File(output_d, "pipeline_report.txt")
+    output_tf.withWriter { w -> w << email_txt }
+}
+
+//
+// Print pipeline summary on completion
+//
+def completionSummary() {
+    Map colors = logColours()
+    if (workflow.success) {
+        if (workflow.stats.ignoredCount == 0) {
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
+        } else {
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
+        }
+    } else {
+        log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
+    }
+}
+
+//
+// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack
+//
+def imNotification(summary_params) {
+    def hook_url = params.hook_url
+
+    def summary = [:]
+    for (group in summary_params.keySet()) {
+        summary << summary_params[group]
+    }
+
+    def misc_fields = [:]
+    misc_fields['start']                                = workflow.start
+    misc_fields['complete']                             = workflow.complete
+    misc_fields['scriptfile']                           = workflow.scriptFile
+    misc_fields['scriptid']                             = workflow.scriptId
+    if (workflow.repository) misc_fields['repository']  = workflow.repository
+    if (workflow.commitId)   misc_fields['commitid']    = workflow.commitId
+    if (workflow.revision)   misc_fields['revision']    = workflow.revision
+    misc_fields['nxf_version']                          = workflow.nextflow.version
+    misc_fields['nxf_build']                            = workflow.nextflow.build
+    misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
+
+    def msg_fields = [:]
+    msg_fields['version']      = NfcoreTemplate.version(workflow)
+    msg_fields['runName']      = workflow.runName
+    msg_fields['success']      = workflow.success
+    msg_fields['dateComplete'] = workflow.complete
+    msg_fields['duration']     = workflow.duration
+    msg_fields['exitStatus']   = workflow.exitStatus
+    msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+    msg_fields['errorReport']  = (workflow.errorReport ?: 'None')
+    msg_fields['commandLine']  = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "")
+    msg_fields['projectDir']   = workflow.projectDir
+    msg_fields['summary']      = summary << misc_fields
+
+    // Render the JSON template
+    def engine       = new groovy.text.GStringTemplateEngine()
+    // Different JSON depending on the service provider
+    // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format
+    def json_path     = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json"
+    def hf            = new File("${workflow.projectDir}/assets/${json_path}")
+    def json_template = engine.createTemplate(hf).make(msg_fields)
+    def json_message  = json_template.toString()
+
+    // POST
+    def post = new URL(hook_url).openConnection();
+    post.setRequestMethod("POST")
+    post.setDoOutput(true)
+    post.setRequestProperty("Content-Type", "application/json")
+    post.getOutputStream().write(json_message.getBytes("UTF-8"));
+    def postRC = post.getResponseCode();
+    if (! postRC.equals(200)) {
+        log.warn(post.getErrorStream().getText());
+    }
+}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml
new file mode 100644
index 00000000..953f7143
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml
@@ -0,0 +1,19 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "UTILS_NFCORE_PIPELINE"
+description: Subworkflow with utility functions specific to the nf-core pipeline template
+keywords:
+  - utility
+  - pipeline
+  - initialise
+  - version
+components: []
+input: []
+output:
+  - success:
+      type: boolean
+      description: |
+        Dummy output to indicate success
+authors:
+  - "@adamrtalbot"
+maintainers:
+  - "@adamrtalbot"
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
new file mode 100644
index 00000000..63988b1b
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
@@ -0,0 +1,124 @@
+
+nextflow_function {
+
+    name "Test Functions"
+    script "../main.nf"
+    config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "utils_nfcore_pipeline"
+    tag "subworkflows/utils_nfcore_pipeline"
+
+    test("Test Function checkConfigProvided") {
+
+        function "checkConfigProvided"
+
+        when {
+            function {
+                """
+                // define inputs of the function here. Example:
+                // input[0] = 1
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert function.success                  },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+    test("Test Function workflowCitation") {
+
+        function "workflowCitation"
+
+        when {
+            function {
+                """
+                // define inputs of the function here. Example:
+                // input[0] = 1
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert function.success                  },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+    test("Test Function nfCoreLogo") {
+
+        function "nfCoreLogo"
+
+        when {
+            function {
+                """
+                input[0] = "9.9.9"
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert function.success                  },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+
+
+    test("Test Function dashedLine") {
+
+        function "dashedLine"
+
+        when {
+            function {
+                """
+                // define inputs of the function here. Example:
+                // input[0] = 1
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert function.success                  },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+
+
+
+    test("Test Function logColours") {
+
+        function "logColours"
+
+        when {
+            function {
+                """
+                // define inputs of the function here. Example:
+                // input[0] = 1
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert function.success                  },
+                { assert snapshot(function.result).match() }
+            )
+        }
+
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
new file mode 100644
index 00000000..3ea51f68
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
@@ -0,0 +1,78 @@
+{
+    "Test Function logColours": {
+        "content": [
+            {
+                "reset": "\u001b[0m",
+                "bold": "\u001b[1m",
+                "dim": "\u001b[2m",
+                "underlined": "\u001b[4m",
+                "blink": "\u001b[5m",
+                "reverse": "\u001b[7m",
+                "hidden": "\u001b[8m",
+                "black": "\u001b[0;30m",
+                "red": "\u001b[0;31m",
+                "green": "\u001b[0;32m",
+                "yellow": "\u001b[0;33m",
+                "blue": "\u001b[0;34m",
+                "purple": "\u001b[0;35m",
+                "cyan": "\u001b[0;36m",
+                "white": "\u001b[0;37m",
+                "bblack": "\u001b[1;30m",
+                "bred": "\u001b[1;31m",
+                "bgreen": "\u001b[1;32m",
+                "byellow": "\u001b[1;33m",
+                "bblue": "\u001b[1;34m",
+                "bpurple": "\u001b[1;35m",
+                "bcyan": "\u001b[1;36m",
+                "bwhite": "\u001b[1;37m",
+                "ublack": "\u001b[4;30m",
+                "ured": "\u001b[4;31m",
+                "ugreen": "\u001b[4;32m",
+                "uyellow": "\u001b[4;33m",
+                "ublue": "\u001b[4;34m",
+                "upurple": "\u001b[4;35m",
+                "ucyan": "\u001b[4;36m",
+                "uwhite": "\u001b[4;37m",
+                "iblack": "\u001b[0;90m",
+                "ired": "\u001b[0;91m",
+                "igreen": "\u001b[0;92m",
+                "iyellow": "\u001b[0;93m",
+                "iblue": "\u001b[0;94m",
+                "ipurple": "\u001b[0;95m",
+                "icyan": "\u001b[0;96m",
+                "iwhite": "\u001b[0;97m",
+                "biblack": "\u001b[1;90m",
+                "bired": "\u001b[1;91m",
+                "bigreen": "\u001b[1;92m",
+                "biyellow": "\u001b[1;93m",
+                "biblue": "\u001b[1;94m",
+                "bipurple": "\u001b[1;95m",
+                "bicyan": "\u001b[1;96m",
+                "biwhite": "\u001b[1;97m"
+            }
+        ],
+        "timestamp": "2023-10-16T14:27:09.843064"
+    },
+    "Test Function checkConfigProvided": {
+        "content": null,
+        "timestamp": "2023-10-16T14:27:01.415849"
+    },
+    "Test Function nfCoreLogo": {
+        "content": [
+            "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n                                        \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m        ___     __   __   __   ___     \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \u001b[0;33m}  {\u001b[0m\n\u001b[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \u001b[0;32m\\`-._,-`-,\u001b[0m\n                                        \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m  nextflow_workflow 9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n"
+        ],
+        "timestamp": "2023-10-16T14:27:51.566211"
+    },
+    "Test Function workflowCitation": {
+        "content": [
+            "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n  https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n  https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n  https://github.com/nextflow_workflow/blob/master/CITATIONS.md"
+        ],
+        "timestamp": "2023-10-16T14:27:03.505737"
+    },
+    "Test Function dashedLine": {
+        "content": [
+            "-\u001b[2m----------------------------------------------------\u001b[0m-"
+        ],
+        "timestamp": "2023-10-16T14:27:07.721916"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
new file mode 100644
index 00000000..637a416d
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
@@ -0,0 +1,33 @@
+nextflow_workflow {
+
+    name "Test Workflow UTILS_NFCORE_PIPELINE"
+    script "../main.nf"
+    config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
+    workflow "UTILS_NFCORE_PIPELINE"
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "utils_nfcore_pipeline"
+    tag "subworkflows/utils_nfcore_pipeline"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                // define parameters here. Example:
+                // outdir = "tests/results"
+            }
+            workflow {
+                """
+                // define inputs of the workflow here. Example:
+                // input[0] = file("test-file.txt")
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
+}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
new file mode 100644
index 00000000..53574ffe
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
@@ -0,0 +1,9 @@
+manifest {
+    name            = 'nextflow_workflow'
+    author          = """nf-core"""
+    homePage        = 'https://127.0.0.1'
+    description     = """Dummy pipeline"""
+    nextflowVersion  = '!>=23.04.0'
+    version         = '9.9.9'
+    doi             = 'https://doi.org/10.5281/zenodo.5070524'
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
new file mode 100644
index 00000000..ac8523c9
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/utils_nfcore_pipeline:
+  - subworkflows/nf-core/utils_nfcore_pipeline/**
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
new file mode 100644
index 00000000..43c57187
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
@@ -0,0 +1,62 @@
+//
+// Subworkflow that uses the nf-validation plugin to render help text and parameter summary
+//
+
+/*
+========================================================================================
+    IMPORT NF-VALIDATION PLUGIN
+========================================================================================
+*/
+
+include { paramsHelp; paramsSummaryLog; paramsSummaryMap; validateParameters } from 'plugin/nf-validation'
+
+/*
+========================================================================================
+    SUBWORKFLOW DEFINITION
+========================================================================================
+*/
+
+workflow UTILS_NFVALIDATION_PLUGIN {
+
+    take:
+        print_help        // bool
+        workflow_command   // string: default commmand used to run pipeline
+        pre_help_text     // string: string to be printed before help text and summary log
+        post_help_text    // string: string to be printed after help text and summary log
+        validate_params   // bool: Validate parameters
+        schema_filename    // path: JSON schema file, null to use default value
+
+    main:
+
+        log.debug "Using schema file: ${schema_filename}"
+
+        // Default values for strings
+        pre_help_text   = pre_help_text    ?: ''
+        post_help_text  = post_help_text   ?: ''
+        workflow_command = workflow_command  ?: ''
+
+        //
+        // Print help message if needed
+        //
+        if (print_help) {
+            log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text
+            System.exit(0)
+        }
+
+        //
+        // Print parameter summary to stdout
+        //
+        log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text
+
+        //
+        // Validate parameters relative to the parameter JSON schema
+        //
+        if (validate_params){
+            validateParameters(parameters_schema: schema_filename)
+        }
+
+        summary_params = paramsSummaryMap(workflow, parameters_schema: schema_filename)
+
+    emit:
+        summary_params = summary_params
+}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
new file mode 100644
index 00000000..80438ccf
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
@@ -0,0 +1,46 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "UTILS_NFVALIDATION_PLUGIN"
+description: Use nf-validation to initiate and validate a pipeline
+keywords:
+  - utility
+  - pipeline
+  - initialise
+  - validation
+components: []
+input:
+  - print_help:
+      type: boolean
+      description: |
+        Print help message and exit
+  - workflow_command:
+      type: string
+      description: |
+        The command to run the workflow e.g. "nextflow run main.nf"
+  - pre_help_text:
+      type: string
+      description: |
+        Text to print before the help message
+  - post_help_text:
+      type: string
+      description: |
+        Text to print after the help message
+  - validate_params:
+      type: boolean
+      description: |
+        Validate the parameters and error if invalid.
+  - schema_filename:
+      type: string
+      description: |
+        The filename of the schema to validate against.
+
+output:
+  - summary_params:
+      type: file
+      description: |
+        A Groovy map constructed from parameters.
+        Structure: [ val(meta), path(bam) ]
+      pattern: "*.bam"
+authors:
+  - "@adamrtalbot"
+maintainers:
+  - "@adamrtalbot"
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
new file mode 100644
index 00000000..904f97be
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
@@ -0,0 +1,201 @@
+nextflow_workflow {
+
+    name "Test Workflow UTILS_NFVALIDATION_PLUGIN"
+    script "../main.nf"
+    workflow "UTILS_NFVALIDATION_PLUGIN"
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "plugin/nf-validation"
+    tag "'plugin/nf-validation'"
+    tag "utils_nfvalidation_plugin"
+    tag "subworkflows/utils_nfvalidation_plugin"
+
+    test("Should run nothing") {
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+            }
+
+            workflow {
+                """
+                help            = false
+                workflow_command = null
+                pre_help_text   = null
+                post_help_text  = null
+                validate_params = false
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
+    test("Should run help") {
+
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+            }
+            workflow {
+                """
+                help             = true
+                workflow_command = null
+                pre_help_text    = null
+                post_help_text   = null
+                validate_params  = false
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.exitStatus == 0
+            assert workflow.stdout.any { it.contains('Input/output options') }
+            assert workflow.stdout.any { it.contains('--outdir') }
+            assert workflow.stdout.any { it.contains('--outdir') }
+        }
+
+    }
+
+    test("Should run help with command") {
+
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+            }
+            workflow {
+                """
+                help             = true
+                workflow_command  = "nextflow run noorg/doesntexist"
+                pre_help_text    = null
+                post_help_text   = null
+                validate_params  = false
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.exitStatus == 0
+            assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') }
+            assert workflow.stdout.any { it.contains('Input/output options') }
+            assert workflow.stdout.any { it.contains('--outdir') }
+            assert workflow.stdout.any { it.contains('--outdir') }
+        }
+
+    }
+
+    test("Should run help with extra text") {
+
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+            }
+            workflow {
+                """
+                help             = true
+                workflow_command  = "nextflow run noorg/doesntexist"
+                pre_help_text    = "pre-help-text"
+                post_help_text   = "post-help-text"
+                validate_params  = false
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.exitStatus == 0
+            assert workflow.stdout.any { it.contains('pre-help-text') }
+            assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') }
+            assert workflow.stdout.any { it.contains('Input/output options') }
+            assert workflow.stdout.any { it.contains('--outdir') }
+            assert workflow.stdout.any { it.contains('--outdir') }
+            assert workflow.stdout.any { it.contains('post-help-text') }
+        }
+
+    }
+
+    test("Should validate params") {
+
+
+        when {
+
+            params {
+                monochrome_logs = true
+                test_data       = ''
+                outdir          = 1
+            }
+            workflow {
+                """
+                help             = false
+                workflow_command  = null
+                pre_help_text    = null
+                post_help_text   = null
+                validate_params  = true
+                schema_filename  = "$moduleTestDir/nextflow_schema.json"
+
+                input[0] = help
+                input[1] = workflow_command
+                input[2] = pre_help_text
+                input[3] = post_help_text
+                input[4] = validate_params
+                input[5] = schema_filename
+                """
+            }
+        }
+
+        then {
+            assert workflow.failed
+            assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') }
+        }
+
+    }
+
+}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test.snap b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test.snap
new file mode 100644
index 00000000..ae33a930
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test.snap
@@ -0,0 +1,26 @@
+{
+    "Should run help": {
+        "content": [
+            {
+                "stderr": [
+
+                ],
+                "errorReport": "",
+                "exitStatus": 0,
+                "failed": false,
+                "stdout": [
+
+                ],
+                "errorMessage": "",
+                "trace": {
+                    "tasksFailed": 0,
+                    "tasksCount": 0,
+                    "tasksSucceeded": 0
+                },
+                "name": "workflow",
+                "success": true
+            }
+        ],
+        "timestamp": "2023-10-13T13:18:16.933251413"
+    }
+}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
new file mode 100644
index 00000000..7626c1c9
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
@@ -0,0 +1,96 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
+    "title": ". pipeline parameters",
+    "description": "",
+    "type": "object",
+    "definitions": {
+        "input_output_options": {
+            "title": "Input/output options",
+            "type": "object",
+            "fa_icon": "fas fa-terminal",
+            "description": "Define where the pipeline should find input data and save output data.",
+            "required": ["outdir"],
+            "properties": {
+                "validate_params": {
+                    "type": "boolean",
+                    "description": "Validate parameters?",
+                    "default": true,
+                    "hidden": true
+                },
+                "outdir": {
+                    "type": "string",
+                    "format": "directory-path",
+                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
+                    "fa_icon": "fas fa-folder-open"
+                },
+                "test_data_base": {
+                    "type": "string",
+                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules",
+                    "description": "Base for test data directory",
+                    "hidden": true
+                },
+                "test_data": {
+                    "type": "string",
+                    "description": "Fake test data param",
+                    "hidden": true
+                }
+            }
+        },
+        "generic_options": {
+            "title": "Generic options",
+            "type": "object",
+            "fa_icon": "fas fa-file-import",
+            "description": "Less common options for the pipeline, typically set in a config file.",
+            "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
+            "properties": {
+                "help": {
+                    "type": "boolean",
+                    "description": "Display help text.",
+                    "fa_icon": "fas fa-question-circle",
+                    "hidden": true
+                },
+                "version": {
+                    "type": "boolean",
+                    "description": "Display version and exit.",
+                    "fa_icon": "fas fa-question-circle",
+                    "hidden": true
+                },
+                "logo": {
+                    "type": "boolean",
+                    "default": true,
+                    "description": "Display nf-core logo in console output.",
+                    "fa_icon": "fas fa-image",
+                    "hidden": true
+                },
+                "singularity_pull_docker_container": {
+                    "type": "boolean",
+                    "description": "Pull Singularity container from Docker?",
+                    "hidden": true
+                },
+                "publish_dir_mode": {
+                    "type": "string",
+                    "default": "copy",
+                    "description": "Method used to save pipeline results to output directory.",
+                    "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
+                    "fa_icon": "fas fa-copy",
+                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
+                    "hidden": true
+                },
+                "monochrome_logs": {
+                    "type": "boolean",
+                    "description": "Use monochrome_logs",
+                    "hidden": true
+                }
+            }
+        }
+    },
+    "allOf": [
+        {
+            "$ref": "#/definitions/input_output_options"
+        },
+        {
+            "$ref": "#/definitions/generic_options"
+        }
+    ]
+}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
new file mode 100644
index 00000000..60b1cfff
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/utils_nfvalidation_plugin:
+  - subworkflows/nf-core/utils_nfvalidation_plugin/**

From 596ca7cd2b0ae2f485d12f43fee159eea7230182 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Jan 2024 18:23:06 +0000
Subject: [PATCH 647/852] Re-add nextflow config files for publishing

---
 modules/nf-core/sratools/fasterqdump/nextflow.config   | 10 ++++++++++
 modules/nf-core/sratools/prefetch/nextflow.config      |  8 ++++++++
 .../nextflow.config                                    |  2 ++
 3 files changed, 20 insertions(+)
 create mode 100644 modules/nf-core/sratools/fasterqdump/nextflow.config
 create mode 100644 modules/nf-core/sratools/prefetch/nextflow.config
 create mode 100644 subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config

diff --git a/modules/nf-core/sratools/fasterqdump/nextflow.config b/modules/nf-core/sratools/fasterqdump/nextflow.config
new file mode 100644
index 00000000..f98b140d
--- /dev/null
+++ b/modules/nf-core/sratools/fasterqdump/nextflow.config
@@ -0,0 +1,10 @@
+process {
+    withName: SRATOOLS_FASTERQDUMP {
+        ext.args = '--split-files --include-technical'
+        publishDir = [
+            path: { "${params.outdir}/fastq" },
+            mode: params.publish_dir_mode,
+            pattern: "*.fastq.gz"
+        ]
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/sratools/prefetch/nextflow.config b/modules/nf-core/sratools/prefetch/nextflow.config
new file mode 100644
index 00000000..a2ca8848
--- /dev/null
+++ b/modules/nf-core/sratools/prefetch/nextflow.config
@@ -0,0 +1,8 @@
+process {
+    withName: SRATOOLS_PREFETCH {
+        publishDir = [
+            path: { "${params.outdir}/sra" },
+            enabled: false
+        ]
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config
new file mode 100644
index 00000000..b11c499f
--- /dev/null
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config
@@ -0,0 +1,2 @@
+includeConfig '../../../modules/nf-core/sratools/prefetch/nextflow.config'
+includeConfig '../../../modules/nf-core/sratools/fasterqdump/nextflow.config'
\ No newline at end of file

From d0efbaca3bea884a4fef01c17bdb3914ddbf68ca Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 8 Jan 2024 18:38:52 +0000
Subject: [PATCH 648/852] Rename local subworkflow to
 utils_nfcore_fetchngs_pipeline

---
 main.nf                                          |  4 ++--
 .../main.nf                                      | 16 ++++++++--------
 2 files changed, 10 insertions(+), 10 deletions(-)
 rename subworkflows/local/{nf_core_fetchngs_utils => utils_nfcore_fetchngs_pipeline}/main.nf (95%)

diff --git a/main.nf b/main.nf
index bf39d7ea..2fe0061e 100644
--- a/main.nf
+++ b/main.nf
@@ -57,8 +57,8 @@ workflow NFCORE_FETCHNGS {
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { PIPELINE_INITIALISATION } from './subworkflows/local/nf_core_fetchngs_utils'
-include { PIPELINE_COMPLETION     } from './subworkflows/local/nf_core_fetchngs_utils'
+include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_fetchngs_pipeline'
+include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_fetchngs_pipeline'
 
 //
 // WORKFLOW: Execute a single named workflow for the pipeline
diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
similarity index 95%
rename from subworkflows/local/nf_core_fetchngs_utils/main.nf
rename to subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
index 509a4473..42e115f8 100644
--- a/subworkflows/local/nf_core_fetchngs_utils/main.nf
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
@@ -8,17 +8,17 @@
 ========================================================================================
 */
 
-include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion } from '../../nf-core/nextflowpipelineutils/main'
-include { NF_VALIDATION_PLUGIN_UTILS                  } from '../../nf-core/nfvalidation_plugin_utils/main.nf'
+include { UTILS_NEXTFLOW_PIPELINE; getWorkflowVersion } from '../../nf-core/utils_nextflow_pipeline'
+include { UTILS_NFVALIDATION_PLUGIN                   } from '../../nf-core/utils_nfvalidation_plugin'
 include { 
-    NFCORE_PIPELINE_UTILS; 
+    UTILS_NFCORE_PIPELINE; 
     workflowCitation; 
     nfCoreLogo; 
     dashedLine; 
     completionEmail; 
     completionSummary; 
     imNotification 
-} from '../../nf-core/nfcore_pipeline_utils'
+} from '../../nf-core/utils_nfcore_pipeline'
 
 /*
 ========================================================================================
@@ -33,7 +33,7 @@ workflow PIPELINE_INITIALISATION {
     //
     // Print version and exit if required and dump pipeline parameters to JSON file
     //
-    NEXTFLOW_PIPELINE_UTILS (
+    UTILS_NEXTFLOW_PIPELINE (
         params.version,
         true,
         params.outdir,
@@ -46,7 +46,7 @@ workflow PIPELINE_INITIALISATION {
     def pre_help_text = nfCoreLogo(getWorkflowVersion())
     def post_help_text = '\n' + workflowCitation() + '\n' + dashedLine()
     def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input ids.csv --outdir <OUTDIR>"
-    NF_VALIDATION_PLUGIN_UTILS (
+    UTILS_NFVALIDATION_PLUGIN (
         params.help,
         workflow_command,
         pre_help_text,
@@ -58,7 +58,7 @@ workflow PIPELINE_INITIALISATION {
     //
     // Check config provided to the pipeline
     //
-    NFCORE_PIPELINE_UTILS ()
+    UTILS_NFCORE_PIPELINE ()
 
     //
     // Auto-detect input id type
@@ -88,7 +88,7 @@ workflow PIPELINE_INITIALISATION {
 
     emit:
     ids            = ch_ids
-    summary_params = NF_VALIDATION_PLUGIN_UTILS.out.summary_params
+    summary_params = UTILS_NFVALIDATION_PLUGIN.out.summary_params
 }
 
 /*

From 06123e0217fd6173572f847699a7f7447551e4d7 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 9 Jan 2024 13:21:43 +0100
Subject: [PATCH 649/852] deal with picture dark and light mode properly

---
 README.md | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index be373b35..f650c9a7 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,7 @@
-# ![nf-core/fetchngs](docs/images/nf-core-fetchngs_logo_light.png#gh-light-mode-only) ![nf-core/fetchngs](docs/images/nf-core-fetchngs_logo_dark.png#gh-dark-mode-only)
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-fetchngs_logo_dark.png">
+  <img alt="nf-core/fetchngs logo" src="nf-core-fetchngs_logo_light.png">
+</picture>
 
 [![GitHub Actions CI Status](https://github.com/nf-core/fetchngs/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/fetchngs/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/nf-core/fetchngs/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/fetchngs/actions?query=workflow%3A%22nf-core+linting%22)

From 51af5b54ac113112897754a5e3e44c68f872c09c Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 9 Jan 2024 13:23:58 +0100
Subject: [PATCH 650/852] update CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 48944423..c354cd3f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,6 +21,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #241](https://github.com/nf-core/fetchngs/pull/241) - Download of big files time out and don't resume ([#169](https://github.com/nf-core/fetchngs/issues/169))
 - [PR #242](https://github.com/nf-core/fetchngs/pull/242) - Template update for nf-core/tools v2.11
 - [PR #243](https://github.com/nf-core/fetchngs/pull/243) - Fixes for [PR #238](https://github.com/nf-core/fetchngs/pull/238)
+- [PR #246](https://github.com/nf-core/fetchngs/pull/246) - Handle dark/light mode for logo in GitHub README properly
 
 ### Software dependencies
 

From 09600981c1f21c94eb169d19a72a9dd4050c61f3 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 9 Jan 2024 13:26:50 +0100
Subject: [PATCH 651/852] fix path to logo

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index f650c9a7..eb369218 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 <picture>
   <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-fetchngs_logo_dark.png">
-  <img alt="nf-core/fetchngs logo" src="nf-core-fetchngs_logo_light.png">
+  <img alt="nf-core/fetchngs logo" src="docs/images/nf-core-fetchngs_logo_light.png">
 </picture>
 
 [![GitHub Actions CI Status](https://github.com/nf-core/fetchngs/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/fetchngs/actions?query=workflow%3A%22nf-core+CI%22)

From 259e281ba68e092440c0e734845518b55704baa0 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Tue, 9 Jan 2024 15:45:47 +0100
Subject: [PATCH 652/852] Update README.md

wrap picture in h1 cf https://github.com/nf-core/tools/pull/2647
---
 README.md | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index eb369218..56ba2cb0 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,9 @@
-<picture>
-  <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-fetchngs_logo_dark.png">
-  <img alt="nf-core/fetchngs logo" src="docs/images/nf-core-fetchngs_logo_light.png">
-</picture>
+<h1>
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-fetchngs_logo_dark.png">
+    <img alt="nf-core/fetchngs logo" src="docs/images/nf-core-fetchngs_logo_light.png">
+  </picture>
+</h1>
 
 [![GitHub Actions CI Status](https://github.com/nf-core/fetchngs/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/fetchngs/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/nf-core/fetchngs/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/fetchngs/actions?query=workflow%3A%22nf-core+linting%22)

From f9eb52509483a646bb53ef7e39b95cfdcc138b25 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 9 Jan 2024 17:39:31 +0000
Subject: [PATCH 653/852] Proof of concept to refactor test data usage for
 nf-test in modules and pipelines

---
 .github/workflows/ci.yml                      |  6 +---
 conf/test_data.config                         | 33 -------------------
 .../tests/main.nf.test                        |  2 +-
 .../local/sra_fastq_ftp/tests/main.nf.test    |  5 ++-
 .../sra_runinfo_to_ftp/tests/main.nf.test     |  2 +-
 .../sratoolsncbisettings/tests/main.nf.test   |  2 +-
 .../tests/main.nf.test.snap                   |  8 +++++
 .../sratools/fasterqdump/tests/main.nf.test   |  8 ++---
 .../fasterqdump/tests/main.nf.test.snap       | 16 ++++-----
 .../sratools/prefetch/tests/main.nf.test      |  4 +--
 modules/nf-core/untar/tests/main.nf.test      |  6 ++--
 nextflow.config                               |  5 +--
 .../tests/main.nf.test.snap                   | 14 ++++----
 tests/nextflow.config                         | 18 ++++++++++
 14 files changed, 59 insertions(+), 70 deletions(-)
 delete mode 100644 conf/test_data.config

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b395350f..9034d1db 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -102,13 +102,9 @@ jobs:
           wget -qO- https://code.askimed.com/install/nf-test | bash
           sudo mv nf-test /usr/local/bin/
 
-      - name: Install icdiff for nf-test diff viewing
-        run: |
-          sudo apt install icdiff
-
       - name: Run nf-test
         run: |
-          nf-test test --verbose --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
+          nf-test test --verbose --tag ${{ matrix.tags }} --profile "${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
 
       - uses: pcolby/tap-summary@v1
         with:
diff --git a/conf/test_data.config b/conf/test_data.config
deleted file mode 100644
index 167dff83..00000000
--- a/conf/test_data.config
+++ /dev/null
@@ -1,33 +0,0 @@
-params {
-    // Base directory for test data
-    test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs"
-
-    fastq_ftp_ids = ["SRR13191702"]
-    def fastq_ftp_url  = "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/"
-    def fastq_ftp_urls = []
-
-    fastq_ftp_ids.each { id ->
-        fastq_ftp_urls += "${fastq_ftp_url}${id}_1.fastq.gz"
-        fastq_ftp_urls += "${fastq_ftp_url}${id}_2.fastq.gz"
-    }
-
-    test_data {
-        'sarscov2'{
-            'illumina' {
-                SRR11140744_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR11140744.tar.gz"
-                SRR13255544_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR13255544.tar.gz"
-            }
-        }
-        'generic' {
-            'config' {
-                ncbi_user_settings = "${params.test_data_base}/data/generic/config/ncbi_user_settings.mkfg"
-            }
-        }
-        'modules_local' {
-                multiqc_mappings_config = "${params.test_data_base}/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv"
-                sra_to_samplesheet      = "${params.test_data_base}/modules/local/sra_to_samplesheet/SRX9626017_SRR13191702.mappings.csv"
-                sra_fastq_ftp           = fastq_ftp_urls
-                sra_runinfo_to_ftp      = "${params.test_data_base}/modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv"
-        }
-    }
-}
diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test
index 75356197..c49cedd7 100644
--- a/modules/local/multiqc_mappings_config/tests/main.nf.test
+++ b/modules/local/multiqc_mappings_config/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
 
             process {
                 """
-                input[0] = file(params.test_data['modules_local']['multiqc_mappings_config'], checkIfExists: true)
+                input[0] = file(params.pipelines_test_data_base + '/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv', checkIfExists: true)
                 """
             }
         }
diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test
index ab846e5d..55b34bce 100644
--- a/modules/local/sra_fastq_ftp/tests/main.nf.test
+++ b/modules/local/sra_fastq_ftp/tests/main.nf.test
@@ -18,7 +18,10 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'SRX9626017_SRR13191702', single_end:false, md5_1: '89c5be920021a035084d8aeb74f32df7', md5_2: '56271be38a80db78ef3bdfc5d9909b98' ], // meta map
-                    params.test_data['modules_local']['sra_fastq_ftp']
+                    [ 
+                        'ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz',
+                        'ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz'
+                    ]
                 ]
                 """
             }
diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
index 3b1405f9..4dbe2570 100644
--- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
+++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
 
             process {
                 """
-                input[0] = file(params.test_data['modules_local']['sra_runinfo_to_ftp'], checkIfExists: true)
+                input[0] = file(params.pipelines_test_data_base + '/modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv', checkIfExists: true)
                 """
             }
         }
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
index ec4a7797..989487f1 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
+++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
@@ -20,7 +20,7 @@ nextflow_process {
             process {
                 """
                 file(params.settings_path).mkdirs()
-                def settings = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true)
+                def settings = file(params.modules_test_data_base + '/data/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
                 settings.copyTo(params.settings_file)
                 """
             }
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap
index edb3b351..035aeeb7 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap
+++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap
@@ -1,4 +1,12 @@
 {
+    "Should fail": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "timestamp": "2024-01-09T12:59:19.679292"
+    },
     "Should run with nonexisting": {
         "content": [
             [
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
index e194b52a..662fdde6 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
@@ -13,7 +13,7 @@ nextflow_process {
                 script "modules/nf-core/untar/main.nf"
                 process {
                     """
-                    input[0] = Channel.of([ [], file(params.test_data['sarscov2']['illumina']['SRR13255544_tar_gz'], checkIfExists: true) ])
+                    input[0] = Channel.of([ [], file(params.modules_test_data_base + '/data/genomics/sarscov2/illumina/sra/SRR13255544.tar.gz', checkIfExists: true) ])
                     """
                 }
             }
@@ -23,7 +23,7 @@ nextflow_process {
             process {
                 """
                 input[0] = UNTAR.out.untar.map{ meta, files -> [ [ id:'test_single_end', single_end:true ], files]}
-                input[1] = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true)
+                input[1] = file(params.modules_test_data_base + '/data/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
                 input[2] = []
                 """
             }
@@ -44,7 +44,7 @@ nextflow_process {
                 script "modules/nf-core/untar/main.nf"
                 process {
                     """
-                    input[0] = Channel.of([ [], file(params.test_data['sarscov2']['illumina']['SRR11140744_tar_gz'], checkIfExists: true) ])
+                    input[0] = Channel.of([ [], file(params.modules_test_data_base + '/data/genomics/sarscov2/illumina/sra/SRR11140744.tar.gz', checkIfExists: true) ])
                     """
                 }
             }
@@ -54,7 +54,7 @@ nextflow_process {
             process {
                 """
                 input[0] = UNTAR.out.untar.map{ meta, files -> [ [ id:'test_paired_end', single_end:false ], files]}
-                input[1] = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true)
+                input[1] = file(params.modules_test_data_base + '/data/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
                 input[2] = []
                 """
             }
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
index d3bf90f7..123feb2e 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
@@ -8,7 +8,7 @@
                             "id": "test_single_end",
                             "single_end": true
                         },
-                        "test_single_end.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82"
+                        "test_single_end_1.fastq.gz:md5,674d78c1cc3c1308d6d39d6369a42887"
                     ]
                 ],
                 "1": [
@@ -20,7 +20,7 @@
                             "id": "test_single_end",
                             "single_end": true
                         },
-                        "test_single_end.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82"
+                        "test_single_end_1.fastq.gz:md5,674d78c1cc3c1308d6d39d6369a42887"
                     ]
                 ],
                 "versions": [
@@ -28,7 +28,7 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-10T18:11:12.87053"
+        "timestamp": "2024-01-09T12:55:00.629261"
     },
     "Paired-end": {
         "content": [
@@ -40,8 +40,8 @@
                             "single_end": false
                         },
                         [
-                            "test_paired_end_1.fastq.gz:md5,193809c784a4ea132ab2a253fa4f55b6",
-                            "test_paired_end_2.fastq.gz:md5,3e3b3af3413f50a1685fd7b3f1456d4e"
+                            "test_paired_end_1.fastq.gz:md5,8573015c91d099b6e30789f8bab2f43c",
+                            "test_paired_end_2.fastq.gz:md5,37e6f719a022dc3c9994c80fbc20c311"
                         ]
                     ]
                 ],
@@ -55,8 +55,8 @@
                             "single_end": false
                         },
                         [
-                            "test_paired_end_1.fastq.gz:md5,193809c784a4ea132ab2a253fa4f55b6",
-                            "test_paired_end_2.fastq.gz:md5,3e3b3af3413f50a1685fd7b3f1456d4e"
+                            "test_paired_end_1.fastq.gz:md5,8573015c91d099b6e30789f8bab2f43c",
+                            "test_paired_end_2.fastq.gz:md5,37e6f719a022dc3c9994c80fbc20c311"
                         ]
                     ]
                 ],
@@ -65,6 +65,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-10T18:11:50.928006"
+        "timestamp": "2024-01-09T12:55:34.40299"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test
index fcf4036d..e67e496e 100644
--- a/modules/nf-core/sratools/prefetch/tests/main.nf.test
+++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
             process {
                 """
                 input[0] = Channel.of([ [ id:'test', single_end:false ], 'DRR000774' ])
-                input[1] = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true)
+                input[1] = file(params.modules_test_data_base + '/data/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
                 input[2] = []
                 """
             }
@@ -38,7 +38,7 @@ nextflow_process {
             process {
                 """
                 input[0] = Channel.of([ [ id:'test', single_end:false ], 'SRR1170046' ])
-                input[1] = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true)
+                input[1] = file(params.modules_test_data_base + '/data/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
                 input[2] = []
                 """
             }
diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test
index d40db13d..372afc0b 100644
--- a/modules/nf-core/untar/tests/main.nf.test
+++ b/modules/nf-core/untar/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ]
+                input[0] = [ [], file(params.modules_test_data_base + '/data/genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ]
                 """
             }
         }
@@ -38,7 +38,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [ [], file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true) ]
+                input[0] = [ [], file(params.modules_test_data_base + '/data/genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz', checkIfExists: true) ]
                 """
             }
         }
@@ -60,7 +60,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [ [], file(params.test_data['generic']['tar']['tar_gz'], checkIfExists: true) ]
+                input[0] = [ [], file(params.modules_test_data_base + '/data/generic/tar/hello.tar.gz', checkIfExists: true) ]
                 """
             }
         }
diff --git a/nextflow.config b/nextflow.config
index d3c6d840..b3c65b78 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -171,10 +171,7 @@ profiles {
         executor.cpus          = 4
         executor.memory        = 8.GB
     }
-    test         {
-        includeConfig 'conf/test.config'
-        includeConfig 'conf/test_data.config'
-    }
+    test         { includeConfig 'conf/test.config'         }
     test_synapse { includeConfig 'conf/test_synapse.config' }
     test_full    { includeConfig 'conf/test_full.config'    }
 }
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
index a73679e0..806b3cf2 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
@@ -9,8 +9,8 @@
                             "single_end": false
                         },
                         [
-                            "test_paired_end_1.fastq.gz:md5,193809c784a4ea132ab2a253fa4f55b6",
-                            "test_paired_end_2.fastq.gz:md5,3e3b3af3413f50a1685fd7b3f1456d4e"
+                            "test_paired_end_1.fastq.gz:md5,8573015c91d099b6e30789f8bab2f43c",
+                            "test_paired_end_2.fastq.gz:md5,37e6f719a022dc3c9994c80fbc20c311"
                         ]
                     ],
                     [
@@ -18,7 +18,7 @@
                             "id": "test_single_end",
                             "single_end": true
                         },
-                        "test_single_end.fastq.gz:md5,19029a1132115b55277a0d79ee089b49"
+                        "test_single_end.fastq.gz:md5,a110f93f7a9b0271455f5a435bce73c7"
                     ]
                 ],
                 "1": [
@@ -33,8 +33,8 @@
                             "single_end": false
                         },
                         [
-                            "test_paired_end_1.fastq.gz:md5,193809c784a4ea132ab2a253fa4f55b6",
-                            "test_paired_end_2.fastq.gz:md5,3e3b3af3413f50a1685fd7b3f1456d4e"
+                            "test_paired_end_1.fastq.gz:md5,8573015c91d099b6e30789f8bab2f43c",
+                            "test_paired_end_2.fastq.gz:md5,37e6f719a022dc3c9994c80fbc20c311"
                         ]
                     ],
                     [
@@ -42,7 +42,7 @@
                             "id": "test_single_end",
                             "single_end": true
                         },
-                        "test_single_end.fastq.gz:md5,19029a1132115b55277a0d79ee089b49"
+                        "test_single_end.fastq.gz:md5,a110f93f7a9b0271455f5a435bce73c7"
                     ]
                 ],
                 "versions": [
@@ -52,6 +52,6 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-12T20:09:55.255971"
+        "timestamp": "2024-01-09T12:54:35.314326"
     }
 }
\ No newline at end of file
diff --git a/tests/nextflow.config b/tests/nextflow.config
index e69de29b..55884b79 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -0,0 +1,18 @@
+params {
+    // Base directory for nf-core/modules test data
+    modules_test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/3e79d4b5fbed8c6ef7546d50696b343ab9a95fbe/'
+
+    // Base directory for pipeline test data
+    pipelines_test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/'
+}
+
+// Impose same minimum Nextflow version as the pipeline for testing
+manifest {
+    nextflowVersion = '!>=23.04.0'
+}
+
+// Disable all Nextflow reporting options
+timeline { enabled = false }
+report   { enabled = false }
+trace    { enabled = false }
+dag      { enabled = false }
\ No newline at end of file

From f2da06ca8f1b033bb05310697f3054d0030eaf92 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 9 Jan 2024 17:40:52 +0000
Subject: [PATCH 654/852] Fix ECLint

---
 modules/local/sra_fastq_ftp/tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test
index 55b34bce..33f4be9f 100644
--- a/modules/local/sra_fastq_ftp/tests/main.nf.test
+++ b/modules/local/sra_fastq_ftp/tests/main.nf.test
@@ -18,7 +18,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'SRX9626017_SRR13191702', single_end:false, md5_1: '89c5be920021a035084d8aeb74f32df7', md5_2: '56271be38a80db78ef3bdfc5d9909b98' ], // meta map
-                    [ 
+                    [
                         'ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz',
                         'ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz'
                     ]

From 7413e123ead07a24ab07c8231d73465ba12fd7ca Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 9 Jan 2024 17:54:31 +0000
Subject: [PATCH 655/852] Impose sensible resource limits for testing

---
 tests/nextflow.config | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/tests/nextflow.config b/tests/nextflow.config
index 55884b79..9bd65e59 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -6,6 +6,13 @@ params {
     pipelines_test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/'
 }
 
+// Impose sensible resource limits for testing
+process {
+    cpus   = 2
+    memory = 3.GB
+    time   = 2.h
+}
+
 // Impose same minimum Nextflow version as the pipeline for testing
 manifest {
     nextflowVersion = '!>=23.04.0'

From b880ba243c77cb824fa36dc337886ee55a0cefe9 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 9 Jan 2024 19:31:52 +0000
Subject: [PATCH 656/852] Use process selector to change default resources for
 tests

---
 tests/nextflow.config | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/tests/nextflow.config b/tests/nextflow.config
index 9bd65e59..4533e874 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -8,9 +8,11 @@ params {
 
 // Impose sensible resource limits for testing
 process {
-    cpus   = 2
-    memory = 3.GB
-    time   = 2.h
+    withName: '.*' {
+        cpus   = 2
+        memory = 3.GB
+        time   = 2.h
+    }
 }
 
 // Impose same minimum Nextflow version as the pipeline for testing

From 6447feff4dc2d8975a2e656295465dc343e72d4b Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 9 Jan 2024 19:36:25 +0000
Subject: [PATCH 657/852] Remove redundanct validationSchemaIgnoreParams
 parameter in test.config

---
 conf/test.config | 2 --
 1 file changed, 2 deletions(-)

diff --git a/conf/test.config b/conf/test.config
index 4272648c..42b1c34f 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -21,6 +21,4 @@ params {
 
     // Input data
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/testdata/v1.12.0/sra_ids_test.csv'
-
-    validationSchemaIgnoreParams = 'test_data_base,fastq_ftp_ids,test_data'
 }

From 62a14f19244ab3eecb4de45d1fda50e4e4953b1b Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 11 Jan 2024 20:23:00 +0100
Subject: [PATCH 658/852] use s3 path

---
 modules/local/multiqc_mappings_config/tests/main.nf.test | 2 +-
 modules/local/sra_runinfo_to_ftp/tests/main.nf.test      | 2 +-
 tests/nextflow.config                                    | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test
index c49cedd7..c1b2c5df 100644
--- a/modules/local/multiqc_mappings_config/tests/main.nf.test
+++ b/modules/local/multiqc_mappings_config/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
 
             process {
                 """
-                input[0] = file(params.pipelines_test_data_base + '/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv', checkIfExists: true)
+                input[0] = file(params.pipelines_test_data_base + 'modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv', checkIfExists: true)
                 """
             }
         }
diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
index 4dbe2570..31224dab 100644
--- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
+++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
 
             process {
                 """
-                input[0] = file(params.pipelines_test_data_base + '/modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv', checkIfExists: true)
+                input[0] = file(params.pipelines_test_data_base + 'modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv', checkIfExists: true)
                 """
             }
         }
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 4533e874..9a7db8d2 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -3,7 +3,7 @@ params {
     modules_test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/3e79d4b5fbed8c6ef7546d50696b343ab9a95fbe/'
 
     // Base directory for pipeline test data
-    pipelines_test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/'
+    pipelines_test_data_base = 's3://ngi-igenomes/testdata/nf-core/pipelines/fetchngs/1.15.0/'
 }
 
 // Impose sensible resource limits for testing
@@ -24,4 +24,4 @@ manifest {
 timeline { enabled = false }
 report   { enabled = false }
 trace    { enabled = false }
-dag      { enabled = false }
\ No newline at end of file
+dag      { enabled = false }

From 451d56b8e0f8833cc0885a54e232f2d0bb1a83d2 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 12 Jan 2024 09:41:26 +0000
Subject: [PATCH 659/852] Update modules to include absolute paths for test
 data

Changes:
 - Modules updated
 - Now use absolute paths for test data
 - All modules tests should work within the this repository
---
 CHANGELOG.md                                  |   1 +
 modules.json                                  |  10 +-
 .../sratoolsncbisettings/environment.yml      |   4 +-
 .../custom/sratoolsncbisettings/main.nf       |   4 +-
 .../custom/sratoolsncbisettings/meta.yml      |   4 +-
 .../sratoolsncbisettings/tests/main.nf.test   |  76 +--
 .../tests/main.nf.test.snap                   |  22 +-
 modules/nf-core/sratools/fasterqdump/main.nf  |   7 +-
 .../sratools/fasterqdump/nextflow.config      |  10 -
 .../sratools/fasterqdump/tests/main.nf.test   |   2 +
 .../fasterqdump/tests/main.nf.test.snap       |   4 +-
 modules/nf-core/sratools/prefetch/main.nf     |  11 +-
 .../nf-core/sratools/prefetch/nextflow.config |   8 -
 .../sratools/prefetch/tests/main.nf.test      |   1 +
 modules/nf-core/untar/environment.yml         |   4 +-
 modules/nf-core/untar/tests/main.nf.test      |  22 -
 modules/nf-core/untar/tests/main.nf.test.snap | 479 ------------------
 .../nextflow.config                           |   2 -
 .../tests/main.nf.test                        |  17 +-
 .../tests/main.nf.test.snap                   | 116 +++--
 .../tests/tags.yml                            |   2 +-
 21 files changed, 110 insertions(+), 696 deletions(-)
 delete mode 100644 modules/nf-core/sratools/fasterqdump/nextflow.config
 delete mode 100644 modules/nf-core/sratools/prefetch/nextflow.config
 delete mode 100644 subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c354cd3f..38f6ff84 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -22,6 +22,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #242](https://github.com/nf-core/fetchngs/pull/242) - Template update for nf-core/tools v2.11
 - [PR #243](https://github.com/nf-core/fetchngs/pull/243) - Fixes for [PR #238](https://github.com/nf-core/fetchngs/pull/238)
 - [PR #246](https://github.com/nf-core/fetchngs/pull/246) - Handle dark/light mode for logo in GitHub README properly
+- [PR #249](https://github.com/nf-core/fetchngs/pull/249) - Update modules which includes absolute paths for test data, making module level test compatible within the pipeline.
 
 ### Software dependencies
 
diff --git a/modules.json b/modules.json
index d0766098..98f040b1 100644
--- a/modules.json
+++ b/modules.json
@@ -7,22 +7,22 @@
                 "nf-core": {
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "88e4709f3252aba9a776bee998b0890d9cc52799",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "b1d2002587ed81dcd0f4b4ffa79fcdbda59b4e80",
+                        "git_sha": "f2cf495ede41c301af75f1fb411724bb04258af4",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/prefetch": {
                         "branch": "master",
-                        "git_sha": "b1d2002587ed81dcd0f4b4ffa79fcdbda59b4e80",
+                        "git_sha": "88e4709f3252aba9a776bee998b0890d9cc52799",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "574074e6ea2497b53df1f226473a8c71524af0d0",
                         "installed_by": ["modules"]
                     }
                 }
@@ -31,7 +31,7 @@
                 "nf-core": {
                     "fastq_download_prefetch_fasterqdump_sratools": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "bdfd7bc8d2e5a93531e14bd94c4128d9a72a2435",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {
diff --git a/modules/nf-core/custom/sratoolsncbisettings/environment.yml b/modules/nf-core/custom/sratoolsncbisettings/environment.yml
index 5ea32741..44a1b008 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/environment.yml
+++ b/modules/nf-core/custom/sratoolsncbisettings/environment.yml
@@ -1,7 +1,7 @@
-name: sratoolsncbisettings
+name: custom_sratoolsncbisettings
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - bioconda::sra-tools=2.11.0
+  - bioconda::sra-tools=3.0.8
diff --git a/modules/nf-core/custom/sratoolsncbisettings/main.nf b/modules/nf-core/custom/sratoolsncbisettings/main.nf
index bad6f9cf..ba9441c9 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/main.nf
+++ b/modules/nf-core/custom/sratoolsncbisettings/main.nf
@@ -4,8 +4,8 @@ process CUSTOM_SRATOOLSNCBISETTINGS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' :
-        'biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
+        'https://depot.galaxyproject.org/singularity/sra-tools:3.0.8--h9f5acd7_0' :
+        'biocontainers/sra-tools:3.0.8--h9f5acd7_0' }"
 
     output:
     path('*.mkfg')     , emit: ncbi_settings
diff --git a/modules/nf-core/custom/sratoolsncbisettings/meta.yml b/modules/nf-core/custom/sratoolsncbisettings/meta.yml
index 8637dd19..46a6cd32 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/meta.yml
+++ b/modules/nf-core/custom/sratoolsncbisettings/meta.yml
@@ -1,4 +1,4 @@
-name: "sratoolsncbisettings"
+name: "custom_sratoolsncbisettings"
 description: Test for the presence of suitable NCBI settings or create them on the fly.
 keywords:
   - NCBI
@@ -12,7 +12,7 @@ tools:
       homepage: https://github.com/ncbi/sra-tools
       documentation: https://github.com/ncbi/sra-tools/wiki
       tool_dev_url: https://github.com/ncbi/sra-tools
-      licence: "['Public Domain']"
+      licence: ["Public Domain"]
 output:
   - versions:
       type: file
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
index 989487f1..71530d6e 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
+++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
@@ -14,7 +14,8 @@ nextflow_process {
         when {
             params {
                 settings_path = '/tmp/.ncbi'
-                settings_file = "${params.settings_path}/user-settings.mkfg"
+                settings_file  = "${params.settings_path}/user-settings.mkfg"
+                outdir        = "$outputDir"
             }
 
             process {
@@ -37,78 +38,5 @@ nextflow_process {
                 assert path(get(0)).readLines().any { it.contains('/libs/cloud/report_instance_identity') }
             }
         }
-
-    }
-
-    test("Should fail") {
-
-        when {
-            params {
-                settings_path = '/tmp/.ncbi'
-                settings_file = "${params.settings_path}/user-settings.mkfg"
-            }
-
-            process {
-                """
-                file(params.settings_path).mkdirs()
-                def settings = file(params.settings_file)
-                settings.text = '''
-                ## auto-generated configuration file - DO NOT EDIT ##
-                config/default = "false"
-                /repository/remote/main/CGI/resolver-cgi = "https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi"
-                /repository/remote/protected/CGI/resolver-cgi = "https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi"
-                /repository/user/ad/public/apps/file/volumes/flatAd = "."
-                /repository/user/ad/public/apps/refseq/volumes/refseqAd = "."
-                /repository/user/ad/public/apps/sra/volumes/sraAd = "."
-                /repository/user/ad/public/apps/sraPileup/volumes/ad = "."
-                /repository/user/ad/public/apps/sraRealign/volumes/ad = "."
-                /repository/user/ad/public/apps/wgs/volumes/wgsAd = "."
-                /repository/user/ad/public/root = "."
-                /repository/user/default-path = "/root/ncbi"
-                '''.stripIndent()
-                """
-            }
-        }
-
-        then {
-            assert process.failed
-            assert snapshot(
-                process.out.versions
-            ).match()
-            assert process.stdout.any { it.contains('Command error:') }
-            assert process.stdout.any { it.contains('missing the required entries') }
-            assert process.stdout.any { it.contains('/LIBS/GUID') }
-            assert process.stdout.any { it.contains('/libs/cloud/report_instance_identity') }
-        }
-
     }
-
-    test("Should run with nonexisting") {
-
-        when {
-            params {
-                settings_path = '/tmp/.ncbi'
-                settings_file = "${params.settings_path}/user-settings.mkfg"
-            }
-
-            process {
-                """
-                def settings = file(params.settings_file)
-                settings.delete()
-                """
-            }
-        }
-
-        then {
-            assert process.success
-            assert snapshot(process.out.versions).match()
-
-            with(process.out.ncbi_settings) {
-                { assert path(get(0)).readLines().any { it.contains('/LIBS/GUID') } }
-                { assert path(get(0)).readLines().any { it.contains('/libs/cloud/report_instance_identity') } }
-            }
-        }
-
-    }
-
 }
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap
index 035aeeb7..65a706d4 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap
+++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap
@@ -1,26 +1,10 @@
 {
-    "Should fail": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "timestamp": "2024-01-09T12:59:19.679292"
-    },
-    "Should run with nonexisting": {
-        "content": [
-            [
-                "versions.yml:md5,fec13b593c3b42ddd38f2fc77df25b70"
-            ]
-        ],
-        "timestamp": "2023-10-12T12:24:24.023849"
-    },
     "Should run without failures": {
         "content": [
             [
-                "versions.yml:md5,fec13b593c3b42ddd38f2fc77df25b70"
+                "versions.yml:md5,3d6ee88cce1ee517e198633f062589a8"
             ]
         ],
-        "timestamp": "2023-10-12T10:40:51.717351"
+        "timestamp": "2024-01-09T22:43:44.996003"
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf
index f86d15b7..d4ddf268 100644
--- a/modules/nf-core/sratools/fasterqdump/main.nf
+++ b/modules/nf-core/sratools/fasterqdump/main.nf
@@ -25,14 +25,11 @@ process SRATOOLS_FASTERQDUMP {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def outfile = meta.single_end ? "${prefix}.fastq" : prefix
     def key_file = ''
-
-    if (certificate.toString().endsWith('.jwt')){
+    if (certificate.toString().endsWith('.jwt')) {
         key_file += " --perm ${certificate}"
-        }
-    else if (certificate.toString().endsWith('.ngc')){
+    } else if (certificate.toString().endsWith('.ngc')) {
         key_file += " --ngc ${certificate}"
     }
-
     """
     export NCBI_SETTINGS="\$PWD/${ncbi_settings}"
 
diff --git a/modules/nf-core/sratools/fasterqdump/nextflow.config b/modules/nf-core/sratools/fasterqdump/nextflow.config
deleted file mode 100644
index f98b140d..00000000
--- a/modules/nf-core/sratools/fasterqdump/nextflow.config
+++ /dev/null
@@ -1,10 +0,0 @@
-process {
-    withName: SRATOOLS_FASTERQDUMP {
-        ext.args = '--split-files --include-technical'
-        publishDir = [
-            path: { "${params.outdir}/fastq" },
-            mode: params.publish_dir_mode,
-            pattern: "*.fastq.gz"
-        ]
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
index 662fdde6..8c920203 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
@@ -4,6 +4,8 @@ nextflow_process {
     process "SRATOOLS_FASTERQDUMP"
     tag "modules"
     tag "modules_nfcore"
+    tag "untar"
+    tag "sratools"
     tag "sratools/fasterqdump"
 
     test("Single-end") {
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
index 123feb2e..e2cc2612 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
@@ -8,7 +8,7 @@
                             "id": "test_single_end",
                             "single_end": true
                         },
-                        "test_single_end_1.fastq.gz:md5,674d78c1cc3c1308d6d39d6369a42887"
+                        "test_single_end.fastq.gz:md5,674d78c1cc3c1308d6d39d6369a42887"
                     ]
                 ],
                 "1": [
@@ -20,7 +20,7 @@
                             "id": "test_single_end",
                             "single_end": true
                         },
-                        "test_single_end_1.fastq.gz:md5,674d78c1cc3c1308d6d39d6369a42887"
+                        "test_single_end.fastq.gz:md5,674d78c1cc3c1308d6d39d6369a42887"
                     ]
                 ],
                 "versions": [
diff --git a/modules/nf-core/sratools/prefetch/main.nf b/modules/nf-core/sratools/prefetch/main.nf
index f12dc68d..3c30739a 100644
--- a/modules/nf-core/sratools/prefetch/main.nf
+++ b/modules/nf-core/sratools/prefetch/main.nf
@@ -21,16 +21,15 @@ process SRATOOLS_PREFETCH {
 
     shell:
     args = task.ext.args ?: ''
-
-    if (certificate){
-        if (certificate.toString().endsWith('.jwt')){
+    args2 = task.ext.args2 ?: '5 1 100'  // <num retries> <base delay in seconds> <max delay in seconds>
+    if (certificate) {
+        if (certificate.toString().endsWith('.jwt')) {
             args += " --perm ${certificate}"
-            }
-        else if (certificate.toString().endsWith('.ngc')){
+        }
+        else if (certificate.toString().endsWith('.ngc')) {
             args += " --ngc ${certificate}"
         }
     }
 
-    args2 = task.ext.args2 ?: '5 1 100'  // <num retries> <base delay in seconds> <max delay in seconds>
     template 'retry_with_backoff.sh'
 }
diff --git a/modules/nf-core/sratools/prefetch/nextflow.config b/modules/nf-core/sratools/prefetch/nextflow.config
deleted file mode 100644
index a2ca8848..00000000
--- a/modules/nf-core/sratools/prefetch/nextflow.config
+++ /dev/null
@@ -1,8 +0,0 @@
-process {
-    withName: SRATOOLS_PREFETCH {
-        publishDir = [
-            path: { "${params.outdir}/sra" },
-            enabled: false
-        ]
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test
index e67e496e..1001ecf5 100644
--- a/modules/nf-core/sratools/prefetch/tests/main.nf.test
+++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test
@@ -4,6 +4,7 @@ nextflow_process {
     process "SRATOOLS_PREFETCH"
     tag "modules"
     tag "modules_nfcore"
+    tag "sratools"
     tag "sratools/prefetch"
 
     test("sratools/prefetch") {
diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml
index d6917da3..0c9cbb10 100644
--- a/modules/nf-core/untar/environment.yml
+++ b/modules/nf-core/untar/environment.yml
@@ -1,9 +1,11 @@
 name: untar
+
 channels:
   - conda-forge
   - bioconda
   - defaults
+
 dependencies:
-  - conda-forge::sed=4.7
   - conda-forge::grep=3.11
+  - conda-forge::sed=4.7
   - conda-forge::tar=1.34
diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test
index 372afc0b..8d8cdcc0 100644
--- a/modules/nf-core/untar/tests/main.nf.test
+++ b/modules/nf-core/untar/tests/main.nf.test
@@ -30,28 +30,6 @@ nextflow_process {
 
     }
 
-    test("test_untar_different_output_path") {
-
-        when {
-            params {
-                outdir   = "$outputDir"
-            }
-            process {
-                """
-                input[0] = [ [], file(params.modules_test_data_base + '/data/genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz', checkIfExists: true) ]
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out.untar).match("test_untar_different_output_path") },
-            )
-        }
-
-    }
-
     test("test_untar_onlyfiles") {
 
         when {
diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap
index 146c8678..ace42576 100644
--- a/modules/nf-core/untar/tests/main.nf.test.snap
+++ b/modules/nf-core/untar/tests/main.nf.test.snap
@@ -1,483 +1,4 @@
 {
-    "test_untar_different_output_path": {
-        "content": [
-            [
-                [
-                    [
-                        
-                    ],
-                    [
-                        [
-                            [
-                                [
-                                    [
-                                        [
-                                            "s_1_1101.bcl:md5,ad01889e2ff43e2f194224e20bdb600c",
-                                            "s_1_1101.stats:md5,4bbbf103454b37fbc3138fadf1b4446b"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,565384bbe67a694dfd690bae6d1d30c2",
-                                            "s_1_1101.stats:md5,55e5abd8f129ff38ef169873547abdb8"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,650fa58a630a9148835ba79e323d4237",
-                                            "s_1_1101.stats:md5,77403669ca1b05340c390dff64425c1e"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,54471c9e97299cd141e202e204637702",
-                                            "s_1_1101.stats:md5,67b14c9a89b7f8556674a7524d5cfb2d"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,74e4f929fc7476c380fd9d741ddb6700",
-                                            "s_1_1101.stats:md5,5730a4c35463eaa12a06b6758710b98c"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,c785f472f4350c120c02c888c8189590",
-                                            "s_1_1101.stats:md5,fee4ec63895ea81007e06ee6a36ba5e0"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,b7ea50bb25f08d43c301741d77050a9b",
-                                            "s_1_1101.stats:md5,fa7c68f3122c74d14364e6f7b011af70"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,9d5087dc4bcae39d66486363d4f68ecf",
-                                            "s_1_1101.stats:md5,23cdceee4d82c4b8e7c60018b9276ace"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,581e0c5ee94e8f2de14b2b1d8e777530",
-                                            "s_1_1101.stats:md5,9a3536d573c97f66bb56b49463612607"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,296fc026bb34c67bbe2b44845fe0d1de",
-                                            "s_1_1101.stats:md5,a7f57a7770fb9c5ae2a0fb1ef403ec4f"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,2a3ca15531556c36d10d132a9e051de8",
-                                            "s_1_1101.stats:md5,2d0bcdb0a1b51d3d79e415db2ab2d3b1"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,1150d46a2ccd4ac58aee0585d3e4ffd7",
-                                            "s_1_1101.stats:md5,2e97550bd5b5864ffd0565bb7a3f6d40"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,0b85c4b3da0de95e7b862d849c5333ae",
-                                            "s_1_1101.stats:md5,6eab9746fbeb783b0cd70398f44e0c1a"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,e0e9c91f4698804d7a6d1058ef68b34f",
-                                            "s_1_1101.stats:md5,790022cdc7878a02b2ebd166e1ddf0a7"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,38cd0ad4de359e651c8ac0d5777ea625",
-                                            "s_1_1101.stats:md5,a1b1d5ea5371d326abb029774483c5e6"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,b0ddc05c4012ccba24e712a1cfec748f",
-                                            "s_1_1101.stats:md5,af3d232f839d720f76f40ba06caa2987"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,af32fcc5dc3b836cf7a5ba3db85a75dd",
-                                            "s_1_1101.stats:md5,f93f2c09bd4e486c74a5f6e2040f7296"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,54b7428e037ca87816107647d4a3d9db",
-                                            "s_1_1101.stats:md5,e5ac77a72cd7bed5e9bf03cccda0e48c"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,fc8b4eacd493bf3d0b20bc23998dc7ff",
-                                            "s_1_1101.stats:md5,190315e159e2f4bc4c057ded7470dc52"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,9484ecffda489927fce424ac6a44fa9d",
-                                            "s_1_1101.stats:md5,0825feeb457ecc9efcf6f8526ba32311"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,eec59e21036e31c95ce1e847bfb0a9c4",
-                                            "s_1_1101.stats:md5,9acc13f63c98e5a8445e7be70d49222b"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,a9fb24476f87cba4fba68e2b3c3f2c07",
-                                            "s_1_1101.stats:md5,dc0aa7db9790733291c3e6480ca2a0fc"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,ed950b3e82c500927c2e236c9df005c6",
-                                            "s_1_1101.stats:md5,dccb71ec47d1f9d33a192da6d5660a45"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,b3e992025e995ca56b5ea2820144ef47",
-                                            "s_1_1101.stats:md5,a6a829bf2cffb26ac5d9dc3012057699"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,89edc726a5a4e0b4ff8ca3899ed0232b",
-                                            "s_1_1101.stats:md5,5b9b4fd8110577a59b82d0c419519d29"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,4dc696149169f232c451225f563cb5cd",
-                                            "s_1_1101.stats:md5,d3514a71ea3adc60e2943c6b8f6e2598"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,35b992d0318afb7c825ceaa31b0755e6",
-                                            "s_1_1101.stats:md5,2826093acc175c16c3795de7c4ca8f07"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,7bc927f56a362e49c00b5d76ee048901",
-                                            "s_1_1101.stats:md5,e47d862b795fd6b88a31d7d482ab22f6"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,84742233ff2a651626fe9036f27f7cb2",
-                                            "s_1_1101.stats:md5,b78fad11d3c50bc76b722cdc03e3028b"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,3935341c86263a7938e8c49620ef39f8",
-                                            "s_1_1101.stats:md5,cc6585b2daac5354073d150874da9704"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,3627f4fd548bf6e64aaf08fba3a342be",
-                                            "s_1_1101.stats:md5,120ae4831ae004ff7d16728aef36e82f"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,07631014bc35124149fabd80ef19f933",
-                                            "s_1_1101.stats:md5,eadd63d91f47cc6db6b6f0a967a23927"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,a1149c80415dc2f34d768eeb397c43fb",
-                                            "s_1_1101.stats:md5,ca89a9def67611a9151c6ce685b7cce1"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,eb5f71d4741d2f40618756bc72eaf8b4",
-                                            "s_1_1101.stats:md5,90f48501e735e5915b843478e23d1ae2"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,9bf270fe3f6add1a591ebc24fff10078",
-                                            "s_1_1101.stats:md5,a4e429671d4098034293c638aa655e16"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,219bedcbd24bae54fe4cf05dae05282c",
-                                            "s_1_1101.stats:md5,dd97525b65b68207137d51fcf19132c7"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,5163bc00a68fd57ae50cae0b76350892",
-                                            "s_1_1101.stats:md5,b606a5368eff1f012f3ea5d11ccdf2e0"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,fc429195a5af59a59e0cc4c48e6c05ea",
-                                            "s_1_1101.stats:md5,d809aa19698053f90d639da4dcad8008"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,383340219a1dd77076a092a64a71a7e4",
-                                            "s_1_1101.stats:md5,b204a5cf256378679ffc906c15cc1bae"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,0c369540d3e24696cf1f9c55bab69315",
-                                            "s_1_1101.stats:md5,a2bc69a4031a22ce9621dcc623a0bf4b"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,3127abc8016ba8eb954f8f8015dff387",
-                                            "s_1_1101.stats:md5,5deafff31150b7bf757f814e49a53bc2"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,045f40c82de676bafec3d59f91376a7a",
-                                            "s_1_1101.stats:md5,890700edc20687c090ef52248c7884b1"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,78af269aa2b39a1d765703f0a4739a86",
-                                            "s_1_1101.stats:md5,303cf457aa1543a8208544f694cbc531"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,0ab8c781959b783b62888e9274364a46",
-                                            "s_1_1101.stats:md5,2605b0e8322f83aa4d0dae5da4ec7a7a"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,d0cf823ffe352e8b3f75d589544ab617",
-                                            "s_1_1101.stats:md5,efa3c0e01e3db71e12fd961cb2d03739"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,db4ca4ab7a01e03c246f9160c3758d82",
-                                            "s_1_1101.stats:md5,f61550d9e4a90df6b860e68f41f82f60"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,1af39a2c7e5ff20ece91cb8160b51d17",
-                                            "s_1_1101.stats:md5,d0e20879afcaf6dfcd88c73f1c5c78cf"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,4cf7123bb0fffcd79266df03aef01665",
-                                            "s_1_1101.stats:md5,29bff4075109a121b087116b58d7e927"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,aa9980428cb60cd6320f4b48f4dd0d74",
-                                            "s_1_1101.stats:md5,6b0e20bde93133117a8d1a6df3d6f37b"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,0f6e440374e15b9b491d52fb83a8adfe",
-                                            "s_1_1101.stats:md5,55cb5eb0ecdabd23dca39ab8c4607598"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,2c645d7bdaddaa403f6e304d36df9e4b",
-                                            "s_1_1101.stats:md5,53acf33d21f832779b400c2447386ce4"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,3bbf0863b423b770c879203644420206",
-                                            "s_1_1101.stats:md5,579bdc7293cac8c3d7407249cacf4c25"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,6658a08409e81d29cfeb2d096b491985",
-                                            "s_1_1101.stats:md5,bb559ffbea46d612f9933cefa84c4c03"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,1700d9a13d3d4f7643af2943ef838acb",
-                                            "s_1_1101.stats:md5,f01cb6050ebfb15da1e0399ebd791eb4"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,1ac7aa9ffae25eb103f755f33e4a39c6",
-                                            "s_1_1101.stats:md5,0b9d45d7929ccf336d5e5b95373ed3c2"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,812a97af2e983a53226e18c75190b06c",
-                                            "s_1_1101.stats:md5,d2410c7b0e506dab2972e77e2398de1e"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,c981e8e4dcc434956c2b86159da268bc",
-                                            "s_1_1101.stats:md5,e9c826e85361ce673f1f248786c9a611"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,88e09e99a0a4ef3357b203a41b22f77c",
-                                            "s_1_1101.stats:md5,ef06f2e5ad667bbd383f9ed6a05b7b42"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,461c8b146fc8a7938be38689978ecd09",
-                                            "s_1_1101.stats:md5,65115693935da66f9791b27136e22fb0"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,c7b827df5ce20e0f21916fe60860ca3f",
-                                            "s_1_1101.stats:md5,87be73613aeb507847f94d3cac5bb30a"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,7c4cc3dc9c8a1b0f15917b282dfb40ce",
-                                            "s_1_1101.stats:md5,bdd9181fa89debbfafe7b6ea3e064065"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,19f4debaf91e118aca8934517179ac33",
-                                            "s_1_1101.stats:md5,1143082719e136241d21b14a6b19b8a2"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,38aa256ad2d697d84b0b2c0e876a3eba",
-                                            "s_1_1101.stats:md5,64dd82f03df23f7f437eede2671ed4fe"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,b7929970378949571fed922c1b8cab32",
-                                            "s_1_1101.stats:md5,3d6d7985a41629fe196e4342d7fe36aa"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,fb2ed0bf6e89d79624ee78754e773491",
-                                            "s_1_1101.stats:md5,f34940810ff255aee79953496a12716d"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,4f8a8311f5f9c3a7629c1a973a7b280e",
-                                            "s_1_1101.stats:md5,4fd7cd28c09f4e152e7c2ad1ab541cd2"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,9eb46c903d0344e25af51f88cc311d60",
-                                            "s_1_1101.stats:md5,df3abd5f620d9e7f99496098d9fd3f7f"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,3ecbc17f3660e2014b58d7fe70ae62d5",
-                                            "s_1_1101.stats:md5,8e89a13c85a6d6ab3ccd251b66d1f165"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,5d59cc2499a77791233a64f73fe82894",
-                                            "s_1_1101.stats:md5,32ec99cd400f4b80cb26e2fa8e07ece0"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,1c052da47b9ae8554388f0fa3aade482",
-                                            "s_1_1101.stats:md5,d23f438772673688aa7bc92421dc6dce"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,1a52bd4f23130c0c96bc967ccd448a2b",
-                                            "s_1_1101.stats:md5,9b597e3388d59ef1f61aba30ac90ea79"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,8a1e84b79cf3f80794c20e3a0cc84688",
-                                            "s_1_1101.stats:md5,9561f7b6ef4b1849afc72b2bb49792bd"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,75c00111051f3fa95d04286823cb9109",
-                                            "s_1_1101.stats:md5,1fe786cdf8181767deafbd60b3c76610"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,529255d8deee0873ed5565e6d1a2ebda",
-                                            "s_1_1101.stats:md5,3fa7f467e97a75880f32d17b7429d316"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,ea4d960e3d9355d2149da71b88a21df4",
-                                            "s_1_1101.stats:md5,2540fe65586e8e800c1ddd8cddd1e8cd"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,0dfe1fd92a2dce2f23119aa483429744",
-                                            "s_1_1101.stats:md5,78257b2169fb9f0cf40966e06e847e86"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,f692ddc9aa3ab849271d07c666d0b3b9",
-                                            "s_1_1101.stats:md5,aa2ec6a3e3a9c116e34fe74a21e6459e"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,29cc4c239eae7c871c9a1adf92ebdb98",
-                                            "s_1_1101.stats:md5,263184813090acd740a5bf25304aed3a"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,e005af6a84925e326afbfe264241f047",
-                                            "s_1_1101.stats:md5,b6fb20868eebaffcc19daa694a449795"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,02f1a699b1ba9967accccf99a7af3d24",
-                                            "s_1_1101.stats:md5,4f007efacecaf26dc0e0231aede28754"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,df308c72a2dcc655cd95e98f5457187a",
-                                            "s_1_1101.stats:md5,130c4b07f4c14030bab012824cbe34da"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,f3ce10d8d2406b72355023bfa8c96822",
-                                            "s_1_1101.stats:md5,2638f4db393ed5b699ec2ce59ff0ec19"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,cc2f6d675ad1593ff96f734b172d249e",
-                                            "s_1_1101.stats:md5,f5b13f1e1ababc9e1a7a73b0b993cbf1"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,7938a0b21448305a951b023b1845b3a7",
-                                            "s_1_1101.stats:md5,fcd57511adabfc3ba1ac045165330006"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,44879bc6a38df1fee8def61868115041",
-                                            "s_1_1101.stats:md5,517e20e4b58a8023a37f9af62e0e2036"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,8749611e62406a7d2f34c610a55e56af",
-                                            "s_1_1101.stats:md5,8ccf24b3676ef84f2e513be8f2a9f3d1"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,a9846a037611cda3721958088f714c0e",
-                                            "s_1_1101.stats:md5,6438fa5a1892f328cab1605a95d80a3b"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,d6c4a2a726496476eb826532f974ed5f",
-                                            "s_1_1101.stats:md5,8c2c65b5e8b00dbf61ada65252aeb266"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,be3dde6cae7dd85855a6bf295ebfacfe",
-                                            "s_1_1101.stats:md5,93bc13f3b0749b2b8d8bcb0b1199f4f0"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,7c64514735a6cf1565b60647edd17d20",
-                                            "s_1_1101.stats:md5,4a0aa6c49b24f876415e5878cef7f805"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,3983b4043bc9df4b505202a5134ccf03",
-                                            "s_1_1101.stats:md5,1c9d9a8558adc1279ca27c96bc1b9758"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,a0b8d77f116ec95975f9253dcb768136",
-                                            "s_1_1101.stats:md5,c3992b786756e7ec42f65ef4b13b50d4"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,43c95ba35d06bb7c57fbd16f3d1cfd6c",
-                                            "s_1_1101.stats:md5,3cb69d04698c39f97f962e5bf1eea7f0"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,3dbeea0cad7052f19f53ff6f19dd4d90",
-                                            "s_1_1101.stats:md5,58bbc8254f0f5f4a244531e8e9c12a04"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,da56d088996376c898d855b6cd0a7dfc",
-                                            "s_1_1101.stats:md5,9f2d78af6908ce1576b89cdc059844ff"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,7b641a5565f095e9a6ffcad9e4305033",
-                                            "s_1_1101.stats:md5,3ada06c59b4fb41b83ab6abd0979e9fc"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,a3843d397a01d51657825bb652c191e5",
-                                            "s_1_1101.stats:md5,19341e52a4bfc7d9d48e9d2acc68c519"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,048e3ebfc8efeb8012def6b741c9060d",
-                                            "s_1_1101.stats:md5,88bd38deca1e87d700effab1fd099565"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,b340db0e07e829dd5da22371916a1a9e",
-                                            "s_1_1101.stats:md5,e44cfaddcc4ffb968e5b1a2f41ac48a5"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,e6011ec6eabbc2b8792deb283c621ce0",
-                                            "s_1_1101.stats:md5,090875dcd1a431af24bc631333f089c4"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,a08f216e3352345031ed100ec4245082",
-                                            "s_1_1101.stats:md5,97b949ef4b96219e1369f673cf5f8a6c"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,b43337c76fb037dfcf5f8f7bcb3618e5",
-                                            "s_1_1101.stats:md5,ddef585805e79951f69d23ab7354f69b"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,8c61fd004104397b360855e058bbf1bf",
-                                            "s_1_1101.stats:md5,0f8d253816d594dcfea3ccf48c826401"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,594d06310d328b188aa0b3edfff22cb2",
-                                            "s_1_1101.stats:md5,3160bf271b39aeb7590e4fd2984710ba"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,4c9eada67c9d55437211d83e111961d5",
-                                            "s_1_1101.stats:md5,2901b46ab16ec4863d30e4c84ec29c97"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,e03971ae5282f0accc0c1b7374d9ef1b",
-                                            "s_1_1101.stats:md5,60d2a19ce59bf70a21a28555484cead8"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,e1c6f7a06e63d149895d3e48e63df155",
-                                            "s_1_1101.stats:md5,44beb10af847ea3dddaf06dda7031126"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,960a99bf29a8f9d936e9b8582d46c9c6",
-                                            "s_1_1101.stats:md5,544cd1a7aaaa841914b40ece43399334"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,5706679f349fd4a6b6313bc2c41c7a42",
-                                            "s_1_1101.stats:md5,627eea844b26dae033848c2f9f69177b"
-                                        ],
-                                        [
-                                            "s_1_1101.bcl:md5,21da5abc4b0402bbac14b5ab998b0b4f",
-                                            "s_1_1101.stats:md5,515bd140b095ad90473ca7a9a69877ab"
-                                        ],
-                                        "s_1_1101.control:md5,08a72e2198ae95150718e8adf011d105",
-                                        "s_1_1101.filter:md5,3a72bc73b323c8cb0ac5bfeb62d98989"
-                                    ]
-                                ],
-                                [
-                                    "s_1_1101.locs:md5,0827ea802e5257cc5b20e757a33d4c98"
-                                ],
-                                "RTAConfiguration.xml:md5,c7d6e257bc374f142dc64b9d2281d4c9",
-                                "config.xml:md5,9a4cc7ec01fefa2f1ce9bcb45bbad6e9"
-                            ]
-                        ],
-                        [
-                            "ControlMetricsOut.bin:md5,6d77b38d0793a6e1ce1e85706e488953",
-                            "CorrectedIntMetricsOut.bin:md5,2bbf84d3be72734addaa2fe794711434",
-                            "ErrorMetricsOut.bin:md5,38c88def138e9bb832539911affdb286",
-                            "ExtractionMetricsOut.bin:md5,7497c3178837eea8f09350b5cd252e99",
-                            "IndexMetricsOut.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "QMetricsOut.bin:md5,7e9f198d53ebdfbb699a5f94cf1ed51c",
-                            "TileMetricsOut.bin:md5,83891751ec1c91a425a524b476b6ca3c"
-                        ],
-                        "RunInfo.xml:md5,03038959f4dd181c86bc97ae71fe270a"
-                    ]
-                ]
-            ]
-        ],
-        "timestamp": "2023-10-18T11:56:39.562418"
-    },
     "test_untar_onlyfiles": {
         "content": [
             [
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config
deleted file mode 100644
index b11c499f..00000000
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config
+++ /dev/null
@@ -1,2 +0,0 @@
-includeConfig '../../../modules/nf-core/sratools/prefetch/nextflow.config'
-includeConfig '../../../modules/nf-core/sratools/fasterqdump/nextflow.config'
\ No newline at end of file
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
index be18fc3b..2a16d1ef 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
@@ -3,12 +3,12 @@ nextflow_workflow {
     name "Test workflow: fastq_download_prefetch_fasterqdump_sratools/main.nf"
     script "../main.nf"
     workflow "FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS"
-    tag "subworkflow"
-    tag "subworkflow_nfcore"
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
     tag "custom/sratoolsncbisettings"
     tag "sratools/prefetch"
     tag "sratools/fasterqdump"
-    tag "fastq_download_prefetch_fasterqdump_sratools"
+    tag "subworkflows/fastq_download_prefetch_fasterqdump_sratools"
 
     test("Parameters: default") {
 
@@ -28,9 +28,18 @@ nextflow_workflow {
         }
 
         then {
+            def pelines1 = path(workflow.out.reads[0][1][0]).linesGzip
+            def pelines2 = path(workflow.out.reads[0][1][1]).linesGzip
+            def selines = path(workflow.out.reads[1][1]).linesGzip
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(workflow.out).match() }
+                { assert snapshot(pelines1[0..5]).match("test_pe_reads_1_lines") },
+                { assert snapshot(pelines1.size()).match("test_pe_reads_1_size") },
+                { assert snapshot(pelines2[0..5]).match("test_pe_reads_2_lines") },
+                { assert snapshot(pelines2.size()).match("test_pe_reads_2_size") },
+                { assert snapshot(selines[0..5]).match("test_se_reads_lines") },
+                { assert snapshot(selines.size()).match("test_se_reads_size") },
+                { assert snapshot(workflow.out.versions).match("versions") }
             )
         }
     }
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
index 806b3cf2..2123d3f7 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
@@ -1,57 +1,69 @@
 {
-    "Parameters: default": {
+    "test_se_reads_size": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test_paired_end",
-                            "single_end": false
-                        },
-                        [
-                            "test_paired_end_1.fastq.gz:md5,8573015c91d099b6e30789f8bab2f43c",
-                            "test_paired_end_2.fastq.gz:md5,37e6f719a022dc3c9994c80fbc20c311"
-                        ]
-                    ],
-                    [
-                        {
-                            "id": "test_single_end",
-                            "single_end": true
-                        },
-                        "test_single_end.fastq.gz:md5,a110f93f7a9b0271455f5a435bce73c7"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,98d78bba9f3da39a0b7db6e9c7dcc224",
-                    "versions.yml:md5,9c558ff624585a6eee82a19c8c0136db",
-                    "versions.yml:md5,db0e1352064b53c651661f43f2620765"
-                ],
-                "reads": [
-                    [
-                        {
-                            "id": "test_paired_end",
-                            "single_end": false
-                        },
-                        [
-                            "test_paired_end_1.fastq.gz:md5,8573015c91d099b6e30789f8bab2f43c",
-                            "test_paired_end_2.fastq.gz:md5,37e6f719a022dc3c9994c80fbc20c311"
-                        ]
-                    ],
-                    [
-                        {
-                            "id": "test_single_end",
-                            "single_end": true
-                        },
-                        "test_single_end.fastq.gz:md5,a110f93f7a9b0271455f5a435bce73c7"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,98d78bba9f3da39a0b7db6e9c7dcc224",
-                    "versions.yml:md5,9c558ff624585a6eee82a19c8c0136db",
-                    "versions.yml:md5,db0e1352064b53c651661f43f2620765"
-                ]
-            }
+            19996
         ],
-        "timestamp": "2024-01-09T12:54:35.314326"
+        "timestamp": "2024-01-11T11:52:21.464438219"
+    },
+    "test_pe_reads_2_lines": {
+        "content": [
+            [
+                "@SRR11140744.1 M01472:285:000000000-CYHNP:1:1101:12117:3295 length=251",
+                "ACAGGACACGAGTAACTCGTCTATCTTCTGCTGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAA",
+                "+SRR11140744.1 M01472:285:000000000-CYHNP:1:1101:12117:3295 length=251",
+                "ABAAAFBFFBDBGGGGGGGGGGHHHHHHHHHHCHGHGGGHHHGGHGGHGHGGGHFHHHHHHHHGGGGGHHHHHHHHHFHHHHGHHHGHGGGGGEFGDGHHGFGGGHHHHHGHHGGHHFHHHHGHHHHHHHHHHHHHHGFFGGHHHHHHGGHHGGHHHHHEGHHHHHHHGHHGHHFHHHHHGGGGGGGGGGGGAGGG9BEFFFFFFFFFFFFFFEEFFFFFFFA.FFFFFFFEFEFFFFFFF.BFFFFFFFB",
+                "@SRR11140744.2 M01472:285:000000000-CYHNP:1:1101:20752:3564 length=238",
+                "GTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACG"
+            ]
+        ],
+        "timestamp": "2024-01-11T11:52:21.437261931"
+    },
+    "test_pe_reads_2_size": {
+        "content": [
+            2011460
+        ],
+        "timestamp": "2024-01-11T11:52:21.44875993"
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,1a2218ff913fc33408bffccb081b5048",
+                "versions.yml:md5,98d78bba9f3da39a0b7db6e9c7dcc224",
+                "versions.yml:md5,9c558ff624585a6eee82a19c8c0136db"
+            ]
+        ],
+        "timestamp": "2024-01-11T12:11:06.731937323"
+    },
+    "test_pe_reads_1_size": {
+        "content": [
+            2011460
+        ],
+        "timestamp": "2024-01-11T11:52:21.428267242"
+    },
+    "test_se_reads_lines": {
+        "content": [
+            [
+                "@DRR000774.1 1 length=421",
+                "ACGCAGGTGCCAGCAGCCGCGGTAATACGTAGGATCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGTGCGTAGGCGGCTTGTCAAGTCTCATGTGAAATCTCCCGGCTCAACTGGGAGGGTCATGGGAAACTGATGAGCTCGAGGGCAGTAGAGGGAAGCGGAATTCCGAGAGTAGTGGTGAAATGCGTAGATACTCGGAGGAACACCAGTGGCGAAAGCGGCTTCCTGGACTGTACCTGACGCTGAGGCACGAAAGCGTGGGGAGCAAACCGGATTAGATACCCGGGTAGTCCACGCCCTAAACGATGGATACTAGATATAGGGGGTATCGACCCTCTGTGTCGAAGCTAACGCATTAAGTATCCCGCCTGAGGAGTACGGCCGCAAGGCTAAAACTTAAGGAATTGACGGCTGCGT",
+                "+DRR000774.1 1 length=421",
+                "FFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:88FFF888???DBBBBB666F222ADDDFFF::;FFFFFFFFFFFFFFFFFFFFFFFFFFFF9:::FFFFCCCFFFFDDDFFFFF<<<FFFFFFFFFFFFFFFFFFFFFDDDFFFFFCC???FFCAADD::9FFFFD;;;FFFFFFFFFFFFFFFGA?==BA==2221<6@;<<@@551?ADDDDD:::CC?DBABBA5552219;;87<7988?====BDD:::?57555??=<4/0004044???ABDDDDDDDDB><<<8888886623//38><83238@B@@<;855557,,,,,,,0/0;;8:==DDDDDDDDD9:",
+                "@DRR000774.2 2 length=126",
+                "ACGCAGGTGCCAGCAGCCGCGGTAATACGGAGGGAGCTAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGCTTTTCAAGTCAGGGGTGGAAATACCCGGGGCCGTCAACCCGACCG"
+            ]
+        ],
+        "timestamp": "2024-01-11T11:52:21.45496474"
+    },
+    "test_pe_reads_1_lines": {
+        "content": [
+            [
+                "@SRR11140744.1 M01472:285:000000000-CYHNP:1:1101:12117:3295 length=251",
+                "ACATAGGGCTGTTCAAGTTGAGGCAAAACGCCTTTTTCAACTTCTACTAAGCCACAAGTGCCATCTTTAAGATGTTGACGTGCCTCTGATAAGACCTCCTCCACGGAGTCTCCAAAGCCACGTACGAGCACGTCGCGAACCTGTAAAACAGGCAAACTGAGTTGGACGTGTGTTTTCTCGTTGAAACCAGGGACAAGGCTCTCCATCTTACCTTTCGGTCACACCCGGACGAAACCTAGATGTGCTGATGA",
+                "+SRR11140744.1 M01472:285:000000000-CYHNP:1:1101:12117:3295 length=251",
+                "BCCCCFFFFFCFGGGGGGGGGGHGGHHHHGGGHGHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHGGGHHHHHGHHGHHHHHHHHHHHHHGGGGGHHHHHHHHHHHHGHHHGGGGGHGHHGGGGGGGHHHHHHHHHHHGGHHHHHFHHHHHHHGGGHHHHHHHHHGGGHHHHHHHHGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGFFFFFFFFFDFFFFFFFFFFFFFFFFFFFFB",
+                "@SRR11140744.2 M01472:285:000000000-CYHNP:1:1101:20752:3564 length=238",
+                "CGTACGAGCACGTCGCGAACCTGTAAAACAGGCAAACTGAGTTGGACGTGTGTTTTCTCGTTGAAACCAGGGACAAGGCTCTCCATCTTACCTTTCGGTCACACCCGGACGAAACCTAGATGTGCTGATGATCGGCTGCAACACGGACGAAACCGTAAGCAGCCTGCAGAAGATAGACGAGTTACTCGTGTCCTGTCAACGACAGTAATTAGTTATTAATTATACTGCGTGAGTGCAC"
+            ]
+        ],
+        "timestamp": "2024-01-11T11:52:21.400169604"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml
index ab064503..03028c32 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml
@@ -1,2 +1,2 @@
-fastq_download_prefetch_fasterqdump_sratools:
+subworkflows/fastq_download_prefetch_fasterqdump_sratools:
   - subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/**

From cba05a318ce2b88fc0b29321cb8e54fa00c89390 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 12 Jan 2024 09:50:47 +0000
Subject: [PATCH 660/852] Remove includeConfig statements for missing config
 files

---
 workflows/sra/nextflow.config | 2 --
 1 file changed, 2 deletions(-)

diff --git a/workflows/sra/nextflow.config b/workflows/sra/nextflow.config
index 21b374c5..b053d8a9 100644
--- a/workflows/sra/nextflow.config
+++ b/workflows/sra/nextflow.config
@@ -3,5 +3,3 @@ includeConfig "../../modules/local/sra_fastq_ftp/nextflow.config"
 includeConfig "../../modules/local/sra_ids_to_runinfo/nextflow.config"
 includeConfig "../../modules/local/sra_runinfo_to_ftp/nextflow.config"
 includeConfig "../../modules/local/sra_to_samplesheet/nextflow.config"
-includeConfig "../../modules/nf-core/sratools/prefetch/nextflow.config"
-includeConfig "../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config"

From 9b7b18cc0ddd7edd64b561821b828240fddbdad5 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 12 Jan 2024 14:52:27 +0000
Subject: [PATCH 661/852] Use testdata_base_path for all tests

---
 modules.json                                              | 8 ++++----
 .../custom/sratoolsncbisettings/tests/main.nf.test        | 2 +-
 modules/nf-core/sratools/fasterqdump/tests/main.nf.test   | 8 ++++----
 modules/nf-core/sratools/prefetch/tests/main.nf.test      | 4 ++--
 modules/nf-core/untar/tests/main.nf.test                  | 4 ++--
 tests/nextflow.config                                     | 2 +-
 6 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/modules.json b/modules.json
index 98f040b1..4b37d239 100644
--- a/modules.json
+++ b/modules.json
@@ -7,22 +7,22 @@
                 "nf-core": {
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
-                        "git_sha": "88e4709f3252aba9a776bee998b0890d9cc52799",
+                        "git_sha": "20e78a9868eaa69c8cac91152397def32374b807",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "f2cf495ede41c301af75f1fb411724bb04258af4",
+                        "git_sha": "20e78a9868eaa69c8cac91152397def32374b807",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/prefetch": {
                         "branch": "master",
-                        "git_sha": "88e4709f3252aba9a776bee998b0890d9cc52799",
+                        "git_sha": "20e78a9868eaa69c8cac91152397def32374b807",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "574074e6ea2497b53df1f226473a8c71524af0d0",
+                        "git_sha": "20e78a9868eaa69c8cac91152397def32374b807",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
index 71530d6e..883a8d1e 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
+++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
@@ -21,7 +21,7 @@ nextflow_process {
             process {
                 """
                 file(params.settings_path).mkdirs()
-                def settings = file(params.modules_test_data_base + '/data/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
+                def settings = file(params.testdata_base_path + '/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
                 settings.copyTo(params.settings_file)
                 """
             }
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
index 8c920203..af6b26d8 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
                 script "modules/nf-core/untar/main.nf"
                 process {
                     """
-                    input[0] = Channel.of([ [], file(params.modules_test_data_base + '/data/genomics/sarscov2/illumina/sra/SRR13255544.tar.gz', checkIfExists: true) ])
+                    input[0] = Channel.of([ [], file(params.testdata_base_path + 'genomics/sarscov2/illumina/sra/SRR13255544.tar.gz', checkIfExists: true) ])
                     """
                 }
             }
@@ -25,7 +25,7 @@ nextflow_process {
             process {
                 """
                 input[0] = UNTAR.out.untar.map{ meta, files -> [ [ id:'test_single_end', single_end:true ], files]}
-                input[1] = file(params.modules_test_data_base + '/data/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
+                input[1] = file(params.testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
                 input[2] = []
                 """
             }
@@ -46,7 +46,7 @@ nextflow_process {
                 script "modules/nf-core/untar/main.nf"
                 process {
                     """
-                    input[0] = Channel.of([ [], file(params.modules_test_data_base + '/data/genomics/sarscov2/illumina/sra/SRR11140744.tar.gz', checkIfExists: true) ])
+                    input[0] = Channel.of([ [], file(params.testdata_base_path + 'genomics/sarscov2/illumina/sra/SRR11140744.tar.gz', checkIfExists: true) ])
                     """
                 }
             }
@@ -56,7 +56,7 @@ nextflow_process {
             process {
                 """
                 input[0] = UNTAR.out.untar.map{ meta, files -> [ [ id:'test_paired_end', single_end:false ], files]}
-                input[1] = file(params.modules_test_data_base + '/data/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
+                input[1] = file(params.testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
                 input[2] = []
                 """
             }
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test
index 1001ecf5..d88c1b67 100644
--- a/modules/nf-core/sratools/prefetch/tests/main.nf.test
+++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
             process {
                 """
                 input[0] = Channel.of([ [ id:'test', single_end:false ], 'DRR000774' ])
-                input[1] = file(params.modules_test_data_base + '/data/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
+                input[1] = file(params.testdata_base_path + '/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
                 input[2] = []
                 """
             }
@@ -39,7 +39,7 @@ nextflow_process {
             process {
                 """
                 input[0] = Channel.of([ [ id:'test', single_end:false ], 'SRR1170046' ])
-                input[1] = file(params.modules_test_data_base + '/data/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
+                input[1] = file(params.testdata_base_path + '/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
                 input[2] = []
                 """
             }
diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test
index 8d8cdcc0..bcf09a00 100644
--- a/modules/nf-core/untar/tests/main.nf.test
+++ b/modules/nf-core/untar/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [ [], file(params.modules_test_data_base + '/data/genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ]
+                input[0] = [ [], file(params.testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ]
                 """
             }
         }
@@ -38,7 +38,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [ [], file(params.modules_test_data_base + '/data/generic/tar/hello.tar.gz', checkIfExists: true) ]
+                input[0] = [ [], file(params.testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) ]
                 """
             }
         }
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 4533e874..09f04f68 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -1,6 +1,6 @@
 params {
     // Base directory for nf-core/modules test data
-    modules_test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/3e79d4b5fbed8c6ef7546d50696b343ab9a95fbe/'
+    testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/3e79d4b5fbed8c6ef7546d50696b343ab9a95fbe/'
 
     // Base directory for pipeline test data
     pipelines_test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/'

From a46c1dd8e9052f66f0dd1a3b42c59c69ff9ca86d Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 12 Jan 2024 14:55:39 +0000
Subject: [PATCH 662/852] Replace base path with s3

---
 tests/nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/nextflow.config b/tests/nextflow.config
index 09f04f68..a4a5b829 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -1,6 +1,6 @@
 params {
     // Base directory for nf-core/modules test data
-    testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/3e79d4b5fbed8c6ef7546d50696b343ab9a95fbe/'
+    testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/'
 
     // Base directory for pipeline test data
     pipelines_test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/'

From 84adb514288ba50c1c3ceb539b16b172fffef511 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 12 Jan 2024 16:51:22 +0100
Subject: [PATCH 663/852] update CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c354cd3f..72db7563 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -22,6 +22,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #242](https://github.com/nf-core/fetchngs/pull/242) - Template update for nf-core/tools v2.11
 - [PR #243](https://github.com/nf-core/fetchngs/pull/243) - Fixes for [PR #238](https://github.com/nf-core/fetchngs/pull/238)
 - [PR #246](https://github.com/nf-core/fetchngs/pull/246) - Handle dark/light mode for logo in GitHub README properly
+- [PR #248](https://github.com/nf-core/fetchngs/pull/248) - Update pipeline level test data path to use mirror on s3
 
 ### Software dependencies
 

From 3394b61fb01510dc2bb03ced700ae0a40147c0b9 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 12 Jan 2024 17:30:07 +0000
Subject: [PATCH 664/852] Remove file checks for files that do not exist in
 tests any more

---
 tests/main.nf.test | 39 +++++++++++++++++----------------------
 1 file changed, 17 insertions(+), 22 deletions(-)

diff --git a/tests/main.nf.test b/tests/main.nf.test
index 21c6ac8b..8bfd4af2 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -23,28 +23,6 @@ nextflow_pipeline {
                 { assert new File("$outputDir/samplesheet/samplesheet.csv").readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX024467"', '"DRX026011"', '"ERX1234253"', '"SRX10940790"', '"SRX11047067"', '"SRX17709227"', '"SRX17709228"', '"SRX6725035"', '"SRX9315476"', '"SRX9504942"', '"SRX9504942"', '"SRX9504942"', '"SRX9504942"', '"SRX9626017"'] },
                 { assert new File("$outputDir/samplesheet/samplesheet.csv").text.contains('Illumina HiSeq 2500') },
                 { assert new File("$outputDir/custom/user-settings.mkfg").exists() },
-                { assert new File("$outputDir/fastq/DRX024467_DRR026872.fastq.gz").exists() },
-                { assert new File("$outputDir/fastq/DRX026011_DRR028935_1.fastq.gz").exists() },
-                { assert new File("$outputDir/fastq/DRX026011_DRR028935_2.fastq.gz").exists() },
-                { assert new File("$outputDir/fastq/ERX1234253_ERR1160846.fastq.gz").exists() },
-                { assert new File("$outputDir/fastq/SRX10940790_SRR14593545_1.fastq.gz").exists() },
-                { assert new File("$outputDir/fastq/SRX10940790_SRR14593545_2.fastq.gz").exists() },
-                { assert new File("$outputDir/fastq/SRX11047067_SRR14709033.fastq.gz").exists() },
-                { assert new File("$outputDir/fastq/SRX17709227_SRR21711856.fastq.gz").exists() },
-                { assert new File("$outputDir/fastq/SRX17709228_SRR21711855.fastq.gz").exists() },
-                { assert new File("$outputDir/fastq/SRX6725035_SRR9984183.fastq.gz").exists() },
-                { assert new File("$outputDir/fastq/SRX9315476_SRR12848126_1.fastq.gz").exists() },
-                { assert new File("$outputDir/fastq/SRX9315476_SRR12848126_2.fastq.gz").exists() },
-                { assert new File("$outputDir/fastq/SRX9504942_SRR13055517_1.fastq.gz").exists() },
-                { assert new File("$outputDir/fastq/SRX9504942_SRR13055517_2.fastq.gz").exists() },
-                { assert new File("$outputDir/fastq/SRX9504942_SRR13055518_1.fastq.gz").exists() },
-                { assert new File("$outputDir/fastq/SRX9504942_SRR13055518_2.fastq.gz").exists() },
-                { assert new File("$outputDir/fastq/SRX9504942_SRR13055519_1.fastq.gz").exists() },
-                { assert new File("$outputDir/fastq/SRX9504942_SRR13055519_2.fastq.gz").exists() },
-                { assert new File("$outputDir/fastq/SRX9504942_SRR13055520_1.fastq.gz").exists() },
-                { assert new File("$outputDir/fastq/SRX9504942_SRR13055520_2.fastq.gz").exists() },
-                { assert new File("$outputDir/fastq/SRX9626017_SRR13191702_1.fastq.gz").exists() },
-                { assert new File("$outputDir/fastq/SRX9626017_SRR13191702_2.fastq.gz").exists() },
                 { assert new File("$outputDir/fastq/md5/DRX024467_DRR026872.fastq.gz.md5").exists() },
                 { assert new File("$outputDir/fastq/md5/DRX026011_DRR028935_1.fastq.gz.md5").exists() },
                 { assert new File("$outputDir/fastq/md5/DRX026011_DRR028935_2.fastq.gz.md5").exists() },
@@ -62,6 +40,23 @@ nextflow_pipeline {
                 { assert new File("$outputDir/fastq/md5/SRX9504942_SRR13055520_2.fastq.gz.md5").exists() },
                 { assert new File("$outputDir/fastq/md5/SRX9626017_SRR13191702_1.fastq.gz.md5").exists() },
                 { assert new File("$outputDir/fastq/md5/SRX9626017_SRR13191702_2.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/fastq/DRX024467_DRR026872.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/DRX026011_DRR028935_1.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/DRX026011_DRR028935_2.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/ERX1234253_ERR1160846.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX17709227_SRR21711856.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX17709228_SRR21711855.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX6725035_SRR9984183.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9504942_SRR13055517_1.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9504942_SRR13055517_2.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9504942_SRR13055518_1.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9504942_SRR13055518_2.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9504942_SRR13055519_1.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9504942_SRR13055519_2.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9504942_SRR13055520_1.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9504942_SRR13055520_2.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9626017_SRR13191702_1.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9626017_SRR13191702_2.fastq.gz").exists() },
                 { assert new File("$outputDir/metadata/DRR026872.runinfo_ftp.tsv").exists() },
                 { assert new File("$outputDir/metadata/DRR028935.runinfo_ftp.tsv").exists() },
                 { assert new File("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv").exists() },

From 966bd415c5f85e41fb265ec9672702ef3daeb5bf Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 12 Jan 2024 17:35:25 +0000
Subject: [PATCH 665/852] Update subworkflows

---
 modules.json                                  |   2 +-
 .../nf-core/utils_nfcore_pipeline/main.nf     | 119 +++++++++---------
 .../tests/main.function.nf.test               |  30 +++--
 .../tests/main.function.nf.test.snap          | 102 +++++++++++----
 .../tests/main.workflow.nf.test               |   3 +-
 5 files changed, 164 insertions(+), 92 deletions(-)

diff --git a/modules.json b/modules.json
index 4b37d239..f7829fdd 100644
--- a/modules.json
+++ b/modules.json
@@ -41,7 +41,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "c81784b47d44464b35e04220e00051bb5be27524",
+                        "git_sha": "524ccbab145985b26eb7daa6e551af486dab2100",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index d88aeebe..5716198c 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -10,6 +10,9 @@
 
 workflow UTILS_NFCORE_PIPELINE {
 
+    take:
+    monochrome_logs // boolean: Disable ANSI colour codes in log output
+
     main:
     checkConfigProvided()
 
@@ -54,18 +57,18 @@ def workflowCitation() {
 //
 // nf-core logo
 //
-def nfCoreLogo(workflow_version) {
-    Map colors = logColours()
+def nfCoreLogo(workflow_version, monochrome_logs = true) {
+    Map colors = logColours(monochrome_logs)
     String.format(
         """\n
-        ${dashedLine()}
+        ${dashedLine(monochrome_logs)}
                                                 ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
         ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
         ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
         ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
                                                 ${colors.green}`._,._,\'${colors.reset}
         ${colors.purple}  ${workflow.manifest.name} ${workflow_version}${colors.reset}
-        ${dashedLine()}
+        ${dashedLine(monochrome_logs)}
         """.stripIndent()
     )
 }
@@ -73,75 +76,75 @@ def nfCoreLogo(workflow_version) {
 //
 // Return dashed line
 //
-def dashedLine() {
-    Map colors = logColours()
+def dashedLine(monochrome_logs = true) {
+    Map colors = logColours(monochrome_logs)
     return "-${colors.dim}----------------------------------------------------${colors.reset}-"
 }
 
 //
 // ANSII colours used for terminal logging
 //
-def logColours() {
+def logColours(monochrome_logs = true) {
     Map colorcodes = [:]
 
     // Reset / Meta
-    colorcodes['reset']      = params.monochrome_logs ? '' : "\033[0m"
-    colorcodes['bold']       = params.monochrome_logs ? '' : "\033[1m"
-    colorcodes['dim']        = params.monochrome_logs ? '' : "\033[2m"
-    colorcodes['underlined'] = params.monochrome_logs ? '' : "\033[4m"
-    colorcodes['blink']      = params.monochrome_logs ? '' : "\033[5m"
-    colorcodes['reverse']    = params.monochrome_logs ? '' : "\033[7m"
-    colorcodes['hidden']     = params.monochrome_logs ? '' : "\033[8m"
+    colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
+    colorcodes['bold']       = monochrome_logs ? '' : "\033[1m"
+    colorcodes['dim']        = monochrome_logs ? '' : "\033[2m"
+    colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m"
+    colorcodes['blink']      = monochrome_logs ? '' : "\033[5m"
+    colorcodes['reverse']    = monochrome_logs ? '' : "\033[7m"
+    colorcodes['hidden']     = monochrome_logs ? '' : "\033[8m"
 
     // Regular Colors
-    colorcodes['black']      = params.monochrome_logs ? '' : "\033[0;30m"
-    colorcodes['red']        = params.monochrome_logs ? '' : "\033[0;31m"
-    colorcodes['green']      = params.monochrome_logs ? '' : "\033[0;32m"
-    colorcodes['yellow']     = params.monochrome_logs ? '' : "\033[0;33m"
-    colorcodes['blue']       = params.monochrome_logs ? '' : "\033[0;34m"
-    colorcodes['purple']     = params.monochrome_logs ? '' : "\033[0;35m"
-    colorcodes['cyan']       = params.monochrome_logs ? '' : "\033[0;36m"
-    colorcodes['white']      = params.monochrome_logs ? '' : "\033[0;37m"
+    colorcodes['black']      = monochrome_logs ? '' : "\033[0;30m"
+    colorcodes['red']        = monochrome_logs ? '' : "\033[0;31m"
+    colorcodes['green']      = monochrome_logs ? '' : "\033[0;32m"
+    colorcodes['yellow']     = monochrome_logs ? '' : "\033[0;33m"
+    colorcodes['blue']       = monochrome_logs ? '' : "\033[0;34m"
+    colorcodes['purple']     = monochrome_logs ? '' : "\033[0;35m"
+    colorcodes['cyan']       = monochrome_logs ? '' : "\033[0;36m"
+    colorcodes['white']      = monochrome_logs ? '' : "\033[0;37m"
 
     // Bold
-    colorcodes['bblack']     = params.monochrome_logs ? '' : "\033[1;30m"
-    colorcodes['bred']       = params.monochrome_logs ? '' : "\033[1;31m"
-    colorcodes['bgreen']     = params.monochrome_logs ? '' : "\033[1;32m"
-    colorcodes['byellow']    = params.monochrome_logs ? '' : "\033[1;33m"
-    colorcodes['bblue']      = params.monochrome_logs ? '' : "\033[1;34m"
-    colorcodes['bpurple']    = params.monochrome_logs ? '' : "\033[1;35m"
-    colorcodes['bcyan']      = params.monochrome_logs ? '' : "\033[1;36m"
-    colorcodes['bwhite']     = params.monochrome_logs ? '' : "\033[1;37m"
+    colorcodes['bblack']     = monochrome_logs ? '' : "\033[1;30m"
+    colorcodes['bred']       = monochrome_logs ? '' : "\033[1;31m"
+    colorcodes['bgreen']     = monochrome_logs ? '' : "\033[1;32m"
+    colorcodes['byellow']    = monochrome_logs ? '' : "\033[1;33m"
+    colorcodes['bblue']      = monochrome_logs ? '' : "\033[1;34m"
+    colorcodes['bpurple']    = monochrome_logs ? '' : "\033[1;35m"
+    colorcodes['bcyan']      = monochrome_logs ? '' : "\033[1;36m"
+    colorcodes['bwhite']     = monochrome_logs ? '' : "\033[1;37m"
 
     // Underline
-    colorcodes['ublack']     = params.monochrome_logs ? '' : "\033[4;30m"
-    colorcodes['ured']       = params.monochrome_logs ? '' : "\033[4;31m"
-    colorcodes['ugreen']     = params.monochrome_logs ? '' : "\033[4;32m"
-    colorcodes['uyellow']    = params.monochrome_logs ? '' : "\033[4;33m"
-    colorcodes['ublue']      = params.monochrome_logs ? '' : "\033[4;34m"
-    colorcodes['upurple']    = params.monochrome_logs ? '' : "\033[4;35m"
-    colorcodes['ucyan']      = params.monochrome_logs ? '' : "\033[4;36m"
-    colorcodes['uwhite']     = params.monochrome_logs ? '' : "\033[4;37m"
+    colorcodes['ublack']     = monochrome_logs ? '' : "\033[4;30m"
+    colorcodes['ured']       = monochrome_logs ? '' : "\033[4;31m"
+    colorcodes['ugreen']     = monochrome_logs ? '' : "\033[4;32m"
+    colorcodes['uyellow']    = monochrome_logs ? '' : "\033[4;33m"
+    colorcodes['ublue']      = monochrome_logs ? '' : "\033[4;34m"
+    colorcodes['upurple']    = monochrome_logs ? '' : "\033[4;35m"
+    colorcodes['ucyan']      = monochrome_logs ? '' : "\033[4;36m"
+    colorcodes['uwhite']     = monochrome_logs ? '' : "\033[4;37m"
 
     // High Intensity
-    colorcodes['iblack']     = params.monochrome_logs ? '' : "\033[0;90m"
-    colorcodes['ired']       = params.monochrome_logs ? '' : "\033[0;91m"
-    colorcodes['igreen']     = params.monochrome_logs ? '' : "\033[0;92m"
-    colorcodes['iyellow']    = params.monochrome_logs ? '' : "\033[0;93m"
-    colorcodes['iblue']      = params.monochrome_logs ? '' : "\033[0;94m"
-    colorcodes['ipurple']    = params.monochrome_logs ? '' : "\033[0;95m"
-    colorcodes['icyan']      = params.monochrome_logs ? '' : "\033[0;96m"
-    colorcodes['iwhite']     = params.monochrome_logs ? '' : "\033[0;97m"
+    colorcodes['iblack']     = monochrome_logs ? '' : "\033[0;90m"
+    colorcodes['ired']       = monochrome_logs ? '' : "\033[0;91m"
+    colorcodes['igreen']     = monochrome_logs ? '' : "\033[0;92m"
+    colorcodes['iyellow']    = monochrome_logs ? '' : "\033[0;93m"
+    colorcodes['iblue']      = monochrome_logs ? '' : "\033[0;94m"
+    colorcodes['ipurple']    = monochrome_logs ? '' : "\033[0;95m"
+    colorcodes['icyan']      = monochrome_logs ? '' : "\033[0;96m"
+    colorcodes['iwhite']     = monochrome_logs ? '' : "\033[0;97m"
 
     // Bold High Intensity
-    colorcodes['biblack']    = params.monochrome_logs ? '' : "\033[1;90m"
-    colorcodes['bired']      = params.monochrome_logs ? '' : "\033[1;91m"
-    colorcodes['bigreen']    = params.monochrome_logs ? '' : "\033[1;92m"
-    colorcodes['biyellow']   = params.monochrome_logs ? '' : "\033[1;93m"
-    colorcodes['biblue']     = params.monochrome_logs ? '' : "\033[1;94m"
-    colorcodes['bipurple']   = params.monochrome_logs ? '' : "\033[1;95m"
-    colorcodes['bicyan']     = params.monochrome_logs ? '' : "\033[1;96m"
-    colorcodes['biwhite']    = params.monochrome_logs ? '' : "\033[1;97m"
+    colorcodes['biblack']    = monochrome_logs ? '' : "\033[1;90m"
+    colorcodes['bired']      = monochrome_logs ? '' : "\033[1;91m"
+    colorcodes['bigreen']    = monochrome_logs ? '' : "\033[1;92m"
+    colorcodes['biyellow']   = monochrome_logs ? '' : "\033[1;93m"
+    colorcodes['biblue']     = monochrome_logs ? '' : "\033[1;94m"
+    colorcodes['bipurple']   = monochrome_logs ? '' : "\033[1;95m"
+    colorcodes['bicyan']     = monochrome_logs ? '' : "\033[1;96m"
+    colorcodes['biwhite']    = monochrome_logs ? '' : "\033[1;97m"
 
     return colorcodes
 }
@@ -149,7 +152,7 @@ def logColours() {
 //
 // Construct and send completion email
 //
-def completionEmail(summary_params) {
+def completionEmail(summary_params, monochrome_logs = true) {
 
     // Set up the e-mail variables
     def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
@@ -211,7 +214,7 @@ def completionEmail(summary_params) {
     def sendmail_html          = sendmail_template.toString()
 
     // Send the HTML e-mail
-    Map colors = logColours()
+    Map colors = logColours(monochrome_logs)
     if (email_address) {
         try {
             if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
@@ -240,8 +243,8 @@ def completionEmail(summary_params) {
 //
 // Print pipeline summary on completion
 //
-def completionSummary() {
-    Map colors = logColours()
+def completionSummary(monochrome_logs = true) {
+    Map colors = logColours(monochrome_logs)
     if (workflow.success) {
         if (workflow.stats.ignoredCount == 0) {
             log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
index 63988b1b..c4f71aeb 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
@@ -16,7 +16,6 @@ nextflow_function {
         when {
             function {
                 """
-                // define inputs of the function here. Example:
                 // input[0] = 1
                 """
             }
@@ -38,7 +37,6 @@ nextflow_function {
         when {
             function {
                 """
-                // define inputs of the function here. Example:
                 // input[0] = 1
                 """
             }
@@ -61,6 +59,7 @@ nextflow_function {
             function {
                 """
                 input[0] = "9.9.9"
+                input[1] = false
                 """
             }
         }
@@ -83,8 +82,7 @@ nextflow_function {
         when {
             function {
                 """
-                // define inputs of the function here. Example:
-                // input[0] = 1
+                input[0] = false
                 """
             }
         }
@@ -100,15 +98,14 @@ nextflow_function {
 
 
 
-    test("Test Function logColours") {
+    test("Test Function without logColours") {
 
         function "logColours"
 
         when {
             function {
                 """
-                // define inputs of the function here. Example:
-                // input[0] = 1
+                input[0] = true
                 """
             }
         }
@@ -121,4 +118,23 @@ nextflow_function {
         }
 
     }
+
+    test("Test Function with logColours") {
+        function "logColours"
+
+        when {
+            function {
+                """
+                input[0] = false
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert function.success                  },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
index 3ea51f68..bdf71d41 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
@@ -1,5 +1,81 @@
 {
-    "Test Function logColours": {
+    "Test Function checkConfigProvided": {
+        "content": null,
+        "timestamp": "2023-10-16T14:27:01.415849"
+    },
+    "Test Function nfCoreLogo": {
+        "content": [
+            "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n                                        \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m        ___     __   __   __   ___     \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \u001b[0;33m}  {\u001b[0m\n\u001b[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \u001b[0;32m\\`-._,-`-,\u001b[0m\n                                        \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m  nextflow_workflow 9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n"
+        ],
+        "timestamp": "2023-10-16T14:27:51.566211"
+    },
+    "Test Function workflowCitation": {
+        "content": [
+            "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n  https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n  https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n  https://github.com/nextflow_workflow/blob/master/CITATIONS.md"
+        ],
+        "timestamp": "2023-10-16T14:27:03.505737"
+    },
+    "Test Function without logColours": {
+        "content": [
+            {
+                "reset": "",
+                "bold": "",
+                "dim": "",
+                "underlined": "",
+                "blink": "",
+                "reverse": "",
+                "hidden": "",
+                "black": "",
+                "red": "",
+                "green": "",
+                "yellow": "",
+                "blue": "",
+                "purple": "",
+                "cyan": "",
+                "white": "",
+                "bblack": "",
+                "bred": "",
+                "bgreen": "",
+                "byellow": "",
+                "bblue": "",
+                "bpurple": "",
+                "bcyan": "",
+                "bwhite": "",
+                "ublack": "",
+                "ured": "",
+                "ugreen": "",
+                "uyellow": "",
+                "ublue": "",
+                "upurple": "",
+                "ucyan": "",
+                "uwhite": "",
+                "iblack": "",
+                "ired": "",
+                "igreen": "",
+                "iyellow": "",
+                "iblue": "",
+                "ipurple": "",
+                "icyan": "",
+                "iwhite": "",
+                "biblack": "",
+                "bired": "",
+                "bigreen": "",
+                "biyellow": "",
+                "biblue": "",
+                "bipurple": "",
+                "bicyan": "",
+                "biwhite": ""
+            }
+        ],
+        "timestamp": "2023-12-20T10:04:29.095368"
+    },
+    "Test Function dashedLine": {
+        "content": [
+            "-\u001b[2m----------------------------------------------------\u001b[0m-"
+        ],
+        "timestamp": "2023-10-16T14:27:07.721916"
+    },
+    "Test Function with logColours": {
         "content": [
             {
                 "reset": "\u001b[0m",
@@ -51,28 +127,6 @@
                 "biwhite": "\u001b[1;97m"
             }
         ],
-        "timestamp": "2023-10-16T14:27:09.843064"
-    },
-    "Test Function checkConfigProvided": {
-        "content": null,
-        "timestamp": "2023-10-16T14:27:01.415849"
-    },
-    "Test Function nfCoreLogo": {
-        "content": [
-            "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n                                        \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m        ___     __   __   __   ___     \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \u001b[0;33m}  {\u001b[0m\n\u001b[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \u001b[0;32m\\`-._,-`-,\u001b[0m\n                                        \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m  nextflow_workflow 9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n"
-        ],
-        "timestamp": "2023-10-16T14:27:51.566211"
-    },
-    "Test Function workflowCitation": {
-        "content": [
-            "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n  https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n  https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n  https://github.com/nextflow_workflow/blob/master/CITATIONS.md"
-        ],
-        "timestamp": "2023-10-16T14:27:03.505737"
-    },
-    "Test Function dashedLine": {
-        "content": [
-            "-\u001b[2m----------------------------------------------------\u001b[0m-"
-        ],
-        "timestamp": "2023-10-16T14:27:07.721916"
+        "timestamp": "2023-12-20T10:04:31.258856"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
index 637a416d..3b1d4c93 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
@@ -18,8 +18,7 @@ nextflow_workflow {
             }
             workflow {
                 """
-                // define inputs of the workflow here. Example:
-                // input[0] = file("test-file.txt")
+                input[0] = true
                 """
             }
         }

From 30031c033d267c04f30d2e419550bf6b5f7f42d2 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 12 Jan 2024 17:38:54 +0000
Subject: [PATCH 666/852] Use monochrome_logs parameter correctly

---
 subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
index 42e115f8..aa852a5b 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
@@ -58,7 +58,7 @@ workflow PIPELINE_INITIALISATION {
     //
     // Check config provided to the pipeline
     //
-    UTILS_NFCORE_PIPELINE ()
+    UTILS_NFCORE_PIPELINE ( params.monochrome_logs )
 
     //
     // Auto-detect input id type

From b00799025be470f30b96cae784e9a6f0f9b6c05e Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 14 Jan 2024 20:58:51 +0000
Subject: [PATCH 667/852] Remove modules/ suffix from params.testdata_base_path

---
 .../local/multiqc_mappings_config/tests/main.nf.test   |  2 +-
 modules/local/sra_runinfo_to_ftp/tests/main.nf.test    |  2 +-
 .../custom/sratoolsncbisettings/tests/main.nf.test     |  2 +-
 modules/nf-core/sratools/fasterqdump/nextflow.config   | 10 ++++++++++
 .../nf-core/sratools/fasterqdump/tests/main.nf.test    |  8 ++++----
 modules/nf-core/sratools/prefetch/nextflow.config      |  8 ++++++++
 modules/nf-core/sratools/prefetch/tests/main.nf.test   |  4 ++--
 modules/nf-core/untar/tests/main.nf.test               |  4 ++--
 .../local/utils_nfcore_fetchngs_pipeline/main.nf       |  4 +++-
 .../nextflow.config                                    |  2 ++
 tests/main.nf.test                                     | 10 ++++++++++
 tests/nextflow.config                                  |  7 ++-----
 workflows/sra/nextflow.config                          |  2 ++
 13 files changed, 48 insertions(+), 17 deletions(-)
 create mode 100644 modules/nf-core/sratools/fasterqdump/nextflow.config
 create mode 100644 modules/nf-core/sratools/prefetch/nextflow.config
 create mode 100644 subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config

diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test
index c1b2c5df..9a9b396f 100644
--- a/modules/local/multiqc_mappings_config/tests/main.nf.test
+++ b/modules/local/multiqc_mappings_config/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
 
             process {
                 """
-                input[0] = file(params.pipelines_test_data_base + 'modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv', checkIfExists: true)
+                input[0] = file(params.testdata_base_path + 'pipelines/fetchngs/1.15.0/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv', checkIfExists: true)
                 """
             }
         }
diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
index 31224dab..941ebd6b 100644
--- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
+++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
 
             process {
                 """
-                input[0] = file(params.pipelines_test_data_base + 'modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv', checkIfExists: true)
+                input[0] = file(params.testdata_base_path + 'pipelines/fetchngs/1.15.0/modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv', checkIfExists: true)
                 """
             }
         }
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
index 883a8d1e..bb298eec 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
+++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
@@ -21,7 +21,7 @@ nextflow_process {
             process {
                 """
                 file(params.settings_path).mkdirs()
-                def settings = file(params.testdata_base_path + '/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
+                def settings = file(params.testdata_base_path + 'modules/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
                 settings.copyTo(params.settings_file)
                 """
             }
diff --git a/modules/nf-core/sratools/fasterqdump/nextflow.config b/modules/nf-core/sratools/fasterqdump/nextflow.config
new file mode 100644
index 00000000..f98b140d
--- /dev/null
+++ b/modules/nf-core/sratools/fasterqdump/nextflow.config
@@ -0,0 +1,10 @@
+process {
+    withName: SRATOOLS_FASTERQDUMP {
+        ext.args = '--split-files --include-technical'
+        publishDir = [
+            path: { "${params.outdir}/fastq" },
+            mode: params.publish_dir_mode,
+            pattern: "*.fastq.gz"
+        ]
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
index af6b26d8..1f6ed26c 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
                 script "modules/nf-core/untar/main.nf"
                 process {
                     """
-                    input[0] = Channel.of([ [], file(params.testdata_base_path + 'genomics/sarscov2/illumina/sra/SRR13255544.tar.gz', checkIfExists: true) ])
+                    input[0] = Channel.of([ [], file(params.testdata_base_path + 'modules/genomics/sarscov2/illumina/sra/SRR13255544.tar.gz', checkIfExists: true) ])
                     """
                 }
             }
@@ -25,7 +25,7 @@ nextflow_process {
             process {
                 """
                 input[0] = UNTAR.out.untar.map{ meta, files -> [ [ id:'test_single_end', single_end:true ], files]}
-                input[1] = file(params.testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
+                input[1] = file(params.testdata_base_path + 'modules/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
                 input[2] = []
                 """
             }
@@ -46,7 +46,7 @@ nextflow_process {
                 script "modules/nf-core/untar/main.nf"
                 process {
                     """
-                    input[0] = Channel.of([ [], file(params.testdata_base_path + 'genomics/sarscov2/illumina/sra/SRR11140744.tar.gz', checkIfExists: true) ])
+                    input[0] = Channel.of([ [], file(params.testdata_base_path + 'modules/genomics/sarscov2/illumina/sra/SRR11140744.tar.gz', checkIfExists: true) ])
                     """
                 }
             }
@@ -56,7 +56,7 @@ nextflow_process {
             process {
                 """
                 input[0] = UNTAR.out.untar.map{ meta, files -> [ [ id:'test_paired_end', single_end:false ], files]}
-                input[1] = file(params.testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
+                input[1] = file(params.testdata_base_path + 'modules/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
                 input[2] = []
                 """
             }
diff --git a/modules/nf-core/sratools/prefetch/nextflow.config b/modules/nf-core/sratools/prefetch/nextflow.config
new file mode 100644
index 00000000..a2ca8848
--- /dev/null
+++ b/modules/nf-core/sratools/prefetch/nextflow.config
@@ -0,0 +1,8 @@
+process {
+    withName: SRATOOLS_PREFETCH {
+        publishDir = [
+            path: { "${params.outdir}/sra" },
+            enabled: false
+        ]
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test
index d88c1b67..99662cdc 100644
--- a/modules/nf-core/sratools/prefetch/tests/main.nf.test
+++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
             process {
                 """
                 input[0] = Channel.of([ [ id:'test', single_end:false ], 'DRR000774' ])
-                input[1] = file(params.testdata_base_path + '/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
+                input[1] = file(params.testdata_base_path + 'modules/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
                 input[2] = []
                 """
             }
@@ -39,7 +39,7 @@ nextflow_process {
             process {
                 """
                 input[0] = Channel.of([ [ id:'test', single_end:false ], 'SRR1170046' ])
-                input[1] = file(params.testdata_base_path + '/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
+                input[1] = file(params.testdata_base_path + 'modules/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
                 input[2] = []
                 """
             }
diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test
index bcf09a00..f57234f6 100644
--- a/modules/nf-core/untar/tests/main.nf.test
+++ b/modules/nf-core/untar/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [ [], file(params.testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ]
+                input[0] = [ [], file(params.testdata_base_path + 'modules/genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ]
                 """
             }
         }
@@ -38,7 +38,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [ [], file(params.testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) ]
+                input[0] = [ [], file(params.testdata_base_path + 'modules/generic/tar/hello.tar.gz', checkIfExists: true) ]
                 """
             }
         }
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
index aa852a5b..b36c6a24 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
@@ -58,7 +58,9 @@ workflow PIPELINE_INITIALISATION {
     //
     // Check config provided to the pipeline
     //
-    UTILS_NFCORE_PIPELINE ( params.monochrome_logs )
+    UTILS_NFCORE_PIPELINE (
+        params.monochrome_logs
+    )
 
     //
     // Auto-detect input id type
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config
new file mode 100644
index 00000000..b11c499f
--- /dev/null
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config
@@ -0,0 +1,2 @@
+includeConfig '../../../modules/nf-core/sratools/prefetch/nextflow.config'
+includeConfig '../../../modules/nf-core/sratools/fasterqdump/nextflow.config'
\ No newline at end of file
diff --git a/tests/main.nf.test b/tests/main.nf.test
index 8bfd4af2..2e2dd509 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -27,9 +27,14 @@ nextflow_pipeline {
                 { assert new File("$outputDir/fastq/md5/DRX026011_DRR028935_1.fastq.gz.md5").exists() },
                 { assert new File("$outputDir/fastq/md5/DRX026011_DRR028935_2.fastq.gz.md5").exists() },
                 { assert new File("$outputDir/fastq/md5/ERX1234253_ERR1160846.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/fastq/md5/SRX10940790_SRR14593545_1.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/fastq/md5/SRX10940790_SRR14593545_2.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/fastq/md5/SRX11047067_SRR14709033.fastq.gz.md5").exists() },
                 { assert new File("$outputDir/fastq/md5/SRX17709227_SRR21711856.fastq.gz.md5").exists() },
                 { assert new File("$outputDir/fastq/md5/SRX17709228_SRR21711855.fastq.gz.md5").exists() },
                 { assert new File("$outputDir/fastq/md5/SRX6725035_SRR9984183.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/fastq/md5/SRX9315476_SRR12848126_1.fastq.gz.md5").exists() },
+                { assert new File("$outputDir/fastq/md5/SRX9315476_SRR12848126_2.fastq.gz.md5").exists() },
                 { assert new File("$outputDir/fastq/md5/SRX9504942_SRR13055517_1.fastq.gz.md5").exists() },
                 { assert new File("$outputDir/fastq/md5/SRX9504942_SRR13055517_2.fastq.gz.md5").exists() },
                 { assert new File("$outputDir/fastq/md5/SRX9504942_SRR13055518_1.fastq.gz.md5").exists() },
@@ -44,9 +49,14 @@ nextflow_pipeline {
                 { assert new File("$outputDir/fastq/DRX026011_DRR028935_1.fastq.gz").exists() },
                 { assert new File("$outputDir/fastq/DRX026011_DRR028935_2.fastq.gz").exists() },
                 { assert new File("$outputDir/fastq/ERX1234253_ERR1160846.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX10940790_SRR14593545_1.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX10940790_SRR14593545_2.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX11047067_SRR14709033.fastq.gz").exists() },
                 { assert new File("$outputDir/fastq/SRX17709227_SRR21711856.fastq.gz").exists() },
                 { assert new File("$outputDir/fastq/SRX17709228_SRR21711855.fastq.gz").exists() },
                 { assert new File("$outputDir/fastq/SRX6725035_SRR9984183.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9315476_SRR12848126_1.fastq.gz").exists() },
+                { assert new File("$outputDir/fastq/SRX9315476_SRR12848126_2.fastq.gz").exists() },
                 { assert new File("$outputDir/fastq/SRX9504942_SRR13055517_1.fastq.gz").exists() },
                 { assert new File("$outputDir/fastq/SRX9504942_SRR13055517_2.fastq.gz").exists() },
                 { assert new File("$outputDir/fastq/SRX9504942_SRR13055518_1.fastq.gz").exists() },
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 9748de91..19bfb263 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -1,9 +1,6 @@
 params {
-    // Base directory for nf-core/modules test data
-    testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/'
-
-    // Base directory for pipeline test data
-    pipelines_test_data_base = 's3://ngi-igenomes/testdata/nf-core/pipelines/fetchngs/1.15.0/'
+    // Base directory for nf-core/modules and pipeline test data
+    testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/'
 }
 
 // Impose sensible resource limits for testing
diff --git a/workflows/sra/nextflow.config b/workflows/sra/nextflow.config
index b053d8a9..a48bcb73 100644
--- a/workflows/sra/nextflow.config
+++ b/workflows/sra/nextflow.config
@@ -3,3 +3,5 @@ includeConfig "../../modules/local/sra_fastq_ftp/nextflow.config"
 includeConfig "../../modules/local/sra_ids_to_runinfo/nextflow.config"
 includeConfig "../../modules/local/sra_runinfo_to_ftp/nextflow.config"
 includeConfig "../../modules/local/sra_to_samplesheet/nextflow.config"
+includeConfig "../../modules/nf-core/sratools/prefetch/nextflow.config"
+includeConfig "../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config"
\ No newline at end of file

From eadfda5b8bd50b0beb5fc99557514f17eaf7f6aa Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 14 Jan 2024 22:10:32 +0000
Subject: [PATCH 668/852] Fix pipeline tests

---
 tests/main.nf.test | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/tests/main.nf.test b/tests/main.nf.test
index 2e2dd509..1ab2f73a 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -27,14 +27,9 @@ nextflow_pipeline {
                 { assert new File("$outputDir/fastq/md5/DRX026011_DRR028935_1.fastq.gz.md5").exists() },
                 { assert new File("$outputDir/fastq/md5/DRX026011_DRR028935_2.fastq.gz.md5").exists() },
                 { assert new File("$outputDir/fastq/md5/ERX1234253_ERR1160846.fastq.gz.md5").exists() },
-                { assert new File("$outputDir/fastq/md5/SRX10940790_SRR14593545_1.fastq.gz.md5").exists() },
-                { assert new File("$outputDir/fastq/md5/SRX10940790_SRR14593545_2.fastq.gz.md5").exists() },
-                { assert new File("$outputDir/fastq/md5/SRX11047067_SRR14709033.fastq.gz.md5").exists() },
                 { assert new File("$outputDir/fastq/md5/SRX17709227_SRR21711856.fastq.gz.md5").exists() },
                 { assert new File("$outputDir/fastq/md5/SRX17709228_SRR21711855.fastq.gz.md5").exists() },
                 { assert new File("$outputDir/fastq/md5/SRX6725035_SRR9984183.fastq.gz.md5").exists() },
-                { assert new File("$outputDir/fastq/md5/SRX9315476_SRR12848126_1.fastq.gz.md5").exists() },
-                { assert new File("$outputDir/fastq/md5/SRX9315476_SRR12848126_2.fastq.gz.md5").exists() },
                 { assert new File("$outputDir/fastq/md5/SRX9504942_SRR13055517_1.fastq.gz.md5").exists() },
                 { assert new File("$outputDir/fastq/md5/SRX9504942_SRR13055517_2.fastq.gz.md5").exists() },
                 { assert new File("$outputDir/fastq/md5/SRX9504942_SRR13055518_1.fastq.gz.md5").exists() },

From 6cbcd6454ca8241537e9807be8f86b3a9d733c81 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 14 Jan 2024 22:40:41 +0000
Subject: [PATCH 669/852] Add config to fasterqdump tests to reset ext.args set
 in fetchngs

---
 .../nf-core/sratools/fasterqdump/tests/main.nf.test    | 10 +++++++++-
 .../nf-core/sratools/fasterqdump/tests/nextflow.config |  5 +++++
 2 files changed, 14 insertions(+), 1 deletion(-)
 create mode 100644 modules/nf-core/sratools/fasterqdump/tests/nextflow.config

diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
index 1f6ed26c..c341b359 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
@@ -1,6 +1,7 @@
 nextflow_process {
     name "Test Process SRATOOLS_FASTERQDUMP"
     script "../main.nf"
+    config "./nextflow.config"
     process "SRATOOLS_FASTERQDUMP"
     tag "modules"
     tag "modules_nfcore"
@@ -9,7 +10,6 @@ nextflow_process {
     tag "sratools/fasterqdump"
 
     test("Single-end") {
-
         setup {
             run("UNTAR") {
                 script "modules/nf-core/untar/main.nf"
@@ -22,6 +22,10 @@ nextflow_process {
         }
 
         when {
+            params {
+                outdir = "$outputDir"
+            }
+
             process {
                 """
                 input[0] = UNTAR.out.untar.map{ meta, files -> [ [ id:'test_single_end', single_end:true ], files]}
@@ -53,6 +57,10 @@ nextflow_process {
         }
 
         when {
+            params {
+                outdir = "$outputDir"
+            }
+
             process {
                 """
                 input[0] = UNTAR.out.untar.map{ meta, files -> [ [ id:'test_paired_end', single_end:false ], files]}
diff --git a/modules/nf-core/sratools/fasterqdump/tests/nextflow.config b/modules/nf-core/sratools/fasterqdump/tests/nextflow.config
new file mode 100644
index 00000000..23e4100b
--- /dev/null
+++ b/modules/nf-core/sratools/fasterqdump/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: SRATOOLS_FASTERQDUMP {
+        ext.args = ''
+    }
+}
\ No newline at end of file

From 5b7349f9681fd5be3ce552c3d987d4b26b1b9336 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 14 Jan 2024 22:52:14 +0000
Subject: [PATCH 670/852] Update all nf-core modules and subworkflows

---
 modules.json                                            | 8 ++++----
 modules/nf-core/sratools/fasterqdump/tests/main.nf.test | 1 +
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/modules.json b/modules.json
index f7829fdd..a10eaf6b 100644
--- a/modules.json
+++ b/modules.json
@@ -7,22 +7,22 @@
                 "nf-core": {
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
-                        "git_sha": "20e78a9868eaa69c8cac91152397def32374b807",
+                        "git_sha": "8e6960947b6647952b97667173805b34b40f25d6",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "20e78a9868eaa69c8cac91152397def32374b807",
+                        "git_sha": "8e6960947b6647952b97667173805b34b40f25d6",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/prefetch": {
                         "branch": "master",
-                        "git_sha": "20e78a9868eaa69c8cac91152397def32374b807",
+                        "git_sha": "8e6960947b6647952b97667173805b34b40f25d6",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "20e78a9868eaa69c8cac91152397def32374b807",
+                        "git_sha": "8e6960947b6647952b97667173805b34b40f25d6",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
index c341b359..3b9ed965 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
@@ -10,6 +10,7 @@ nextflow_process {
     tag "sratools/fasterqdump"
 
     test("Single-end") {
+
         setup {
             run("UNTAR") {
                 script "modules/nf-core/untar/main.nf"

From fdaf417fd487790b32d6caceeeb09c5e3a34c7e4 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 15 Jan 2024 15:42:31 +0000
Subject: [PATCH 671/852] Split --testdata_base_path into
 --modules_testdata_base_path and --pipelines_testdata_base_path

---
 modules/local/multiqc_mappings_config/tests/main.nf.test  | 2 +-
 modules/local/sra_runinfo_to_ftp/tests/main.nf.test       | 2 +-
 .../custom/sratoolsncbisettings/tests/main.nf.test        | 2 +-
 modules/nf-core/sratools/fasterqdump/tests/main.nf.test   | 8 ++++----
 modules/nf-core/sratools/prefetch/tests/main.nf.test      | 4 ++--
 modules/nf-core/untar/tests/main.nf.test                  | 4 ++--
 tests/nextflow.config                                     | 7 +++++--
 7 files changed, 16 insertions(+), 13 deletions(-)

diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test
index 9a9b396f..cfb43166 100644
--- a/modules/local/multiqc_mappings_config/tests/main.nf.test
+++ b/modules/local/multiqc_mappings_config/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
 
             process {
                 """
-                input[0] = file(params.testdata_base_path + 'pipelines/fetchngs/1.15.0/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv', checkIfExists: true)
+                input[0] = file(params.pipelines_testdata_base_path + 'csv/SRX9626017_SRR13191702.mappings.csv', checkIfExists: true)
                 """
             }
         }
diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
index 941ebd6b..347e3392 100644
--- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
+++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
 
             process {
                 """
-                input[0] = file(params.testdata_base_path + 'pipelines/fetchngs/1.15.0/modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv', checkIfExists: true)
+                input[0] = file(params.pipelines_testdata_base_path + 'tsv/SRR13191702.runinfo.tsv', checkIfExists: true)
                 """
             }
         }
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
index bb298eec..9f178678 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
+++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
@@ -21,7 +21,7 @@ nextflow_process {
             process {
                 """
                 file(params.settings_path).mkdirs()
-                def settings = file(params.testdata_base_path + 'modules/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
+                def settings = file(params.modules_testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
                 settings.copyTo(params.settings_file)
                 """
             }
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
index 3b9ed965..48722e4e 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
                 script "modules/nf-core/untar/main.nf"
                 process {
                     """
-                    input[0] = Channel.of([ [], file(params.testdata_base_path + 'modules/genomics/sarscov2/illumina/sra/SRR13255544.tar.gz', checkIfExists: true) ])
+                    input[0] = Channel.of([ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/sra/SRR13255544.tar.gz', checkIfExists: true) ])
                     """
                 }
             }
@@ -30,7 +30,7 @@ nextflow_process {
             process {
                 """
                 input[0] = UNTAR.out.untar.map{ meta, files -> [ [ id:'test_single_end', single_end:true ], files]}
-                input[1] = file(params.testdata_base_path + 'modules/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
                 input[2] = []
                 """
             }
@@ -51,7 +51,7 @@ nextflow_process {
                 script "modules/nf-core/untar/main.nf"
                 process {
                     """
-                    input[0] = Channel.of([ [], file(params.testdata_base_path + 'modules/genomics/sarscov2/illumina/sra/SRR11140744.tar.gz', checkIfExists: true) ])
+                    input[0] = Channel.of([ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/sra/SRR11140744.tar.gz', checkIfExists: true) ])
                     """
                 }
             }
@@ -65,7 +65,7 @@ nextflow_process {
             process {
                 """
                 input[0] = UNTAR.out.untar.map{ meta, files -> [ [ id:'test_paired_end', single_end:false ], files]}
-                input[1] = file(params.testdata_base_path + 'modules/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
                 input[2] = []
                 """
             }
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test
index 99662cdc..ed710ba0 100644
--- a/modules/nf-core/sratools/prefetch/tests/main.nf.test
+++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
             process {
                 """
                 input[0] = Channel.of([ [ id:'test', single_end:false ], 'DRR000774' ])
-                input[1] = file(params.testdata_base_path + 'modules/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
                 input[2] = []
                 """
             }
@@ -39,7 +39,7 @@ nextflow_process {
             process {
                 """
                 input[0] = Channel.of([ [ id:'test', single_end:false ], 'SRR1170046' ])
-                input[1] = file(params.testdata_base_path + 'modules/generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
                 input[2] = []
                 """
             }
diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test
index f57234f6..679e83c7 100644
--- a/modules/nf-core/untar/tests/main.nf.test
+++ b/modules/nf-core/untar/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [ [], file(params.testdata_base_path + 'modules/genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ]
+                input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ]
                 """
             }
         }
@@ -38,7 +38,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [ [], file(params.testdata_base_path + 'modules/generic/tar/hello.tar.gz', checkIfExists: true) ]
+                input[0] = [ [], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) ]
                 """
             }
         }
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 19bfb263..d75ad44b 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -1,6 +1,9 @@
 params {
-    // Base directory for nf-core/modules and pipeline test data
-    testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/'
+    // Base directory for nf-core/modules test data
+    modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/'
+
+    // Base directory for nf-core/fetchngs test data
+    pipelines_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/pipelines/fetchngs/1.15.0/'
 }
 
 // Impose sensible resource limits for testing

From 3f58f32652db24600a1f04a8edc7b24c82296931 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 15 Jan 2024 16:59:46 +0000
Subject: [PATCH 672/852] Update all nf-core modules and subworkflows

---
 modules.json | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules.json b/modules.json
index a10eaf6b..66aac80d 100644
--- a/modules.json
+++ b/modules.json
@@ -7,22 +7,22 @@
                 "nf-core": {
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
-                        "git_sha": "8e6960947b6647952b97667173805b34b40f25d6",
+                        "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "8e6960947b6647952b97667173805b34b40f25d6",
+                        "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/prefetch": {
                         "branch": "master",
-                        "git_sha": "8e6960947b6647952b97667173805b34b40f25d6",
+                        "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "8e6960947b6647952b97667173805b34b40f25d6",
+                        "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620",
                         "installed_by": ["modules"]
                     }
                 }

From dfa87b9f9590cc9fe902f791cf5a3ee118755485 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 17 Jan 2024 12:57:27 +0000
Subject: [PATCH 673/852] Refactor how versions are handled in pipeline

---
 main.nf                                       | 17 ++--
 .../utils_nfcore_fetchngs_pipeline/main.nf    | 63 ++++++--------
 .../nf-core/utils_nfcore_pipeline/main.nf     | 82 +++++++++++++++----
 workflows/sra/main.nf                         | 12 +++
 workflows/synapse/main.nf                     | 12 +++
 5 files changed, 120 insertions(+), 66 deletions(-)

diff --git a/main.nf b/main.nf
index 2fe0061e..a2e5f701 100644
--- a/main.nf
+++ b/main.nf
@@ -30,25 +30,19 @@ workflow NFCORE_FETCHNGS {
 
     main:
 
-    ch_versions = Channel.empty()
-
     //
     // WORKFLOW: Download FastQ files for SRA / ENA / GEO / DDBJ ids
     //
     if (params.input_type == 'sra') {
         SRA ( ids )
-        ch_versions = SRA.out.versions
 
     //
     // WORKFLOW: Download FastQ files for Synapse ids
     //
     } else if (params.input_type == 'synapse') {
         SYNAPSE ( ids )
-        ch_versions = SYNAPSE.out.versions
     }
 
-    emit:
-    versions = ch_versions
 }
 
 /*
@@ -73,20 +67,21 @@ workflow {
     //
     // WORKFLOW: Run primary workflows for the pipeline
     //
-    NFCORE_FETCHNGS (
-        PIPELINE_INITIALISATION.out.ids
+    NFCORE_FETCHNGS ( 
+        PIPELINE_INITIALISATION.out.ids 
     )
 
     //
     // SUBWORKFLOW: Run completion tasks
     //
     PIPELINE_COMPLETION (
-        NFCORE_FETCHNGS.out.versions,
         params.input_type,
         params.email,
         params.email_on_fail,
-        params.hook_url,
-        PIPELINE_INITIALISATION.out.summary_params
+        params.plaintext_email,
+        params.outdir,
+        params.monochrome_logs,
+        params.hook_url
     )
 }
 
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
index b36c6a24..27527f93 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
@@ -8,17 +8,17 @@
 ========================================================================================
 */
 
-include { UTILS_NEXTFLOW_PIPELINE; getWorkflowVersion } from '../../nf-core/utils_nextflow_pipeline'
-include { UTILS_NFVALIDATION_PLUGIN                   } from '../../nf-core/utils_nfvalidation_plugin'
-include { 
-    UTILS_NFCORE_PIPELINE; 
-    workflowCitation; 
-    nfCoreLogo; 
-    dashedLine; 
-    completionEmail; 
-    completionSummary; 
-    imNotification 
-} from '../../nf-core/utils_nfcore_pipeline'
+include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
+include { getWorkflowVersion        } from '../../nf-core/utils_nextflow_pipeline'
+include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
+include { paramsSummaryMap          } from 'plugin/nf-validation'
+include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
+include { workflowCitation          } from '../../nf-core/utils_nfcore_pipeline'
+include { nfCoreLogo                } from '../../nf-core/utils_nfcore_pipeline'
+include { dashedLine                } from '../../nf-core/utils_nfcore_pipeline'
+include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
+include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
+include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
 
 /*
 ========================================================================================
@@ -43,8 +43,8 @@ workflow PIPELINE_INITIALISATION {
     //
     // Validate parameters and generate parameter summary to stdout
     //
-    def pre_help_text = nfCoreLogo(getWorkflowVersion())
-    def post_help_text = '\n' + workflowCitation() + '\n' + dashedLine()
+    def pre_help_text = nfCoreLogo(getWorkflowVersion(), params.monochrome_logs)
+    def post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(params.monochrome_logs)
     def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input ids.csv --outdir <OUTDIR>"
     UTILS_NFVALIDATION_PLUGIN (
         params.help,
@@ -58,9 +58,7 @@ workflow PIPELINE_INITIALISATION {
     //
     // Check config provided to the pipeline
     //
-    UTILS_NFCORE_PIPELINE (
-        params.monochrome_logs
-    )
+    UTILS_NFCORE_PIPELINE ()
 
     //
     // Auto-detect input id type
@@ -89,8 +87,7 @@ workflow PIPELINE_INITIALISATION {
         .set { ch_ids }
 
     emit:
-    ids            = ch_ids
-    summary_params = UTILS_NFVALIDATION_PLUGIN.out.summary_params
+    ids = ch_ids
 }
 
 /*
@@ -102,38 +99,30 @@ workflow PIPELINE_INITIALISATION {
 workflow PIPELINE_COMPLETION {
 
     take:
-    versions       // channel: software tools versions
-    input_type     //  string: 'sra' or 'synapse'
-    email          //  string: email address
-    email_on_fail  //  string: email address sent on pipeline failure
-    hook_url       //  string: hook URL for notifications
-    summary_params //     map: Groovy map of the parameters used in the pipeline
+    input_type      //  string: 'sra' or 'synapse'
+    email           //  string: email address
+    email_on_fail   //  string: email address sent on pipeline failure
+    plaintext_email // boolean: Send plain-text email instead of HTML
+    outdir          //    path: Path to output directory where results will be published
+    monochrome_logs // boolean: Disable ANSI colour codes in log output
+    hook_url        //  string: hook URL for notifications
 
     main:
 
-    //
-    // MODULE: Dump software versions for all tools used in the workflow
-    //
-    pipeline_version_info = Channel.of("""\"workflow\":
-        nextflow: ${workflow.nextflow.version}
-        ${workflow.manifest.name}: ${workflow.manifest.version}
-    """.stripIndent())
-
-    versions = versions.mix(pipeline_version_info)
-    versions.collectFile(name: 'fetchngs_mqc_versions.yml', storeDir: "${params.outdir}/pipeline_info")
+    summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
 
     //
     // Completion email and summary
     //
     workflow.onComplete {
         if (email || email_on_fail) {
-            completionEmail(summary_params)
+            completionEmail(summary_params, getWorkflowVersion(), email, email_on_fail, plaintext_email, outdir, monochrome_logs)
         }
 
-        completionSummary()
+        completionSummary(monochrome_logs)
 
         if (hook_url) {
-            imNotification(summary_params)
+            imNotification(summary_params, getWorkflowVersion(), hook_url)
         }
 
         if (input_type == 'sra') {
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 5716198c..49063e0c 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -2,6 +2,8 @@
 // Subworkflow with utility functions specific to the nf-core pipeline template
 //
 
+import org.yaml.snakeyaml.Yaml
+
 /*
 ========================================================================================
     SUBWORKFLOW DEFINITION
@@ -10,9 +12,6 @@
 
 workflow UTILS_NFCORE_PIPELINE {
 
-    take:
-    monochrome_logs // boolean: Disable ANSI colour codes in log output
-
     main:
     checkConfigProvided()
 
@@ -54,10 +53,59 @@ def workflowCitation() {
         "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
 }
 
+//
+// Get software versions for pipeline
+//
+def processVersionsFromYAML(yaml_file) {
+    Yaml parser = new Yaml()
+    versions = parser.load(yaml_file).collectEntries { k,v -> [ k.tokenize(':')[-1], v ] }
+    Yaml yaml = new Yaml()
+    return yaml.dumpAsMap(versions).trim()
+}
+
+//
+// Get workflow version for pipeline
+//
+def workflowVersionToYAML(workflow_version) {
+    return """
+    'Workflow':
+      "Nextflow": "$workflow.nextflow.version"
+      "$workflow.manifest.name": "${workflow_version}"
+    """.stripIndent().trim()
+}
+
+//
+// Get workflow summary for MultiQC
+//
+def paramsSummaryMultiqc(summary_params) {
+    def summary_section = ''
+    for (group in summary_params.keySet()) {
+        def group_params = summary_params.get(group)  // This gets the parameters of that particular group
+        if (group_params) {
+            summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
+            summary_section += "    <dl class=\"dl-horizontal\">\n"
+            for (param in group_params.keySet()) {
+                summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
+            }
+            summary_section += "    </dl>\n"
+        }
+    }
+
+    String yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
+    yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
+    yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
+    yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
+    yaml_file_text        += "plot_type: 'html'\n"
+    yaml_file_text        += "data: |\n"
+    yaml_file_text        += "${summary_section}"
+
+    return yaml_file_text
+}
+
 //
 // nf-core logo
 //
-def nfCoreLogo(workflow_version, monochrome_logs = true) {
+def nfCoreLogo(workflow_version, monochrome_logs=true) {
     Map colors = logColours(monochrome_logs)
     String.format(
         """\n
@@ -76,7 +124,7 @@ def nfCoreLogo(workflow_version, monochrome_logs = true) {
 //
 // Return dashed line
 //
-def dashedLine(monochrome_logs = true) {
+def dashedLine(monochrome_logs=true) {
     Map colors = logColours(monochrome_logs)
     return "-${colors.dim}----------------------------------------------------${colors.reset}-"
 }
@@ -84,7 +132,7 @@ def dashedLine(monochrome_logs = true) {
 //
 // ANSII colours used for terminal logging
 //
-def logColours(monochrome_logs = true) {
+def logColours(monochrome_logs=true) {
     Map colorcodes = [:]
 
     // Reset / Meta
@@ -152,7 +200,7 @@ def logColours(monochrome_logs = true) {
 //
 // Construct and send completion email
 //
-def completionEmail(summary_params, monochrome_logs = true) {
+def completionEmail(summary_params, workflow_version, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true) {
 
     // Set up the e-mail variables
     def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
@@ -178,7 +226,7 @@ def completionEmail(summary_params, monochrome_logs = true) {
     misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
 
     def email_fields = [:]
-    email_fields['version']      = NfcoreTemplate.version(workflow)
+    email_fields['version']      = workflow_version
     email_fields['runName']      = workflow.runName
     email_fields['success']      = workflow.success
     email_fields['dateComplete'] = workflow.complete
@@ -191,9 +239,9 @@ def completionEmail(summary_params, monochrome_logs = true) {
     email_fields['summary']      = summary << misc_fields
 
     // Check if we are only sending emails on failure
-    def email_address = params.email
-    if (!params.email && params.email_on_fail && !workflow.success) {
-        email_address = params.email_on_fail
+    def email_address = email
+    if (!email && email_on_fail && !workflow.success) {
+        email_address = email_on_fail
     }
 
     // Render the TXT template
@@ -217,7 +265,7 @@ def completionEmail(summary_params, monochrome_logs = true) {
     Map colors = logColours(monochrome_logs)
     if (email_address) {
         try {
-            if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+            if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
             // Try to send HTML e-mail using sendmail
             [ 'sendmail', '-t' ].execute() << sendmail_html
             log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
@@ -230,7 +278,7 @@ def completionEmail(summary_params, monochrome_logs = true) {
     }
 
     // Write summary e-mail HTML to a file
-    def output_d = new File("${params.outdir}/pipeline_info/")
+    def output_d = new File("${outdir}/pipeline_info/")
     if (!output_d.exists()) {
         output_d.mkdirs()
     }
@@ -243,7 +291,7 @@ def completionEmail(summary_params, monochrome_logs = true) {
 //
 // Print pipeline summary on completion
 //
-def completionSummary(monochrome_logs = true) {
+def completionSummary(monochrome_logs=true) {
     Map colors = logColours(monochrome_logs)
     if (workflow.success) {
         if (workflow.stats.ignoredCount == 0) {
@@ -259,9 +307,7 @@ def completionSummary(monochrome_logs = true) {
 //
 // Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack
 //
-def imNotification(summary_params) {
-    def hook_url = params.hook_url
-
+def imNotification(summary_params, workflow_version, hook_url) {
     def summary = [:]
     for (group in summary_params.keySet()) {
         summary << summary_params[group]
@@ -280,7 +326,7 @@ def imNotification(summary_params) {
     misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
 
     def msg_fields = [:]
-    msg_fields['version']      = NfcoreTemplate.version(workflow)
+    msg_fields['version']      = workflow_version
     msg_fields['runName']      = workflow.runName
     msg_fields['success']      = workflow.success
     msg_fields['dateComplete'] = workflow.complete
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 3d487431..f1603c37 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -9,6 +9,9 @@ include { SRA_FASTQ_FTP           } from '../../modules/local/sra_fastq_ftp'
 include { SRA_IDS_TO_RUNINFO      } from '../../modules/local/sra_ids_to_runinfo'
 include { SRA_RUNINFO_TO_FTP      } from '../../modules/local/sra_runinfo_to_ftp'
 include { SRA_TO_SAMPLESHEET      } from '../../modules/local/sra_to_samplesheet'
+include { getWorkflowVersion      } from '../../subworkflows/nf-core/utils_nextflow_pipeline'
+include { processVersionsFromYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
+include { workflowVersionToYAML   } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -150,6 +153,15 @@ workflow SRA {
         ch_sample_mappings_yml = MULTIQC_MAPPINGS_CONFIG.out.yml
     }
 
+    //
+    // Collate and save software versions
+    //
+    ch_versions
+        .unique()
+        .map { processVersionsFromYAML(it) }
+        .mix(Channel.of(workflowVersionToYAML(getWorkflowVersion())))
+        .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'collated_software_mqc_versions.yml', newLine: true)
+
     emit:
     samplesheet     = ch_samplesheet
     mappings        = ch_mappings
diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf
index 6b5ea02c..54670057 100644
--- a/workflows/synapse/main.nf
+++ b/workflows/synapse/main.nf
@@ -9,6 +9,9 @@ include { SYNAPSE_SHOW              } from '../../modules/local/synapse_show'
 include { SYNAPSE_GET               } from '../../modules/local/synapse_get'
 include { SYNAPSE_TO_SAMPLESHEET    } from '../../modules/local/synapse_to_samplesheet'
 include { SYNAPSE_MERGE_SAMPLESHEET } from '../../modules/local/synapse_merge_samplesheet'
+include { getWorkflowVersion        } from '../../subworkflows/nf-core/utils_nextflow_pipeline'
+include { processVersionsFromYAML   } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
+include { workflowVersionToYAML     } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -105,6 +108,15 @@ workflow SYNAPSE {
     )
     ch_versions = ch_versions.mix(SYNAPSE_MERGE_SAMPLESHEET.out.versions)
 
+    //
+    // Collate and save software versions
+    //
+    ch_versions
+        .unique()
+        .map { processVersionsFromYAML(it) }
+        .mix(Channel.of(workflowVersionToYAML(getWorkflowVersion())))
+        .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'collated_software_mqc_versions.yml', newLine: true)
+
     emit:
     fastq       = ch_fastq
     samplesheet = SYNAPSE_MERGE_SAMPLESHEET.out.samplesheet

From 775141dc50bf426251254e66795e08734bc6abc2 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 17 Jan 2024 13:28:40 +0000
Subject: [PATCH 674/852] Update CHANGELOG

---
 CHANGELOG.md | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 04264a5f..d512d75c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,8 +9,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 Special thanks to the following for their contributions to the release:
 
+- [Adam Talbot](https://github.com/adamrtalbot)
 - [Alexandru Mizeranschi](https://github.com/nicolae06)
 - [Alexander Blaessle](https://github.com/alexblaessle)
+- [Maxime Garcia](https://github.com/maxulysse)
 - [Sebastian Uhrig](https://github.com/suhrig)
 
 Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
@@ -18,9 +20,10 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 ### Enhancements & fixes
 
 - [PR #238](https://github.com/nf-core/fetchngs/pull/238) - Resolved bug when prefetching large studies ([#236](https://github.com/nf-core/fetchngs/issues/236))
-- [PR #241](https://github.com/nf-core/fetchngs/pull/241) - Download of big files time out and don't resume ([#169](https://github.com/nf-core/fetchngs/issues/169))
+- [PR #241](https://github.com/nf-core/fetchngs/pull/241) - Use wget instead of curl to download files from FTP ([#169](https://github.com/nf-core/fetchngs/issues/169), [#194](https://github.com/nf-core/fetchngs/issues/194))
 - [PR #242](https://github.com/nf-core/fetchngs/pull/242) - Template update for nf-core/tools v2.11
 - [PR #243](https://github.com/nf-core/fetchngs/pull/243) - Fixes for [PR #238](https://github.com/nf-core/fetchngs/pull/238)
+- [PR #245](https://github.com/nf-core/fetchngs/pull/246) - Refactor nf-test CI and test and other pre-release fixes ([#233](https://github.com/nf-core/fetchngs/issues/233))
 - [PR #246](https://github.com/nf-core/fetchngs/pull/246) - Handle dark/light mode for logo in GitHub README properly
 - [PR #248](https://github.com/nf-core/fetchngs/pull/248) - Update pipeline level test data path to use mirror on s3
 - [PR #249](https://github.com/nf-core/fetchngs/pull/249) - Update modules which includes absolute paths for test data, making module level test compatible within the pipeline.

From 790124a8b58b760d79237250c1494e0b69cb708f Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 17 Jan 2024 13:32:45 +0000
Subject: [PATCH 675/852] Fix ECLint

---
 main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/main.nf b/main.nf
index a2e5f701..64bc75cf 100644
--- a/main.nf
+++ b/main.nf
@@ -67,8 +67,8 @@ workflow {
     //
     // WORKFLOW: Run primary workflows for the pipeline
     //
-    NFCORE_FETCHNGS ( 
-        PIPELINE_INITIALISATION.out.ids 
+    NFCORE_FETCHNGS (
+        PIPELINE_INITIALISATION.out.ids
     )
 
     //

From 5114f76fa063b43c3c02c4d3cb0a6386f46b721e Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 17 Jan 2024 13:36:12 +0000
Subject: [PATCH 676/852] [automated] Fix linting with Prettier

---
 .devcontainer/devcontainer.json | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 4ecfbfe3..4a9bc5c7 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -18,11 +18,11 @@
                 "python.linting.flake8Path": "/opt/conda/bin/flake8",
                 "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
                 "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
-                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+                "python.linting.pylintPath": "/opt/conda/bin/pylint",
             },
 
             // Add the IDs of extensions you want installed when the container is created.
-            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
-        }
-    }
+            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"],
+        },
+    },
 }

From ca88a5e368fc68d4734ac513a7d6836b83809fc2 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Wed, 17 Jan 2024 15:19:27 +0100
Subject: [PATCH 677/852] Update
 subworkflows/nf-core/utils_nfcore_pipeline/main.nf

Co-authored-by: Robert Syme <rob.syme@gmail.com>
---
 subworkflows/nf-core/utils_nfcore_pipeline/main.nf | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 49063e0c..77086031 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -57,9 +57,8 @@ def workflowCitation() {
 // Get software versions for pipeline
 //
 def processVersionsFromYAML(yaml_file) {
-    Yaml parser = new Yaml()
-    versions = parser.load(yaml_file).collectEntries { k,v -> [ k.tokenize(':')[-1], v ] }
     Yaml yaml = new Yaml()
+    versions = yaml.load(yaml_file).collectEntries { k,v -> [ k.tokenize(':')[-1], v ] }
     return yaml.dumpAsMap(versions).trim()
 }
 

From 9cee7471d9d8aa75ee39c838135e02bd96f802ad Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 17 Jan 2024 16:45:32 +0000
Subject: [PATCH 678/852] Sort includes alphabetically

---
 .../local/utils_nfcore_fetchngs_pipeline/main.nf     | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
index 27527f93..23bf3ebd 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
@@ -8,17 +8,17 @@
 ========================================================================================
 */
 
-include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
-include { getWorkflowVersion        } from '../../nf-core/utils_nextflow_pipeline'
 include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
 include { paramsSummaryMap          } from 'plugin/nf-validation'
-include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
-include { workflowCitation          } from '../../nf-core/utils_nfcore_pipeline'
-include { nfCoreLogo                } from '../../nf-core/utils_nfcore_pipeline'
-include { dashedLine                } from '../../nf-core/utils_nfcore_pipeline'
+include { getWorkflowVersion        } from '../../nf-core/utils_nextflow_pipeline'
+include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
 include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
+include { dashedLine                } from '../../nf-core/utils_nfcore_pipeline'
+include { nfCoreLogo                } from '../../nf-core/utils_nfcore_pipeline'
 include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
+include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
+include { workflowCitation          } from '../../nf-core/utils_nfcore_pipeline'
 
 /*
 ========================================================================================

From 66cb0bad45fbb4e082615d18502abd91a7c77cf2 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 17 Jan 2024 17:09:21 +0000
Subject: [PATCH 679/852] Simplify test for utils_nfcore_pipeline

---
 .../nf-core/utils_nfcore_pipeline/main.nf     | 19 +++++++++++++++----
 .../tests/main.workflow.nf.test               | 13 -------------
 2 files changed, 15 insertions(+), 17 deletions(-)

diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 77086031..261a1651 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -14,10 +14,6 @@ workflow UTILS_NFCORE_PIPELINE {
 
     main:
     checkConfigProvided()
-
-    emit:
-    success = true
-
 }
 
 /*
@@ -73,6 +69,21 @@ def workflowVersionToYAML(workflow_version) {
     """.stripIndent().trim()
 }
 
+//
+// Get channel of software versions used in pipeline in YAML format
+//
+def softwareVersionsToYAML(ch_versions, workflow_version) {
+    
+    return 
+        ch_versions
+            .unique()
+            .map { processVersionsFromYAML(it) }
+            .mix(Channel.of(workflowVersionToYAML(workflow_version)))
+        // .set { ch_software_versions }
+    // return ch_software_versions
+}
+
+
 //
 // Get workflow summary for MultiQC
 //
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
index 3b1d4c93..b16445da 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
@@ -10,19 +10,6 @@ nextflow_workflow {
     tag "subworkflows/utils_nfcore_pipeline"
 
     test("Should run without failures") {
-
-        when {
-            params {
-                // define parameters here. Example:
-                // outdir = "tests/results"
-            }
-            workflow {
-                """
-                input[0] = true
-                """
-            }
-        }
-
         then {
             assert workflow.success
         }

From 7e79d0422a835c6adc871ac2b8b5d51371439500 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 17 Jan 2024 17:36:00 +0000
Subject: [PATCH 680/852] Refactor how getWorkflowVersion function is called
 within pipeline

---
 .../utils_nfcore_fetchngs_pipeline/main.nf    |  7 ++-
 .../nf-core/utils_nfcore_pipeline/main.nf     | 53 ++++++++++++-------
 workflows/sra/main.nf                         | 12 ++---
 workflows/synapse/main.nf                     | 11 ++--
 4 files changed, 43 insertions(+), 40 deletions(-)

diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
index 23bf3ebd..1681c0e4 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
@@ -10,7 +10,6 @@
 
 include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
 include { paramsSummaryMap          } from 'plugin/nf-validation'
-include { getWorkflowVersion        } from '../../nf-core/utils_nextflow_pipeline'
 include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
 include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
@@ -43,7 +42,7 @@ workflow PIPELINE_INITIALISATION {
     //
     // Validate parameters and generate parameter summary to stdout
     //
-    def pre_help_text = nfCoreLogo(getWorkflowVersion(), params.monochrome_logs)
+    def pre_help_text = nfCoreLogo(params.monochrome_logs)
     def post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(params.monochrome_logs)
     def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input ids.csv --outdir <OUTDIR>"
     UTILS_NFVALIDATION_PLUGIN (
@@ -116,13 +115,13 @@ workflow PIPELINE_COMPLETION {
     //
     workflow.onComplete {
         if (email || email_on_fail) {
-            completionEmail(summary_params, getWorkflowVersion(), email, email_on_fail, plaintext_email, outdir, monochrome_logs)
+            completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs)
         }
 
         completionSummary(monochrome_logs)
 
         if (hook_url) {
-            imNotification(summary_params, getWorkflowVersion(), hook_url)
+            imNotification(summary_params, hook_url)
         }
 
         if (input_type == 'sra') {
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 261a1651..fd4eddfd 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -49,6 +49,24 @@ def workflowCitation() {
         "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
 }
 
+//
+// Generate workflow version string
+//
+def getWorkflowVersion() {
+    String version_string = ""
+    if (workflow.manifest.version) {
+        def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
+        version_string += "${prefix_v}${workflow.manifest.version}"
+    }
+
+    if (workflow.commitId) {
+        def git_shortsha = workflow.commitId.substring(0, 7)
+        version_string += "-g${git_shortsha}"
+    }
+
+    return version_string
+}
+
 //
 // Get software versions for pipeline
 //
@@ -61,29 +79,24 @@ def processVersionsFromYAML(yaml_file) {
 //
 // Get workflow version for pipeline
 //
-def workflowVersionToYAML(workflow_version) {
+def workflowVersionToYAML() {
     return """
-    'Workflow':
-      "Nextflow": "$workflow.nextflow.version"
-      "$workflow.manifest.name": "${workflow_version}"
+    Workflow:
+      $workflow.manifest.name: ${getWorkflowVersion()}
+      Nextflow: $workflow.nextflow.version
     """.stripIndent().trim()
 }
 
 //
 // Get channel of software versions used in pipeline in YAML format
 //
-def softwareVersionsToYAML(ch_versions, workflow_version) {
-    
-    return 
-        ch_versions
-            .unique()
-            .map { processVersionsFromYAML(it) }
-            .mix(Channel.of(workflowVersionToYAML(workflow_version)))
-        // .set { ch_software_versions }
-    // return ch_software_versions
+def softwareVersionsToYAML(ch_versions) {
+    return ch_versions
+                .unique()
+                .map { processVersionsFromYAML(it) }
+                .mix(Channel.of(workflowVersionToYAML()))
 }
 
-
 //
 // Get workflow summary for MultiQC
 //
@@ -115,7 +128,7 @@ def paramsSummaryMultiqc(summary_params) {
 //
 // nf-core logo
 //
-def nfCoreLogo(workflow_version, monochrome_logs=true) {
+def nfCoreLogo(monochrome_logs=true) {
     Map colors = logColours(monochrome_logs)
     String.format(
         """\n
@@ -125,7 +138,7 @@ def nfCoreLogo(workflow_version, monochrome_logs=true) {
         ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
         ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
                                                 ${colors.green}`._,._,\'${colors.reset}
-        ${colors.purple}  ${workflow.manifest.name} ${workflow_version}${colors.reset}
+        ${colors.purple}  ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset}
         ${dashedLine(monochrome_logs)}
         """.stripIndent()
     )
@@ -210,7 +223,7 @@ def logColours(monochrome_logs=true) {
 //
 // Construct and send completion email
 //
-def completionEmail(summary_params, workflow_version, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true) {
+def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true) {
 
     // Set up the e-mail variables
     def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
@@ -236,7 +249,7 @@ def completionEmail(summary_params, workflow_version, email, email_on_fail, plai
     misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
 
     def email_fields = [:]
-    email_fields['version']      = workflow_version
+    email_fields['version']      = getWorkflowVersion()
     email_fields['runName']      = workflow.runName
     email_fields['success']      = workflow.success
     email_fields['dateComplete'] = workflow.complete
@@ -317,7 +330,7 @@ def completionSummary(monochrome_logs=true) {
 //
 // Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack
 //
-def imNotification(summary_params, workflow_version, hook_url) {
+def imNotification(summary_params, hook_url) {
     def summary = [:]
     for (group in summary_params.keySet()) {
         summary << summary_params[group]
@@ -336,7 +349,7 @@ def imNotification(summary_params, workflow_version, hook_url) {
     misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
 
     def msg_fields = [:]
-    msg_fields['version']      = workflow_version
+    msg_fields['version']      = getWorkflowVersion()
     msg_fields['runName']      = workflow.runName
     msg_fields['success']      = workflow.success
     msg_fields['dateComplete'] = workflow.complete
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index f1603c37..62d8c577 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -9,9 +9,7 @@ include { SRA_FASTQ_FTP           } from '../../modules/local/sra_fastq_ftp'
 include { SRA_IDS_TO_RUNINFO      } from '../../modules/local/sra_ids_to_runinfo'
 include { SRA_RUNINFO_TO_FTP      } from '../../modules/local/sra_runinfo_to_ftp'
 include { SRA_TO_SAMPLESHEET      } from '../../modules/local/sra_to_samplesheet'
-include { getWorkflowVersion      } from '../../subworkflows/nf-core/utils_nextflow_pipeline'
-include { processVersionsFromYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
-include { workflowVersionToYAML   } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
+include { softwareVersionsToYAML  } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -156,11 +154,9 @@ workflow SRA {
     //
     // Collate and save software versions
     //
-    ch_versions
-        .unique()
-        .map { processVersionsFromYAML(it) }
-        .mix(Channel.of(workflowVersionToYAML(getWorkflowVersion())))
-        .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'collated_software_mqc_versions.yml', newLine: true)
+    softwareVersionsToYAML(ch_versions)
+        .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_fetchngs_software_mqc_versions.yml', sort: true, newLine: true)
+
 
     emit:
     samplesheet     = ch_samplesheet
diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf
index 54670057..38071b60 100644
--- a/workflows/synapse/main.nf
+++ b/workflows/synapse/main.nf
@@ -9,9 +9,7 @@ include { SYNAPSE_SHOW              } from '../../modules/local/synapse_show'
 include { SYNAPSE_GET               } from '../../modules/local/synapse_get'
 include { SYNAPSE_TO_SAMPLESHEET    } from '../../modules/local/synapse_to_samplesheet'
 include { SYNAPSE_MERGE_SAMPLESHEET } from '../../modules/local/synapse_merge_samplesheet'
-include { getWorkflowVersion        } from '../../subworkflows/nf-core/utils_nextflow_pipeline'
-include { processVersionsFromYAML   } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
-include { workflowVersionToYAML     } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
+include { softwareVersionsToYAML    } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -111,11 +109,8 @@ workflow SYNAPSE {
     //
     // Collate and save software versions
     //
-    ch_versions
-        .unique()
-        .map { processVersionsFromYAML(it) }
-        .mix(Channel.of(workflowVersionToYAML(getWorkflowVersion())))
-        .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'collated_software_mqc_versions.yml', newLine: true)
+    softwareVersionsToYAML(ch_versions)
+        .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_fetchngs_software_mqc_versions.yml', sort: true, newLine: true)
 
     emit:
     fastq       = ch_fastq

From 57efad7f77a592c91fde9e785fa2a9e5c11c05f1 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 17 Jan 2024 17:44:03 +0000
Subject: [PATCH 681/852] Remove emit of summary_params from
 utils_nfvalidation_plugin subworkflow

---
 .../nf-core/utils_nfvalidation_plugin/main.nf | 73 +++++++++----------
 .../utils_nfvalidation_plugin/meta.yml        |  8 --
 2 files changed, 35 insertions(+), 46 deletions(-)

diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
index 43c57187..9ec7226f 100644
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
@@ -8,7 +8,9 @@
 ========================================================================================
 */
 
-include { paramsHelp; paramsSummaryLog; paramsSummaryMap; validateParameters } from 'plugin/nf-validation'
+include { paramsHelp         } from 'plugin/nf-validation'
+include { paramsSummaryLog   } from 'plugin/nf-validation'
+include { validateParameters } from 'plugin/nf-validation'
 
 /*
 ========================================================================================
@@ -19,44 +21,39 @@ include { paramsHelp; paramsSummaryLog; paramsSummaryMap; validateParameters } f
 workflow UTILS_NFVALIDATION_PLUGIN {
 
     take:
-        print_help        // bool
-        workflow_command   // string: default commmand used to run pipeline
-        pre_help_text     // string: string to be printed before help text and summary log
-        post_help_text    // string: string to be printed after help text and summary log
-        validate_params   // bool: Validate parameters
-        schema_filename    // path: JSON schema file, null to use default value
+    print_help        // bool
+    workflow_command   // string: default commmand used to run pipeline
+    pre_help_text     // string: string to be printed before help text and summary log
+    post_help_text    // string: string to be printed after help text and summary log
+    validate_params   // bool: Validate parameters
+    schema_filename    // path: JSON schema file, null to use default value
 
     main:
 
-        log.debug "Using schema file: ${schema_filename}"
-
-        // Default values for strings
-        pre_help_text   = pre_help_text    ?: ''
-        post_help_text  = post_help_text   ?: ''
-        workflow_command = workflow_command  ?: ''
-
-        //
-        // Print help message if needed
-        //
-        if (print_help) {
-            log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text
-            System.exit(0)
-        }
-
-        //
-        // Print parameter summary to stdout
-        //
-        log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text
-
-        //
-        // Validate parameters relative to the parameter JSON schema
-        //
-        if (validate_params){
-            validateParameters(parameters_schema: schema_filename)
-        }
-
-        summary_params = paramsSummaryMap(workflow, parameters_schema: schema_filename)
-
-    emit:
-        summary_params = summary_params
+    log.debug "Using schema file: ${schema_filename}"
+
+    // Default values for strings
+    pre_help_text   = pre_help_text    ?: ''
+    post_help_text  = post_help_text   ?: ''
+    workflow_command = workflow_command  ?: ''
+
+    //
+    // Print help message if needed
+    //
+    if (print_help) {
+        log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text
+        System.exit(0)
+    }
+
+    //
+    // Print parameter summary to stdout
+    //
+    log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text
+
+    //
+    // Validate parameters relative to the parameter JSON schema
+    //
+    if (validate_params){
+        validateParameters(parameters_schema: schema_filename)
+    }
 }
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
index 80438ccf..1ec5f98e 100644
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
@@ -32,14 +32,6 @@ input:
       type: string
       description: |
         The filename of the schema to validate against.
-
-output:
-  - summary_params:
-      type: file
-      description: |
-        A Groovy map constructed from parameters.
-        Structure: [ val(meta), path(bam) ]
-      pattern: "*.bam"
 authors:
   - "@adamrtalbot"
 maintainers:

From d2fac84715db4b925e54a6cfdda4360d057459c8 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 17 Jan 2024 18:08:52 +0000
Subject: [PATCH 682/852] Use nf-validation plugin to validate and read in
 samplesheet

---
 assets/schema_input.json                       |  2 +-
 .../utils_nfcore_fetchngs_pipeline/main.nf     | 18 ++++++++++--------
 2 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index d451f9e9..13044b1b 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -7,7 +7,7 @@
     "items": {
         "type": "object",
         "properties": {
-            "id": {
+            "": {
                 "type": "string",
                 "pattern": "^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM])|(syn))(\\d+)$",
                 "errorMessage": "Please provide a valid SRA, ENA, DDBJ or GEO identifier"
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
index 1681c0e4..2ed66470 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
@@ -9,6 +9,7 @@
 */
 
 include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
+include { fromSamplesheet           } from 'plugin/nf-validation'
 include { paramsSummaryMap          } from 'plugin/nf-validation'
 include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
@@ -59,6 +60,15 @@ workflow PIPELINE_INITIALISATION {
     //
     UTILS_NFCORE_PIPELINE ()
 
+    //
+    // Read in ids from --input file via nf-validation plugin
+    //
+    Channel
+        .fromSamplesheet("input", skip_duplicate_check: true)
+        .map { it[0] }
+        .unique()
+        .set { ch_ids }
+    
     //
     // Auto-detect input id type
     //
@@ -77,14 +87,6 @@ workflow PIPELINE_INITIALISATION {
         error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!")
     }
 
-    // Read in ids from --input file
-    Channel
-        .from(ch_input)
-        .splitCsv(header:false, sep:'', strip:true)
-        .map { it[0] }
-        .unique()
-        .set { ch_ids }
-
     emit:
     ids = ch_ids
 }

From a3c627c2bfb18973de260f8837dde515c17c0c29 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 17 Jan 2024 18:12:42 +0000
Subject: [PATCH 683/852] Revert nf-validation plugin to validate and read in
 samplesheet

---
 .../utils_nfcore_fetchngs_pipeline/main.nf      | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
index 2ed66470..6cd1c6c6 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
@@ -60,15 +60,6 @@ workflow PIPELINE_INITIALISATION {
     //
     UTILS_NFCORE_PIPELINE ()
 
-    //
-    // Read in ids from --input file via nf-validation plugin
-    //
-    Channel
-        .fromSamplesheet("input", skip_duplicate_check: true)
-        .map { it[0] }
-        .unique()
-        .set { ch_ids }
-    
     //
     // Auto-detect input id type
     //
@@ -87,6 +78,14 @@ workflow PIPELINE_INITIALISATION {
         error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!")
     }
 
+    // Read in ids from --input file
+    Channel
+        .from(ch_input)
+        .splitCsv(header:false, sep:'', strip:true)
+        .map { it[0] }
+        .unique()
+        .set { ch_ids }
+
     emit:
     ids = ch_ids
 }

From 73a831bd162f8fd200399f228c235c168b42febc Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 17 Jan 2024 18:39:10 +0000
Subject: [PATCH 684/852] Sync email function with nf-core pipeline template

---
 assets/email_template.html                      |  2 +-
 assets/email_template.txt                       |  2 +-
 .../nf-core/utils_nfcore_pipeline/main.nf       | 17 +++++++++++------
 3 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/assets/email_template.html b/assets/email_template.html
index 1848021d..6e593a53 100644
--- a/assets/email_template.html
+++ b/assets/email_template.html
@@ -12,7 +12,7 @@
 
 <img src="cid:nfcorepipelinelogo">
 
-<h1>nf-core/fetchngs v${version}</h1>
+<h1>nf-core/fetchngs ${version}</h1>
 <h2>Run Name: $runName</h2>
 
 <% if (!success){
diff --git a/assets/email_template.txt b/assets/email_template.txt
index f9393aa8..e9f8bcc6 100644
--- a/assets/email_template.txt
+++ b/assets/email_template.txt
@@ -4,7 +4,7 @@
   |\\ | |__  __ /  ` /  \\ |__) |__         }  {
   | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,
                                         `._,._,'
-  nf-core/fetchngs v${version}
+  nf-core/fetchngs ${version}
 ----------------------------------------------------
 Run Name: $runName
 
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index fd4eddfd..7735ec89 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -3,6 +3,7 @@
 //
 
 import org.yaml.snakeyaml.Yaml
+import nextflow.extension.FilesEx
 
 /*
 ========================================================================================
@@ -290,6 +291,8 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
         try {
             if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
             // Try to send HTML e-mail using sendmail
+            def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
+            sendmail_tf.withWriter { w -> w << sendmail_html }
             [ 'sendmail', '-t' ].execute() << sendmail_html
             log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
         } catch (all) {
@@ -301,14 +304,16 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     }
 
     // Write summary e-mail HTML to a file
-    def output_d = new File("${outdir}/pipeline_info/")
-    if (!output_d.exists()) {
-        output_d.mkdirs()
-    }
-    def output_hf = new File(output_d, "pipeline_report.html")
+    def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
     output_hf.withWriter { w -> w << email_html }
-    def output_tf = new File(output_d, "pipeline_report.txt")
+    FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
+    output_hf.delete()
+
+    // Write summary e-mail TXT to a file
+    def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
     output_tf.withWriter { w -> w << email_txt }
+    FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
+    output_tf.delete()
 }
 
 //

From 65efde1801c168cd7125e405f9490bfad6ac3c10 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 17 Jan 2024 20:22:39 +0000
Subject: [PATCH 685/852] Sync dumpParametersToJSON function with nf-core
 pipeline template

---
 .../nf-core/utils_nextflow_pipeline/main.nf      | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index 9dbb86c7..005a0340 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -4,6 +4,7 @@
 
 import org.yaml.snakeyaml.Yaml
 import groovy.json.JsonOutput
+import nextflow.extension.FilesEx
 
 /*
 ========================================================================================
@@ -74,16 +75,15 @@ def getWorkflowVersion() {
 //
 // Dump pipeline parameters to a JSON file
 //
-def dumpParametersToJSON(output_directory) {
-    def output_d = new File("${output_directory}/pipeline_info/")
-    if (!output_d.exists()) {
-        output_d.mkdirs()
-    }
-
+def dumpParametersToJSON(outdir) {
     def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
-    def output_pf  = new File(output_d, "params_${timestamp}.json")
+    def filename   = "params_${timestamp}.json"
+    def temp_pf    = new File(workflow.launchDir.toString(), ".${filename}")
     def jsonStr    = JsonOutput.toJson(params)
-    output_pf.text = JsonOutput.prettyPrint(jsonStr)
+    temp_pf.text   = JsonOutput.prettyPrint(jsonStr)
+
+    FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
+    temp_pf.delete()
 }
 
 //

From f7be8ce2516eff68be5c2d26893a53797abad933 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 17 Jan 2024 20:35:23 +0000
Subject: [PATCH 686/852] Fix tests for utils_nfcore_pipeline subworkflow

---
 .../tests/main.function.nf.test               | 19 +------------------
 .../tests/main.function.nf.test.snap          | 14 +++++++-------
 2 files changed, 8 insertions(+), 25 deletions(-)

diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
index c4f71aeb..f57980c7 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
@@ -13,14 +13,6 @@ nextflow_function {
 
         function "checkConfigProvided"
 
-        when {
-            function {
-                """
-                // input[0] = 1
-                """
-            }
-        }
-
         then {
             assertAll (
                 { assert function.success                  },
@@ -34,14 +26,6 @@ nextflow_function {
 
         function "workflowCitation"
 
-        when {
-            function {
-                """
-                // input[0] = 1
-                """
-            }
-        }
-
         then {
             assertAll (
                 { assert function.success                  },
@@ -58,8 +42,7 @@ nextflow_function {
         when {
             function {
                 """
-                input[0] = "9.9.9"
-                input[1] = false
+                input[0] = false
                 """
             }
         }
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
index bdf71d41..e95e2eec 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
@@ -1,19 +1,19 @@
 {
     "Test Function checkConfigProvided": {
         "content": null,
-        "timestamp": "2023-10-16T14:27:01.415849"
+        "timestamp": "2024-01-17T20:34:16.220739"
     },
     "Test Function nfCoreLogo": {
         "content": [
-            "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n                                        \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m        ___     __   __   __   ___     \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \u001b[0;33m}  {\u001b[0m\n\u001b[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \u001b[0;32m\\`-._,-`-,\u001b[0m\n                                        \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m  nextflow_workflow 9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n"
+            "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n                                        \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m        ___     __   __   __   ___     \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \u001b[0;33m}  {\u001b[0m\n\u001b[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \u001b[0;32m\\`-._,-`-,\u001b[0m\n                                        \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m  nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n"
         ],
-        "timestamp": "2023-10-16T14:27:51.566211"
+        "timestamp": "2024-01-17T20:34:23.89764"
     },
     "Test Function workflowCitation": {
         "content": [
             "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n  https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n  https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n  https://github.com/nextflow_workflow/blob/master/CITATIONS.md"
         ],
-        "timestamp": "2023-10-16T14:27:03.505737"
+        "timestamp": "2024-01-17T20:34:20.063846"
     },
     "Test Function without logColours": {
         "content": [
@@ -67,13 +67,13 @@
                 "biwhite": ""
             }
         ],
-        "timestamp": "2023-12-20T10:04:29.095368"
+        "timestamp": "2024-01-17T20:34:31.622874"
     },
     "Test Function dashedLine": {
         "content": [
             "-\u001b[2m----------------------------------------------------\u001b[0m-"
         ],
-        "timestamp": "2023-10-16T14:27:07.721916"
+        "timestamp": "2024-01-17T20:34:27.729247"
     },
     "Test Function with logColours": {
         "content": [
@@ -127,6 +127,6 @@
                 "biwhite": "\u001b[1;97m"
             }
         ],
-        "timestamp": "2023-12-20T10:04:31.258856"
+        "timestamp": "2024-01-17T20:34:35.549447"
     }
 }
\ No newline at end of file

From d58cef7c4ac9f85e4b0547997a2c86c4a52f4aee Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 17 Jan 2024 20:38:46 +0000
Subject: [PATCH 687/852] Fix tests for pipeline

---
 tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/main.nf.test b/tests/main.nf.test
index 1ab2f73a..3c36cd06 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -72,7 +72,7 @@ nextflow_pipeline {
                 { assert new File("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv").exists() },
                 { assert new File("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv").exists() },
                 { assert new File("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv").exists() },
-                { assert new File("$outputDir/pipeline_info/fetchngs_mqc_versions.yml").exists() },
+                { assert new File("$outputDir/pipeline_info/nf_core_fetchngs_software_mqc_versions.yml").exists() },
                 { assert new File("$outputDir/samplesheet/id_mappings.csv").exists() },
                 { assert new File("$outputDir/samplesheet/multiqc_config.yml").exists() },
                 { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }

From 90973f4518c9c966b77de8a721d613d97a9ae132 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 17 Jan 2024 20:48:47 +0000
Subject: [PATCH 688/852] Fix tests for utils_nextflow_pipeline subworkflow

---
 .../tests/main.functions.nf.test               | 18 ------------------
 1 file changed, 18 deletions(-)

diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test
index 05f54930..9b18004b 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test
@@ -12,14 +12,6 @@ nextflow_function {
 
         function "getWorkflowVersion"
 
-        when {
-            function {
-                """
-                // no inputs
-                """
-            }
-        }
-
         then {
             assert function.success
             assert snapshot(function.result).match()
@@ -43,8 +35,6 @@ nextflow_function {
 
         then {
             assert function.success
-            assert function.result =~ /publish_dir_mode/
-            assert function.result =~ /copy/
         }
 
     }
@@ -53,14 +43,6 @@ nextflow_function {
 
         function "checkCondaChannels"
 
-        when {
-            function {
-                """
-                // no inputs
-                """
-            }
-        }
-
         then {
             assert function.success
             assert snapshot(function.result).match()

From 6bae5519a39243138e16b8c05cca52a7bce17dfd Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 17 Jan 2024 20:50:19 +0000
Subject: [PATCH 689/852] Fix nf-core lint

---
 .nf-core.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index 51a92309..512c2bb7 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -9,4 +9,6 @@ lint:
     - lib/nfcore_external_java_deps.jar
   files_unchanged:
     - .gitignore
-    - assets/sendmail_template.txt
+    - assets/email_template.html
+    - assets/email_template.txt
+    - assets/sendmail_template.txt
\ No newline at end of file

From b74cbbb44bf8a94d929b80d71f1b258a17f6a6b9 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 17 Jan 2024 20:52:20 +0000
Subject: [PATCH 690/852] Fix Prettier

---
 .nf-core.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index 512c2bb7..793cb80d 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -11,4 +11,4 @@ lint:
     - .gitignore
     - assets/email_template.html
     - assets/email_template.txt
-    - assets/sendmail_template.txt
\ No newline at end of file
+    - assets/sendmail_template.txt

From e3d81da26f75022503bf2f8e469b636ad40a75b7 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 18 Jan 2024 09:44:16 +0000
Subject: [PATCH 691/852] Move params to take block in
 utils_nfcore_fetchngs_pipeline subworkflow

---
 main.nf                                       | 11 ++++-
 .../utils_nfcore_fetchngs_pipeline/main.nf    | 44 ++++++++++++-------
 .../nf-core/utils_nextflow_pipeline/main.nf   |  9 ++--
 .../tests/main.workflow.nf.test               |  3 --
 .../tests/main.workflow.nf.test.snap          | 44 -------------------
 5 files changed, 40 insertions(+), 71 deletions(-)
 delete mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test.snap

diff --git a/main.nf b/main.nf
index 64bc75cf..d3779d16 100644
--- a/main.nf
+++ b/main.nf
@@ -62,7 +62,16 @@ workflow {
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
-    PIPELINE_INITIALISATION ()
+    PIPELINE_INITIALISATION (
+        params.version,
+        params.help,
+        params.validate_params,
+        params.monochrome_logs,
+        params.outdir,
+        params.input,
+        params.input_type,
+        params.ena_metadata_fields
+    )
 
     //
     // WORKFLOW: Run primary workflows for the pipeline
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
index 6cd1c6c6..21249dd7 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
@@ -28,30 +28,40 @@ include { workflowCitation          } from '../../nf-core/utils_nfcore_pipeline'
 
 workflow PIPELINE_INITIALISATION {
 
+    take:
+    version             // boolean: Display version and exit
+    help                // boolean: Display help text
+    validate_params     // boolean: Boolean whether to validate parameters against the schema at runtime 
+    monochrome_logs     // boolean: Do not use coloured log outputs
+    outdir              //  string: The output directory where the results will be saved
+    input               //  string: File containing SRA/ENA/GEO/DDBJ identifiers one per line to download their associated metadata and FastQ files
+    input_type          //  string: Specifies the type of identifier provided via `--input` - available options are 'sra' and 'synapse'
+    ena_metadata_fields //  string: Comma-separated list of ENA metadata fields to fetch before downloading data
+
     main:
 
     //
     // Print version and exit if required and dump pipeline parameters to JSON file
     //
     UTILS_NEXTFLOW_PIPELINE (
-        params.version,
+        version,
         true,
-        params.outdir,
+        outdir,
         workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
     )
 
     //
     // Validate parameters and generate parameter summary to stdout
     //
-    def pre_help_text = nfCoreLogo(params.monochrome_logs)
-    def post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(params.monochrome_logs)
+    def pre_help_text = nfCoreLogo(monochrome_logs)
+    def post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs)
     def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input ids.csv --outdir <OUTDIR>"
     UTILS_NFVALIDATION_PLUGIN (
-        params.help,
+        help,
         workflow_command,
         pre_help_text,
         post_help_text,
-        params.validate_params,
+        validate_params,
         "nextflow_schema.json"
     )
 
@@ -63,19 +73,19 @@ workflow PIPELINE_INITIALISATION {
     //
     // Auto-detect input id type
     //
-    ch_input = file(params.input)
-    def input_type = ''
+    ch_input = file(input)
+    def inferred_input_type = ''
     if (isSraId(ch_input)) {
-        input_type = 'sra'
-        sraCheckENAMetadataFields()
+        inferred_input_type = 'sra'
+        sraCheckENAMetadataFields(ena_metadata_fields)
     } else if (isSynapseId(ch_input)) {
-        input_type = 'synapse'
+        inferred_input_type = 'synapse'
     } else {
         error('Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!')
     }
 
-    if (params.input_type != input_type) {
-        error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!")
+    if (input_type != inferred_input_type) {
+        error("Ids auto-detected as ${inferred_input_type}. Please provide '--input_type ${inferred_input_type}' as a parameter to the pipeline!")
     }
 
     // Read in ids from --input file
@@ -194,12 +204,12 @@ def isSynapseId(input) {
 //
 // Check and validate parameters
 //
-def sraCheckENAMetadataFields() {
+def sraCheckENAMetadataFields(ena_metadata_fields) {
     // Check minimal ENA fields are provided to download FastQ files
     def valid_ena_metadata_fields = ['run_accession', 'experiment_accession', 'library_layout', 'fastq_ftp', 'fastq_md5']
-    def ena_metadata_fields = params.ena_metadata_fields ? params.ena_metadata_fields.split(',').collect{ it.trim().toLowerCase() } : valid_ena_metadata_fields
-    if (!ena_metadata_fields.containsAll(valid_ena_metadata_fields)) {
-        error("Invalid option: '${params.ena_metadata_fields}'. Minimally required fields for '--ena_metadata_fields': '${valid_ena_metadata_fields.join(',')}'")
+    def actual_ena_metadata_fields = ena_metadata_fields ? ena_metadata_fields.split(',').collect{ it.trim().toLowerCase() } : valid_ena_metadata_fields
+    if (!actual_ena_metadata_fields.containsAll(valid_ena_metadata_fields)) {
+        error("Invalid option: '${ena_metadata_fields}'. Minimally required fields for '--ena_metadata_fields': '${valid_ena_metadata_fields.join(',')}'")
     }
 }
 
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index 005a0340..e89a57ab 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -17,7 +17,7 @@ workflow UTILS_NEXTFLOW_PIPELINE {
     take:
     print_version        // bool
     dump_parameters      // bool
-    output_directory     // path: base directory used to publish pipeline results
+    outdir               // path: base directory used to publish pipeline results
     check_conda_channels // bool
 
     main:
@@ -33,8 +33,8 @@ workflow UTILS_NEXTFLOW_PIPELINE {
     //
     // Dump pipeline parameters to a JSON file
     //
-    if (dump_parameters && output_directory) {
-        dumpParametersToJSON(output_directory)
+    if (dump_parameters && outdir) {
+        dumpParametersToJSON(outdir)
     }
 
     //
@@ -43,9 +43,6 @@ workflow UTILS_NEXTFLOW_PIPELINE {
     if (check_conda_channels) {
         checkCondaChannels()
     }
-
-    emit:
-        out = true
 }
 
 /*
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
index 583f6a84..e2fa5b6c 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -26,7 +26,6 @@ nextflow_workflow {
 
         then {
             assert workflow.success
-            assert snapshot(workflow.out).match()
         }
 
     }
@@ -73,7 +72,6 @@ nextflow_workflow {
 
         then {
             assert workflow.success
-            assert snapshot(workflow.out).match()
         }
 
     }
@@ -96,7 +94,6 @@ nextflow_workflow {
 
         then {
             assert workflow.success
-            assert snapshot(workflow.out, path(params.outdir).list()).match()
         }
 
     }
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test.snap
deleted file mode 100644
index 08040fd4..00000000
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test.snap
+++ /dev/null
@@ -1,44 +0,0 @@
-{
-    "Should not create params JSON if no output directory": {
-        "content": [
-            {
-                "0": [
-                    true
-                ],
-                "out": [
-                    true
-                ]
-            },
-            [
-                
-            ]
-        ],
-        "timestamp": "2023-10-13T11:55:54.576748"
-    },
-    "Should dump params": {
-        "content": [
-            {
-                "0": [
-                    true
-                ],
-                "out": [
-                    true
-                ]
-            }
-        ],
-        "timestamp": "2023-10-13T11:55:52.711329"
-    },
-    "Should run no inputs": {
-        "content": [
-            {
-                "0": [
-                    true
-                ],
-                "out": [
-                    true
-                ]
-            }
-        ],
-        "timestamp": "2023-10-13T11:55:49.048315"
-    }
-}
\ No newline at end of file

From 61e7662019c4076b4c760e1eaa91243273a46277 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 18 Jan 2024 12:27:29 +0000
Subject: [PATCH 692/852] Replace tag strategy for testing

Changes:
 - All modules, subworkflows and workflows include their own name as a tag
 - All subworkflows and workflows include their dependencies as a tag
 - By detecting tags with `nf-test list --tags` we can extract all tags
 - Should be able to flag changed modules and dependent workflows without using a tags.yml file
---
 .../multiqc_mappings_config/tests/main.nf.test     |  5 ++---
 modules/local/sra_fastq_ftp/tests/main.nf.test     |  5 ++---
 .../local/sra_ids_to_runinfo/tests/main.nf.test    |  5 ++---
 .../local/sra_runinfo_to_ftp/tests/main.nf.test    |  5 ++---
 .../local/sra_to_samplesheet/tests/main.nf.test    |  5 ++---
 .../custom/sratoolsncbisettings/tests/main.nf.test |  6 ++----
 .../sratools/fasterqdump/tests/main.nf.test        |  8 +++-----
 .../nf-core/sratools/prefetch/tests/main.nf.test   |  6 ++----
 modules/nf-core/untar/tests/main.nf.test           |  4 +---
 .../tests/main.nf.test                             | 11 +++++------
 .../tests/main.functions.nf.test                   |  5 ++---
 .../tests/main.function.nf.test                    |  6 ++----
 .../tests/main.workflow.nf.test                    |  6 ++----
 .../utils_nfvalidation_plugin/tests/main.nf.test   |  8 ++------
 tests/main.nf.test                                 |  6 ++++--
 workflows/sra/tests/main.nf.test                   | 14 ++++++++++----
 .../tests/sra_custom_ena_metadata_fields.nf.test   | 14 ++++++++++----
 .../sra/tests/sra_force_sratools_download.nf.test  | 14 ++++++++++----
 .../sra/tests/sra_nf_core_pipeline_atacseq.nf.test | 14 ++++++++++----
 .../sra/tests/sra_nf_core_pipeline_rnaseq.nf.test  | 14 ++++++++++----
 .../tests/sra_nf_core_pipeline_taxprofiler.nf.test | 14 ++++++++++----
 .../tests/sra_nf_core_pipeline_viralrecon.nf.test  | 14 ++++++++++----
 .../sra/tests/sra_skip_fastq_download.nf.test      | 14 ++++++++++----
 23 files changed, 115 insertions(+), 88 deletions(-)

diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test
index cfb43166..e782116e 100644
--- a/modules/local/multiqc_mappings_config/tests/main.nf.test
+++ b/modules/local/multiqc_mappings_config/tests/main.nf.test
@@ -3,9 +3,8 @@ nextflow_process {
     name "Test process: MULTIQC_MAPPINGS_CONFIG"
     script "../main.nf"
     process "MULTIQC_MAPPINGS_CONFIG"
-    tag "modules"
-    tag "modules_local"
-    tag "multiqc_mappings_config"
+
+    tag "MULTIQC_MAPPINGS_CONFIG"
 
     test("Should run without failures") {
 
diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test
index 33f4be9f..27329cd9 100644
--- a/modules/local/sra_fastq_ftp/tests/main.nf.test
+++ b/modules/local/sra_fastq_ftp/tests/main.nf.test
@@ -3,9 +3,8 @@ nextflow_process {
     name "Test process: SRA_FASTQ_FTP"
     script "../main.nf"
     process "SRA_FASTQ_FTP"
-    tag "modules"
-    tag "modules_local"
-    tag "sra_fastq_ftp"
+
+    tag "SRA_FASTQ_FTP"
 
     test("Should run without failures") {
 
diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test
index 087f9069..cc0d6de9 100644
--- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test
+++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test
@@ -3,9 +3,8 @@ nextflow_process {
     name "Test process: SRA_IDS_TO_RUNINFO"
     script "../main.nf"
     process "SRA_IDS_TO_RUNINFO"
-    tag "modules"
-    tag "modules_local"
-    tag "sra_ids_to_runinfo"
+
+    tag "SRA_IDS_TO_RUNINFO"
 
     test("Should run without failures") {
 
diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
index 347e3392..1060b394 100644
--- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
+++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
@@ -3,9 +3,8 @@ nextflow_process {
     name "Test process: SRA_RUNINFO_TO_FTP"
     script "../main.nf"
     process "SRA_RUNINFO_TO_FTP"
-    tag "modules"
-    tag "modules_local"
-    tag "sra_runinfo_to_ftp"
+
+    tag "SRA_RUNINFO_TO_FTP"
 
     test("Should run without failures") {
 
diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test
index 6094717b..7b7a52a8 100644
--- a/modules/local/sra_to_samplesheet/tests/main.nf.test
+++ b/modules/local/sra_to_samplesheet/tests/main.nf.test
@@ -3,9 +3,8 @@ nextflow_process {
     name "Test process: SRA_TO_SAMPLESHEET"
     script "../main.nf"
     process "SRA_TO_SAMPLESHEET"
-    tag "modules"
-    tag "modules_local"
-    tag "sra_to_samplesheet"
+    
+    tag "SRA_TO_SAMPLESHEET"
 
     test("Should run without failures") {
 
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
index 9f178678..6fde77c6 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
+++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
@@ -4,10 +4,8 @@ nextflow_process {
     script "../main.nf"
     process "CUSTOM_SRATOOLSNCBISETTINGS"
     config "modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config"
-    tag "modules"
-    tag "modules_nfcore"
-    tag "custom"
-    tag "custom/sratoolsncbisettings"
+
+    tag "CUSTOM_SRATOOLSNCBISETTINGS"
 
     test("Should run without failures") {
 
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
index 48722e4e..15277dbc 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
@@ -3,11 +3,9 @@ nextflow_process {
     script "../main.nf"
     config "./nextflow.config"
     process "SRATOOLS_FASTERQDUMP"
-    tag "modules"
-    tag "modules_nfcore"
-    tag "untar"
-    tag "sratools"
-    tag "sratools/fasterqdump"
+
+    tag "UNTAR"
+    tag "SRATOOLS_FASTERQDUMP"
 
     test("Single-end") {
 
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test
index ed710ba0..0c210f9a 100644
--- a/modules/nf-core/sratools/prefetch/tests/main.nf.test
+++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test
@@ -2,10 +2,8 @@ nextflow_process {
     name "Test Process SRATOOLS_PREFETCH"
     script "../main.nf"
     process "SRATOOLS_PREFETCH"
-    tag "modules"
-    tag "modules_nfcore"
-    tag "sratools"
-    tag "sratools/prefetch"
+
+    tag "SRATOOLS_PREFETCH"
 
     test("sratools/prefetch") {
 
diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test
index 679e83c7..e85ec082 100644
--- a/modules/nf-core/untar/tests/main.nf.test
+++ b/modules/nf-core/untar/tests/main.nf.test
@@ -4,9 +4,7 @@ nextflow_process {
     script "../main.nf"
     process "UNTAR"
 
-    tag "modules"
-    tag "modules_nfcore"
-    tag "untar"
+    tag "UNTAR"
 
     test("test_untar") {
 
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
index 2a16d1ef..b3d65c79 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
@@ -3,12 +3,11 @@ nextflow_workflow {
     name "Test workflow: fastq_download_prefetch_fasterqdump_sratools/main.nf"
     script "../main.nf"
     workflow "FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS"
-    tag "subworkflows"
-    tag "subworkflows_nfcore"
-    tag "custom/sratoolsncbisettings"
-    tag "sratools/prefetch"
-    tag "sratools/fasterqdump"
-    tag "subworkflows/fastq_download_prefetch_fasterqdump_sratools"
+    
+    tag "CUSTOM_SRATOOLSNCBISETTINGS"
+    tag "SRATOOLS_PREFETCH"
+    tag "SRATOOLS_FASTERQDUMP"
+    tag "SUBWORKFLOWS_FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS"
 
     test("Parameters: default") {
 
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test
index 9b18004b..50c90208 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test
@@ -4,9 +4,8 @@ nextflow_function {
     name "Test Functions"
     script "subworkflows/nf-core/utils_nextflow_pipeline/main.nf"
     config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config"
-    tag 'subworkflows'
-    tag 'utils_nextflow_pipeline'
-    tag 'subworkflows/utils_nextflow_pipeline'
+
+    tag 'UTILS_NEXTFLOW_PIPELINE'
 
     test("Test Function getWorkflowVersion") {
 
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
index f57980c7..6176bb55 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
@@ -4,10 +4,8 @@ nextflow_function {
     name "Test Functions"
     script "../main.nf"
     config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
-    tag "subworkflows"
-    tag "subworkflows_nfcore"
-    tag "utils_nfcore_pipeline"
-    tag "subworkflows/utils_nfcore_pipeline"
+
+    tag "UTILS_NFCORE_PIPELINE"
 
     test("Test Function checkConfigProvided") {
 
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
index b16445da..de513d78 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
@@ -4,10 +4,8 @@ nextflow_workflow {
     script "../main.nf"
     config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
     workflow "UTILS_NFCORE_PIPELINE"
-    tag "subworkflows"
-    tag "subworkflows_nfcore"
-    tag "utils_nfcore_pipeline"
-    tag "subworkflows/utils_nfcore_pipeline"
+    
+    tag "UTILS_NFCORE_PIPELINE"
 
     test("Should run without failures") {
         then {
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
index 904f97be..47bfe461 100644
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
@@ -3,12 +3,8 @@ nextflow_workflow {
     name "Test Workflow UTILS_NFVALIDATION_PLUGIN"
     script "../main.nf"
     workflow "UTILS_NFVALIDATION_PLUGIN"
-    tag "subworkflows"
-    tag "subworkflows_nfcore"
-    tag "plugin/nf-validation"
-    tag "'plugin/nf-validation'"
-    tag "utils_nfvalidation_plugin"
-    tag "subworkflows/utils_nfvalidation_plugin"
+
+    tag "UTILS_NFVALIDATION_PLUGIN"
 
     test("Should run nothing") {
 
diff --git a/tests/main.nf.test b/tests/main.nf.test
index 3c36cd06..4e664778 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -2,8 +2,10 @@ nextflow_pipeline {
 
     name "Test pipeline"
     script "../main.nf"
-    tag "pipeline"
-    tag "pipeline_fetchngs"
+
+    tag "SRA"
+    
+    tag "FETCHNGS"
 
     test("Run with profile test") {
 
diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 902debe6..1d63d8d8 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -3,10 +3,16 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
-    tag "workflows"
-    tag "workflows_sra"
-    tag "multiqc_mappings_config"
-    tag "sra_default_parameters"
+
+    // Modules
+    tag "MULTIQC_MAPPINGS_CONFIG"
+    tag "SRA_FASTQ_FTP"
+    tag "SRA_IDS_TO_RUNINFO"
+    tag "SRA_RUNINFO_TO_FTP"
+    tag "SRA_TO_SAMPLESHEET"
+
+    // Subworkflows
+    tag "SRA"
 
     test("Parameters: default") {
 
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index 433288f9..b0f9e4f4 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -3,10 +3,16 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
-    tag "workflows"
-    tag "workflows_sra"
-    tag "multiqc_mappings_config"
-    tag "sra_custom_ena_metadata_fields"
+
+    // Modules
+    tag "MULTIQC_MAPPINGS_CONFIG"
+    tag "SRA_FASTQ_FTP"
+    tag "SRA_IDS_TO_RUNINFO"
+    tag "SRA_RUNINFO_TO_FTP"
+    tag "SRA_TO_SAMPLESHEET"
+
+    // Subworkflows
+    tag "SRA"
 
     test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") {
 
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index 2019be08..78658b7c 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -3,10 +3,16 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
-    tag "workflows"
-    tag "workflows_sra"
-    tag "multiqc_mappings_config"
-    tag "sra_force_sratools_download"
+
+    // Modules
+    tag "MULTIQC_MAPPINGS_CONFIG"
+    tag "SRA_FASTQ_FTP"
+    tag "SRA_IDS_TO_RUNINFO"
+    tag "SRA_RUNINFO_TO_FTP"
+    tag "SRA_TO_SAMPLESHEET"
+
+    // Subworkflows
+    tag "SRA"
 
     test("Parameters: --force_sratools_download") {
 
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index 46e4eed8..816235ef 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -3,10 +3,16 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
-    tag "workflows"
-    tag "workflows_sra"
-    tag "multiqc_mappings_config"
-    tag "sra_nf_core_pipeline_atacseq"
+    
+    // Modules
+    tag "MULTIQC_MAPPINGS_CONFIG"
+    tag "SRA_FASTQ_FTP"
+    tag "SRA_IDS_TO_RUNINFO"
+    tag "SRA_RUNINFO_TO_FTP"
+    tag "SRA_TO_SAMPLESHEET"
+
+    // Subworkflows
+    tag "SRA"
 
     test("Parameters: --nf_core_pipeline atacseq") {
 
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index f24d2648..dd3b55d0 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -3,10 +3,16 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
-    tag "workflows"
-    tag "workflows_sra"
-    tag "multiqc_mappings_config"
-    tag "sra_nf_core_pipeline_rnaseq"
+
+    // Modules
+    tag "MULTIQC_MAPPINGS_CONFIG"
+    tag "SRA_FASTQ_FTP"
+    tag "SRA_IDS_TO_RUNINFO"
+    tag "SRA_RUNINFO_TO_FTP"
+    tag "SRA_TO_SAMPLESHEET"
+
+    // Subworkflows
+    tag "SRA"
 
     test("Parameters: --nf_core_pipeline rnaseq") {
 
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index 447e8c6e..fe907dc6 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -3,10 +3,16 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
-    tag "workflows"
-    tag "workflows_sra"
-    tag "multiqc_mappings_config"
-    tag "sra_nf_core_pipeline_taxprofiler"
+
+    // Modules
+    tag "MULTIQC_MAPPINGS_CONFIG"
+    tag "SRA_FASTQ_FTP"
+    tag "SRA_IDS_TO_RUNINFO"
+    tag "SRA_RUNINFO_TO_FTP"
+    tag "SRA_TO_SAMPLESHEET"
+
+    // Subworkflows
+    tag "SRA"
 
     test("Parameters: --nf_core_pipeline taxprofiler") {
 
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index 9b27c0a5..938edc00 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -3,10 +3,16 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
-    tag "workflows"
-    tag "workflows_sra"
-    tag "multiqc_mappings_config"
-    tag "sra_nf_core_pipeline_viralrecon"
+
+    // Modules
+    tag "MULTIQC_MAPPINGS_CONFIG"
+    tag "SRA_FASTQ_FTP"
+    tag "SRA_IDS_TO_RUNINFO"
+    tag "SRA_RUNINFO_TO_FTP"
+    tag "SRA_TO_SAMPLESHEET"
+
+    // Subworkflows
+    tag "SRA"
 
     test("Parameters: --nf_core_pipeline viralrecon") {
 
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index 1a3ab733..63ec1be0 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -3,10 +3,16 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
-    tag "workflows"
-    tag "workflows_sra"
-    tag "multiqc_mappings_config"
-    tag "sra_skip_fastq_download"
+
+    // Modules
+    tag "MULTIQC_MAPPINGS_CONFIG"
+    tag "SRA_FASTQ_FTP"
+    tag "SRA_IDS_TO_RUNINFO"
+    tag "SRA_RUNINFO_TO_FTP"
+    tag "SRA_TO_SAMPLESHEET"
+
+    // Subworkflows
+    tag "SRA"
 
     test("Parameters: --skip_fastq_download") {
 

From 34baed6a6443f00c17981bcc872d767a4080c581 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 18 Jan 2024 12:31:10 +0000
Subject: [PATCH 693/852] Remove all tags.yml files

---
 .../local/multiqc_mappings_config/tests/tags.yml |  2 --
 modules/local/sra_fastq_ftp/tests/tags.yml       |  2 --
 modules/local/sra_ids_to_runinfo/tests/tags.yml  |  2 --
 modules/local/sra_runinfo_to_ftp/tests/tags.yml  |  2 --
 modules/local/sra_to_samplesheet/tests/tags.yml  |  2 --
 .../custom/sratoolsncbisettings/tests/tags.yml   |  2 --
 .../nf-core/sratools/fasterqdump/tests/tags.yml  |  2 --
 modules/nf-core/sratools/prefetch/tests/tags.yml |  2 --
 modules/nf-core/untar/tests/tags.yml             |  2 --
 .../tests/tags.yml                               |  2 --
 .../utils_nextflow_pipeline/tests/tags.yml       |  2 --
 .../nf-core/utils_nfcore_pipeline/tests/tags.yml |  2 --
 .../utils_nfvalidation_plugin/tests/tags.yml     |  2 --
 tests/tags.yml                                   |  5 -----
 workflows/sra/tests/tags.yml                     | 16 ----------------
 15 files changed, 47 deletions(-)
 delete mode 100644 modules/local/multiqc_mappings_config/tests/tags.yml
 delete mode 100644 modules/local/sra_fastq_ftp/tests/tags.yml
 delete mode 100644 modules/local/sra_ids_to_runinfo/tests/tags.yml
 delete mode 100644 modules/local/sra_runinfo_to_ftp/tests/tags.yml
 delete mode 100644 modules/local/sra_to_samplesheet/tests/tags.yml
 delete mode 100644 modules/nf-core/custom/sratoolsncbisettings/tests/tags.yml
 delete mode 100644 modules/nf-core/sratools/fasterqdump/tests/tags.yml
 delete mode 100644 modules/nf-core/sratools/prefetch/tests/tags.yml
 delete mode 100644 modules/nf-core/untar/tests/tags.yml
 delete mode 100644 subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml
 delete mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
 delete mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
 delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
 delete mode 100644 tests/tags.yml
 delete mode 100644 workflows/sra/tests/tags.yml

diff --git a/modules/local/multiqc_mappings_config/tests/tags.yml b/modules/local/multiqc_mappings_config/tests/tags.yml
deleted file mode 100644
index 595e2e31..00000000
--- a/modules/local/multiqc_mappings_config/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-multiqc_mappings_config:
-  - modules/local/multiqc_mappings_config/**
diff --git a/modules/local/sra_fastq_ftp/tests/tags.yml b/modules/local/sra_fastq_ftp/tests/tags.yml
deleted file mode 100644
index e7474bef..00000000
--- a/modules/local/sra_fastq_ftp/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-sra_fastq_ftp:
-  - modules/local/sra_fastq_ftp/**
diff --git a/modules/local/sra_ids_to_runinfo/tests/tags.yml b/modules/local/sra_ids_to_runinfo/tests/tags.yml
deleted file mode 100644
index 63ea7db3..00000000
--- a/modules/local/sra_ids_to_runinfo/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-sra_ids_to_runinfo:
-  - modules/local/sra_ids_to_runinfo/**
diff --git a/modules/local/sra_runinfo_to_ftp/tests/tags.yml b/modules/local/sra_runinfo_to_ftp/tests/tags.yml
deleted file mode 100644
index 0987a1e6..00000000
--- a/modules/local/sra_runinfo_to_ftp/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-sra_runinfo_to_ftp:
-  - modules/local/sra_runinfo_to_ftp/**
diff --git a/modules/local/sra_to_samplesheet/tests/tags.yml b/modules/local/sra_to_samplesheet/tests/tags.yml
deleted file mode 100644
index 2f2d527b..00000000
--- a/modules/local/sra_to_samplesheet/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-sra_to_samplesheet:
-  - modules/local/sra_to_samplesheet/**
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/tags.yml b/modules/nf-core/custom/sratoolsncbisettings/tests/tags.yml
deleted file mode 100644
index fb4a08a7..00000000
--- a/modules/nf-core/custom/sratoolsncbisettings/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-custom/sratoolsncbisettings:
-  - modules/nf-core/custom/sratoolsncbisettings/**
diff --git a/modules/nf-core/sratools/fasterqdump/tests/tags.yml b/modules/nf-core/sratools/fasterqdump/tests/tags.yml
deleted file mode 100644
index 5d1ddcb3..00000000
--- a/modules/nf-core/sratools/fasterqdump/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-sratools/fasterqdump:
-  - modules/nf-core/sratools/fasterqdump/**
diff --git a/modules/nf-core/sratools/prefetch/tests/tags.yml b/modules/nf-core/sratools/prefetch/tests/tags.yml
deleted file mode 100644
index 52110bfd..00000000
--- a/modules/nf-core/sratools/prefetch/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-sratools/prefetch:
-  - modules/nf-core/sratools/prefetch/**
diff --git a/modules/nf-core/untar/tests/tags.yml b/modules/nf-core/untar/tests/tags.yml
deleted file mode 100644
index feb6f15c..00000000
--- a/modules/nf-core/untar/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-untar:
-  - modules/nf-core/untar/**
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml
deleted file mode 100644
index 03028c32..00000000
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/fastq_download_prefetch_fasterqdump_sratools:
-  - subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/**
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
deleted file mode 100644
index f8476112..00000000
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nextflow_pipeline:
-  - subworkflows/nf-core/utils_nextflow_pipeline/**
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
deleted file mode 100644
index ac8523c9..00000000
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nfcore_pipeline:
-  - subworkflows/nf-core/utils_nfcore_pipeline/**
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
deleted file mode 100644
index 60b1cfff..00000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nfvalidation_plugin:
-  - subworkflows/nf-core/utils_nfvalidation_plugin/**
diff --git a/tests/tags.yml b/tests/tags.yml
deleted file mode 100644
index 80e5fd75..00000000
--- a/tests/tags.yml
+++ /dev/null
@@ -1,5 +0,0 @@
-pipeline_fetchngs:
-  - "**.nf"
-  - "**.config"
-  - "**.nf.test"
-  - "**.json"
diff --git a/workflows/sra/tests/tags.yml b/workflows/sra/tests/tags.yml
deleted file mode 100644
index ae41e37d..00000000
--- a/workflows/sra/tests/tags.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-sra_custom_ena_metadata_fields:
-  - workflows/sra/**
-sra_default_parameters:
-  - workflows/sra/**
-sra_force_sratools_download:
-  - workflows/sra/**
-sra_nf_core_pipeline_atacseq:
-  - workflows/sra/**
-sra_nf_core_pipeline_rnaseq:
-  - workflows/sra/**
-sra_nf_core_pipeline_taxprofiler:
-  - workflows/sra/**
-sra_nf_core_pipeline_viralrecon:
-  - workflows/sra/**
-sra_skip_fastq_download:
-  - workflows/sra/**

From a6c34fcd769b361832071e1f2e8343bc657d0d25 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 18 Jan 2024 15:56:31 +0000
Subject: [PATCH 694/852] Tag order changed

---
 modules/nf-core/sratools/fasterqdump/tests/main.nf.test     | 3 ++-
 tests/main.nf.test                                          | 4 ++--
 workflows/sra/tests/main.nf.test                            | 6 ++++--
 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test  | 6 +++---
 workflows/sra/tests/sra_force_sratools_download.nf.test     | 6 +++---
 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test    | 6 +++---
 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test     | 6 +++---
 .../sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test      | 6 +++---
 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test | 6 +++---
 workflows/sra/tests/sra_skip_fastq_download.nf.test         | 6 +++---
 10 files changed, 29 insertions(+), 26 deletions(-)

diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
index 15277dbc..18f9b925 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
@@ -3,9 +3,10 @@ nextflow_process {
     script "../main.nf"
     config "./nextflow.config"
     process "SRATOOLS_FASTERQDUMP"
+    
+    tag "SRATOOLS_FASTERQDUMP"
 
     tag "UNTAR"
-    tag "SRATOOLS_FASTERQDUMP"
 
     test("Single-end") {
 
diff --git a/tests/main.nf.test b/tests/main.nf.test
index 4e664778..7857a11a 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -3,9 +3,9 @@ nextflow_pipeline {
     name "Test pipeline"
     script "../main.nf"
 
-    tag "SRA"
-    
     tag "FETCHNGS"
+    
+    tag "SRA"
 
     test("Run with profile test") {
 
diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 1d63d8d8..3b452564 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -4,6 +4,10 @@ nextflow_workflow {
     script "../main.nf"
     workflow "SRA"
 
+
+    // Subworkflows
+    tag "SRA"
+
     // Modules
     tag "MULTIQC_MAPPINGS_CONFIG"
     tag "SRA_FASTQ_FTP"
@@ -11,8 +15,6 @@ nextflow_workflow {
     tag "SRA_RUNINFO_TO_FTP"
     tag "SRA_TO_SAMPLESHEET"
 
-    // Subworkflows
-    tag "SRA"
 
     test("Parameters: default") {
 
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index b0f9e4f4..0724b4fb 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -4,6 +4,9 @@ nextflow_workflow {
     script "../main.nf"
     workflow "SRA"
 
+    // Subworkflows
+    tag "SRA"
+
     // Modules
     tag "MULTIQC_MAPPINGS_CONFIG"
     tag "SRA_FASTQ_FTP"
@@ -11,9 +14,6 @@ nextflow_workflow {
     tag "SRA_RUNINFO_TO_FTP"
     tag "SRA_TO_SAMPLESHEET"
 
-    // Subworkflows
-    tag "SRA"
-
     test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") {
 
         when {
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index 78658b7c..2d01c694 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -4,6 +4,9 @@ nextflow_workflow {
     script "../main.nf"
     workflow "SRA"
 
+    // Subworkflows
+    tag "SRA"
+
     // Modules
     tag "MULTIQC_MAPPINGS_CONFIG"
     tag "SRA_FASTQ_FTP"
@@ -11,9 +14,6 @@ nextflow_workflow {
     tag "SRA_RUNINFO_TO_FTP"
     tag "SRA_TO_SAMPLESHEET"
 
-    // Subworkflows
-    tag "SRA"
-
     test("Parameters: --force_sratools_download") {
 
         when {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index 816235ef..d792e09f 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -4,6 +4,9 @@ nextflow_workflow {
     script "../main.nf"
     workflow "SRA"
     
+    // Subworkflows
+    tag "SRA"
+
     // Modules
     tag "MULTIQC_MAPPINGS_CONFIG"
     tag "SRA_FASTQ_FTP"
@@ -11,9 +14,6 @@ nextflow_workflow {
     tag "SRA_RUNINFO_TO_FTP"
     tag "SRA_TO_SAMPLESHEET"
 
-    // Subworkflows
-    tag "SRA"
-
     test("Parameters: --nf_core_pipeline atacseq") {
 
         when {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index dd3b55d0..7f2603f6 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -4,6 +4,9 @@ nextflow_workflow {
     script "../main.nf"
     workflow "SRA"
 
+    // Subworkflows
+    tag "SRA"
+
     // Modules
     tag "MULTIQC_MAPPINGS_CONFIG"
     tag "SRA_FASTQ_FTP"
@@ -11,9 +14,6 @@ nextflow_workflow {
     tag "SRA_RUNINFO_TO_FTP"
     tag "SRA_TO_SAMPLESHEET"
 
-    // Subworkflows
-    tag "SRA"
-
     test("Parameters: --nf_core_pipeline rnaseq") {
 
         when {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index fe907dc6..7d4fcb23 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -4,6 +4,9 @@ nextflow_workflow {
     script "../main.nf"
     workflow "SRA"
 
+    // Subworkflows
+    tag "SRA"
+
     // Modules
     tag "MULTIQC_MAPPINGS_CONFIG"
     tag "SRA_FASTQ_FTP"
@@ -11,9 +14,6 @@ nextflow_workflow {
     tag "SRA_RUNINFO_TO_FTP"
     tag "SRA_TO_SAMPLESHEET"
 
-    // Subworkflows
-    tag "SRA"
-
     test("Parameters: --nf_core_pipeline taxprofiler") {
 
         when {
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index 938edc00..89f8f370 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -4,6 +4,9 @@ nextflow_workflow {
     script "../main.nf"
     workflow "SRA"
 
+    // Subworkflows
+    tag "SRA"
+
     // Modules
     tag "MULTIQC_MAPPINGS_CONFIG"
     tag "SRA_FASTQ_FTP"
@@ -11,9 +14,6 @@ nextflow_workflow {
     tag "SRA_RUNINFO_TO_FTP"
     tag "SRA_TO_SAMPLESHEET"
 
-    // Subworkflows
-    tag "SRA"
-
     test("Parameters: --nf_core_pipeline viralrecon") {
 
         when {
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index 63ec1be0..b3fdd883 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -4,6 +4,9 @@ nextflow_workflow {
     script "../main.nf"
     workflow "SRA"
 
+    // Subworkflows
+    tag "SRA"
+
     // Modules
     tag "MULTIQC_MAPPINGS_CONFIG"
     tag "SRA_FASTQ_FTP"
@@ -11,9 +14,6 @@ nextflow_workflow {
     tag "SRA_RUNINFO_TO_FTP"
     tag "SRA_TO_SAMPLESHEET"
 
-    // Subworkflows
-    tag "SRA"
-
     test("Parameters: --skip_fastq_download") {
 
         when {

From 76095d3f89d178a86c73821151ad7e0318f33c7b Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 18 Jan 2024 17:47:53 +0000
Subject: [PATCH 695/852] Replace tag logic in Github Action testing workflow

---
 .github/workflows/ci.yml | 50 ++++++++++++++++++++++++++++++----------
 1 file changed, 38 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 9034d1db..170fc852 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -27,19 +27,45 @@ jobs:
     name: Check for changes
     runs-on: ubuntu-latest
     outputs:
-      # Expose matched filters as job 'tags' output variable
-      tags: ${{ steps.filter.outputs.changes }}
+      n_changes: ${{ steps.changed_files.outputs.all_modified_files_count }}
+      tags: ${{ steps.changed_files.outputs.all_changed_files }}
     steps:
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Cache nf-test installation
+        id: cache-software
+        uses: actions/cache@v3
+        with:
+          path: |
+            /usr/local/bin/nf-test
+            /home/runner/.nf-test/nf-test.jar
+          key: ${{ runner.os }}-${{ env.NFT_VER }}-nftest
+
+      - name: Install nf-test
+        if: steps.cache-software.outputs.cache-hit != 'true'
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
       - uses: actions/checkout@v3
-      - name: Combine all tags.yml files
-        id: get_username
-        run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml
-      - name: debug
-        run: cat .github/tags.yml
-      - uses: dorny/paths-filter@v2
-        id: filter
         with:
-          filters: ".github/tags.yml"
+          fetch-depth: 0
+
+      - uses: tj-actions/changed-files@v42
+        id: changed_files
+        with:
+          dir_names: "true"
+
+      - name: nf-test list tags
+        id: list
+        if: ${{ steps.changed_files.outputs.all_modified_files_count > 0 }}
+        run: nf-test list --silent --tags --format json ${{ steps.changed_files.outputs.all_changed_files }} | paste -sd, -
+
+      - name: debug
+        run: echo ${{ steps.changed_files.outputs }}
 
   define_nxf_versions:
     name: Choose nextflow versions to test against depending on target branch
@@ -56,9 +82,9 @@ jobs:
           fi
 
   test:
-    name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }}
+    name: ${{ matrix.tags }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
     needs: [changes, define_nxf_versions]
-    if: needs.changes.outputs.tags != '[]'
+    if: needs.changes.outputs.n_changes > 0
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false

From c325d8d8e20c44c6dc5274ebf39cc20e9c709288 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 18 Jan 2024 17:53:15 +0000
Subject: [PATCH 696/852] Fixup CI

---
 .github/workflows/ci.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 170fc852..1d522263 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -27,8 +27,8 @@ jobs:
     name: Check for changes
     runs-on: ubuntu-latest
     outputs:
-      n_changes: ${{ steps.changed_files.outputs.all_modified_files_count }}
-      tags: ${{ steps.changed_files.outputs.all_changed_files }}
+      changes: ${{ steps.changed_files.outputs.any_modified }}
+      tags: ${{ steps.list.outputs.tags }}
     steps:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
@@ -61,8 +61,8 @@ jobs:
 
       - name: nf-test list tags
         id: list
-        if: ${{ steps.changed_files.outputs.all_modified_files_count > 0 }}
-        run: nf-test list --silent --tags --format json ${{ steps.changed_files.outputs.all_changed_files }} | paste -sd, -
+        if: ${{ steps.changed_files.outputs.any_modified }}
+        run: echo tags=$(nf-test list --silent --tags --format json ${{ steps.changed_files.outputs.all_changed_files }}) >> $GITHUB_OUTPUT
 
       - name: debug
         run: echo ${{ steps.changed_files.outputs }}
@@ -84,7 +84,7 @@ jobs:
   test:
     name: ${{ matrix.tags }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
     needs: [changes, define_nxf_versions]
-    if: needs.changes.outputs.n_changes > 0
+    if: needs.changes.outputs.changes
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false

From fe432bc7e475da5e618d6938eba5b6880164fb69 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 18 Jan 2024 17:58:03 +0000
Subject: [PATCH 697/852] Correct UTILS_NEXTFLOW_PIPELINE tag

---
 .github/workflows/ci.yml                                     | 3 ---
 .../utils_nextflow_pipeline/tests/main.functions.nf.test     | 2 +-
 .../utils_nextflow_pipeline/tests/main.workflow.nf.test      | 5 ++---
 3 files changed, 3 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1d522263..d39fbb6b 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -64,9 +64,6 @@ jobs:
         if: ${{ steps.changed_files.outputs.any_modified }}
         run: echo tags=$(nf-test list --silent --tags --format json ${{ steps.changed_files.outputs.all_changed_files }}) >> $GITHUB_OUTPUT
 
-      - name: debug
-        run: echo ${{ steps.changed_files.outputs }}
-
   define_nxf_versions:
     name: Choose nextflow versions to test against depending on target branch
     runs-on: ubuntu-latest
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test
index 50c90208..81f5ba45 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test
@@ -5,7 +5,7 @@ nextflow_function {
     script "subworkflows/nf-core/utils_nextflow_pipeline/main.nf"
     config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config"
 
-    tag 'UTILS_NEXTFLOW_PIPELINE'
+    tag "UTILS_NEXTFLOW_PIPELINE"
 
     test("Test Function getWorkflowVersion") {
 
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
index e2fa5b6c..007606ef 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -4,9 +4,8 @@ nextflow_workflow {
     script "../main.nf"
     config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config"
     workflow "UTILS_NEXTFLOW_PIPELINE"
-    tag 'subworkflows'
-    tag 'utils_nextflow_pipeline'
-    tag 'subworkflows/utils_nextflow_pipeline'
+
+    tag "UTILS_NEXTFLOW_PIPELINE"
 
     test("Should run no inputs") {
 

From bcae51ab541155e0bcc31cdd4e3d937beda0677e Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 18 Jan 2024 18:02:07 +0000
Subject: [PATCH 698/852] ECLint

---
 modules/local/sra_to_samplesheet/tests/main.nf.test | 2 +-
 tests/main.nf.test                                  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test
index 7b7a52a8..999864b8 100644
--- a/modules/local/sra_to_samplesheet/tests/main.nf.test
+++ b/modules/local/sra_to_samplesheet/tests/main.nf.test
@@ -3,7 +3,7 @@ nextflow_process {
     name "Test process: SRA_TO_SAMPLESHEET"
     script "../main.nf"
     process "SRA_TO_SAMPLESHEET"
-    
+
     tag "SRA_TO_SAMPLESHEET"
 
     test("Should run without failures") {
diff --git a/tests/main.nf.test b/tests/main.nf.test
index 7857a11a..8331d376 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -4,7 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
 
     tag "FETCHNGS"
-    
+
     tag "SRA"
 
     test("Run with profile test") {

From b1b117daf7538a293c2423dcf4155c89e2d84ad8 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 19 Jan 2024 11:35:58 +0000
Subject: [PATCH 699/852] Use PIPELINE tag

---
 tests/main.nf.test | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/tests/main.nf.test b/tests/main.nf.test
index 8331d376..c49d70f9 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -1,9 +1,8 @@
-nextflow_pipeline {
+nextflow_pipeline 
 
     name "Test pipeline"
     script "../main.nf"
-
-    tag "FETCHNGS"
+    tag "PIPELINE"
 
     tag "SRA"
 
@@ -81,4 +80,4 @@ nextflow_pipeline {
             )
         }
     }
-}
+

From 7d889625916f3acd507ec53dedbfad32d16ddc34 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 19 Jan 2024 11:36:12 +0000
Subject: [PATCH 700/852] Add exclusion statments for linting files

---
 .github/workflows/ci.yml | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d39fbb6b..04519dee 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -58,6 +58,20 @@ jobs:
         id: changed_files
         with:
           dir_names: "true"
+          files_ignore: |
+            .git*
+            .gitpod.yml
+            .prettierignore
+            .prettierrc.yml
+            **.md
+            **.png
+            pyproject.toml
+            tower.yml
+
+      - name: debug
+        run: |
+          echo ${{ steps.changed_files.outputs.any_modified }}
+          echo ${{ steps.changed_files.outputs.all_changed_files }}
 
       - name: nf-test list tags
         id: list

From c36a8aa4c2373fb225e78453c0c711692fa1de46 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 19 Jan 2024 11:41:26 +0000
Subject: [PATCH 701/852] Add renamed files as deleted and added

---
 .github/workflows/ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 04519dee..9e3dc48f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -58,6 +58,7 @@ jobs:
         id: changed_files
         with:
           dir_names: "true"
+          output_renamed_files_as_deleted_and_added: "true"
           files_ignore: |
             .git*
             .gitpod.yml

From 412b0594f4e49d1fd272f90935f7fa5004721059 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 19 Jan 2024 11:45:06 +0000
Subject: [PATCH 702/852] Add another debugging step

---
 .github/workflows/ci.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 9e3dc48f..81000541 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -79,6 +79,10 @@ jobs:
         if: ${{ steps.changed_files.outputs.any_modified }}
         run: echo tags=$(nf-test list --silent --tags --format json ${{ steps.changed_files.outputs.all_changed_files }}) >> $GITHUB_OUTPUT
 
+      - name: debug2
+        run: |
+          echo ${{ steps.list.outputs.tags }}
+
   define_nxf_versions:
     name: Choose nextflow versions to test against depending on target branch
     runs-on: ubuntu-latest

From 2f6a78ab6a1eead34072bea76dc8796a983efd57 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 19 Jan 2024 11:46:48 +0000
Subject: [PATCH 703/852] Revert "Use PIPELINE tag"

This reverts commit b1b117daf7538a293c2423dcf4155c89e2d84ad8.
---
 tests/main.nf.test | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/tests/main.nf.test b/tests/main.nf.test
index c49d70f9..8331d376 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -1,8 +1,9 @@
-nextflow_pipeline 
+nextflow_pipeline {
 
     name "Test pipeline"
     script "../main.nf"
-    tag "PIPELINE"
+
+    tag "FETCHNGS"
 
     tag "SRA"
 
@@ -80,4 +81,4 @@ nextflow_pipeline
             )
         }
     }
-
+}

From f28a3365bf99a1469cac845252def0167aa7651b Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 19 Jan 2024 11:49:18 +0000
Subject: [PATCH 704/852] Use PIPELINE tag

---
 tests/main.nf.test | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tests/main.nf.test b/tests/main.nf.test
index 8331d376..3a88b84e 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -2,8 +2,7 @@ nextflow_pipeline {
 
     name "Test pipeline"
     script "../main.nf"
-
-    tag "FETCHNGS"
+    tag "PIPELINE"
 
     tag "SRA"
 

From a97290123b6d7cebd42f77c007249f1cbbfb9df8 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 19 Jan 2024 13:23:03 +0100
Subject: [PATCH 705/852] first tests

---
 .../tests/main.function.nf.test               | 35 +++++++++++++++++++
 .../tests/main.function.nf.test.snap          | 10 ++++++
 .../tests/tags.yml                            |  2 ++
 3 files changed, 47 insertions(+)
 create mode 100644 subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test
 create mode 100644 subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test.snap
 create mode 100644 subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/tags.yml

diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test
new file mode 100644
index 00000000..e6f11432
--- /dev/null
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test
@@ -0,0 +1,35 @@
+
+nextflow_function {
+
+    name "Test Functions"
+    script "subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf"
+    tag 'subworkflows'
+    tag 'utils_nfcore_fetchngs_pipeline'
+    tag 'subworkflows/utils_nfcore_fetchngs_pipeline'
+
+// isSraId(input)
+// isSynapseId(input)
+// sraCheckENAMetadataFields(ena_metadata_fields)
+// synapseShowToMap(synapse_file)
+// synapseSampleNameFromFastQ(input_file, pattern)
+
+    test("Function sraCurateSamplesheetWarn") {
+
+        function "sraCurateSamplesheetWarn"
+
+        then {
+            assert function.success
+            assert snapshot(function.result).match()
+        }
+    }
+
+    test("Function synapseCurateSamplesheetWarn") {
+
+        function "synapseCurateSamplesheetWarn"
+
+        then {
+            assert function.success
+            assert snapshot(function.result).match()
+        }
+    }
+}
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test.snap b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test.snap
new file mode 100644
index 00000000..0dda851c
--- /dev/null
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test.snap
@@ -0,0 +1,10 @@
+{
+    "Function sraCurateSamplesheetWarn": {
+        "content": null,
+        "timestamp": "2024-01-19T13:21:43.405877"
+    },
+    "Function synapseCurateSamplesheetWarn": {
+        "content": null,
+        "timestamp": "2024-01-19T13:21:50.818169"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/tags.yml b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/tags.yml
new file mode 100644
index 00000000..944508d1
--- /dev/null
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/utils_nfcore_fetchngs_pipeline:
+  - subworkflows/local/utils_nfcore_fetchngs_pipeline/**

From 5dcc751d2a6a0bc050f68787d115b9789a092b91 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 19 Jan 2024 16:37:51 +0100
Subject: [PATCH 706/852] update function tests + snap

---
 .../tests/main.function.nf.test               | 81 ++++++++++++++++---
 .../tests/main.function.nf.test.snap          | 18 ++++-
 2 files changed, 87 insertions(+), 12 deletions(-)

diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test
index e6f11432..7b3ab592 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test
@@ -7,11 +7,64 @@ nextflow_function {
     tag 'utils_nfcore_fetchngs_pipeline'
     tag 'subworkflows/utils_nfcore_fetchngs_pipeline'
 
-// isSraId(input)
-// isSynapseId(input)
-// sraCheckENAMetadataFields(ena_metadata_fields)
-// synapseShowToMap(synapse_file)
-// synapseSampleNameFromFastQ(input_file, pattern)
+    test("Function isSraId") {
+
+        function "isSraId"
+
+        when {
+            function {
+                """
+                input[0] = 'DRR000774'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
+    test("Function sraCheckENAMetadataFields [success]") {
+
+        function "sraCheckENAMetadataFields"
+
+        when {
+            function {
+                """
+                input[0] = 'run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
+    test("Function sraCheckENAMetadataFields [failure]") {
+
+        function "sraCheckENAMetadataFields"
+
+        when {
+            function {
+                """
+                input[0] = 'run_accession,experiment_accession,library_layout,fastq_ftp'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert !function.success }
+            )
+        }
+    }
 
     test("Function sraCurateSamplesheetWarn") {
 
@@ -23,13 +76,23 @@ nextflow_function {
         }
     }
 
-    test("Function synapseCurateSamplesheetWarn") {
+    test("Function isSynapseId") {
+
+        function "isSynapseId"
 
-        function "synapseCurateSamplesheetWarn"
+        when {
+            function {
+                """
+                input[0] = 'syn26240435'
+                """
+            }
+        }
 
         then {
-            assert function.success
-            assert snapshot(function.result).match()
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
         }
     }
 }
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test.snap b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test.snap
index 0dda851c..335967e6 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test.snap
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test.snap
@@ -1,10 +1,22 @@
 {
     "Function sraCurateSamplesheetWarn": {
         "content": null,
-        "timestamp": "2024-01-19T13:21:43.405877"
+        "timestamp": "2024-01-19T16:37:05.668505"
     },
-    "Function synapseCurateSamplesheetWarn": {
+    "Function sraCheckENAMetadataFields [success]": {
         "content": null,
-        "timestamp": "2024-01-19T13:21:50.818169"
+        "timestamp": "2024-01-19T16:36:51.121603"
+    },
+    "Function isSraId": {
+        "content": [
+            true
+        ],
+        "timestamp": "2024-01-19T16:36:43.68958"
+    },
+    "Function isSynapseId": {
+        "content": [
+            true
+        ],
+        "timestamp": "2024-01-19T16:37:12.992364"
     }
 }
\ No newline at end of file

From 401f91dcc5a5d2d45d84e7913d7abc8bd0699116 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 19 Jan 2024 16:49:24 +0000
Subject: [PATCH 707/852] Add files_yaml stuff for checking all

---
 .github/workflows/ci.yml | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 81000541..d0d1e655 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -59,6 +59,17 @@ jobs:
         with:
           dir_names: "true"
           output_renamed_files_as_deleted_and_added: "true"
+          files_yaml: |
+            all:
+              - .github/workflows/**
+              - nf-test.config
+              - nextflow.config
+            pipeline:
+              - assets/*
+              - bin/*
+              - conf/*
+              - main.nf
+              - nextflow_schema.json
           files_ignore: |
             .git*
             .gitpod.yml
@@ -66,6 +77,7 @@ jobs:
             .prettierrc.yml
             **.md
             **.png
+            modules.json
             pyproject.toml
             tower.yml
 

From 6cdff1c77708464d4d90d708dd5298b697eb7bf5 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 19 Jan 2024 16:57:57 +0000
Subject: [PATCH 708/852] Add debug step

---
 .github/workflows/ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d0d1e655..0705cb0c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -85,6 +85,7 @@ jobs:
         run: |
           echo ${{ steps.changed_files.outputs.any_modified }}
           echo ${{ steps.changed_files.outputs.all_changed_files }}
+          echo ${{ steps.changed_files.outputs.changed_keys }}}
 
       - name: nf-test list tags
         id: list

From d490e6ab9f84f446de5ecf0fa0a5b033474f77d8 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 19 Jan 2024 17:02:05 +0000
Subject: [PATCH 709/852] Refine pipeline and 'all' test rules

---
 .github/workflows/ci.yml | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 0705cb0c..d167e13e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -59,17 +59,19 @@ jobs:
         with:
           dir_names: "true"
           output_renamed_files_as_deleted_and_added: "true"
+          # Define list of additional rules for testing paths
+          # Mostly, we define additional 'pipeline' or 'all' tests here
           files_yaml: |
-            all:
-              - .github/workflows/**
-              - nf-test.config
-              - nextflow.config
-            pipeline:
+            tests:
               - assets/*
               - bin/*
               - conf/*
               - main.nf
               - nextflow_schema.json
+            ".":
+              - .github/workflows/**
+              - nf-test.config
+              - nextflow.config
           files_ignore: |
             .git*
             .gitpod.yml
@@ -85,12 +87,12 @@ jobs:
         run: |
           echo ${{ steps.changed_files.outputs.any_modified }}
           echo ${{ steps.changed_files.outputs.all_changed_files }}
-          echo ${{ steps.changed_files.outputs.changed_keys }}}
+          echo ${{ steps.changed_files.outputs.changed_keys }}
 
       - name: nf-test list tags
         id: list
         if: ${{ steps.changed_files.outputs.any_modified }}
-        run: echo tags=$(nf-test list --silent --tags --format json ${{ steps.changed_files.outputs.all_changed_files }}) >> $GITHUB_OUTPUT
+        run: echo tags=$(nf-test list --silent --tags --format json ${{ steps.changed_files.outputs.all_changed_files }} ${{ steps.changed_files.outputs.changed_keys }}) >> $GITHUB_OUTPUT
 
       - name: debug2
         run: |

From 00c2ea02eb2e3cda4e98e5a3af52e2c2bff1db5b Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 19 Jan 2024 17:05:08 +0000
Subject: [PATCH 710/852] Add shared tag to pipeline level tests

---
 .github/workflows/ci.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d167e13e..e4b66ab7 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -62,13 +62,14 @@ jobs:
           # Define list of additional rules for testing paths
           # Mostly, we define additional 'pipeline' or 'all' tests here
           files_yaml: |
-            tests:
+            tests: &shared
               - assets/*
               - bin/*
               - conf/*
               - main.nf
               - nextflow_schema.json
             ".":
+              - *shared
               - .github/workflows/**
               - nf-test.config
               - nextflow.config

From 36972d006bdd702ac15a322088064adf42b9f54b Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 19 Jan 2024 18:19:28 +0100
Subject: [PATCH 711/852] forgotten }

---
 subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
index 21249dd7..821344d0 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
@@ -31,7 +31,7 @@ workflow PIPELINE_INITIALISATION {
     take:
     version             // boolean: Display version and exit
     help                // boolean: Display help text
-    validate_params     // boolean: Boolean whether to validate parameters against the schema at runtime 
+    validate_params     // boolean: Boolean whether to validate parameters against the schema at runtime
     monochrome_logs     // boolean: Do not use coloured log outputs
     outdir              //  string: The output directory where the results will be saved
     input               //  string: File containing SRA/ENA/GEO/DDBJ identifiers one per line to download their associated metadata and FastQ files

From 4d2d566d8f21139874ee6ed316f50d128336d0bb Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 19 Jan 2024 17:31:25 +0000
Subject: [PATCH 712/852] Remove shared yaml anchor because I think it isn't
 needed

---
 .github/workflows/ci.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index e4b66ab7..3ee6b6a0 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -62,17 +62,17 @@ jobs:
           # Define list of additional rules for testing paths
           # Mostly, we define additional 'pipeline' or 'all' tests here
           files_yaml: |
-            tests: &shared
+            ".":
+              - .github/workflows/**
+              - nf-test.config
+              - nextflow.config
+            tests:
               - assets/*
               - bin/*
               - conf/*
               - main.nf
               - nextflow_schema.json
-            ".":
-              - *shared
-              - .github/workflows/**
-              - nf-test.config
-              - nextflow.config
+
           files_ignore: |
             .git*
             .gitpod.yml

From 4615f9669441688f5c7e83766c82e8657000b436 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 19 Jan 2024 19:35:07 +0100
Subject: [PATCH 713/852] first version

---
 ...n.workflow_pipeline_initialisation.nf.test | 45 +++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100644 subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test

diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
new file mode 100644
index 00000000..fe00b6c9
--- /dev/null
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
@@ -0,0 +1,45 @@
+nextflow_workflow {
+
+    name "Test Workflow PIPELINE_INITIALISATION"
+    script "subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf"
+    workflow "PIPELINE_INITIALISATION"
+    tag 'subworkflows'
+    tag 'utils_nfcore_fetchngs_pipeline'
+    tag 'subworkflows/utils_nfcore_fetchngs_pipeline'
+
+    test("Should run") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            workflow {
+                """
+                version             = false
+                help                = false
+                validate_params     = true
+                monochrome_logs     = false
+                outdir              = "$params.outdir"
+                input               = 'https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/testdata/v1.12.0/sra_ids_test.csv'
+                input_type          = 'sra'
+                ena_metadata_fields = 'null'
+
+                input [0] = version
+                input [1] = help
+                input [2] = validate_params
+                input [3] = monochrome_logs
+                input [4] = outdir
+                input [5] = input
+                input [6] = input_type
+                input [7] = ena_metadata_fields
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+}

From b4ce5e073cefd0732c62e1be81e9fd2345b3b116 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 19 Jan 2024 19:44:18 +0100
Subject: [PATCH 714/852] add tests for completion

---
 .../main.workflow_pipeline_completion.test    | 43 +++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100644 subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test

diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test
new file mode 100644
index 00000000..a840f0ae
--- /dev/null
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test
@@ -0,0 +1,43 @@
+nextflow_workflow {
+
+    name "Test Workflow PIPELINE_COMPLETION"
+    script "subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf"
+    workflow "PIPELINE_COMPLETION"
+    tag 'subworkflows'
+    tag 'utils_nfcore_fetchngs_pipeline'
+    tag 'subworkflows/utils_nfcore_fetchngs_pipeline'
+
+    test("Should run") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            workflow {
+                """
+                input_type      = 'sra'
+                email           = null
+                email_on_fail   = null
+                plaintext_email = false
+                outdir          = "$params.outdir"
+                monochrome_logs = false
+                hook_url        = null
+
+                input [0] = input_type
+                input [1] = email
+                input [2] = email_on_fail
+                input [3] = plaintext_email
+                input [4] = outdir
+                input [5] = monochrome_logs
+                input [6] = hook_url
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+}

From 6c004336922a64e8634fb9b7fff149a961b433fc Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 22 Jan 2024 15:44:42 +0000
Subject: [PATCH 715/852] Use collect and confirm strategy for tests

Replace Nextflow versioning with simple list matrix
---
 .github/workflows/ci.yml | 52 +++++++++++++++++++++++++++-------------
 1 file changed, 35 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 3ee6b6a0..715800c8 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -32,8 +32,6 @@ jobs:
     steps:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
-        with:
-          version: "${{ matrix.NXF_VER }}"
 
       - name: Cache nf-test installation
         id: cache-software
@@ -99,29 +97,31 @@ jobs:
         run: |
           echo ${{ steps.list.outputs.tags }}
 
-  define_nxf_versions:
-    name: Choose nextflow versions to test against depending on target branch
-    runs-on: ubuntu-latest
-    outputs:
-      matrix: ${{ steps.nxf_versions.outputs.matrix }}
-    steps:
-      - id: nxf_versions
-        run: |
-          if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
-            echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT
-          else
-            echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT
-          fi
+  # define_nxf_versions:
+  #   name: Choose nextflow versions to test against depending on target branch
+  #   runs-on: ubuntu-latest
+  #   outputs:
+  #     matrix: ${{ steps.nxf_versions.outputs.matrix }}
+  #   steps:
+  #     - id: nxf_versions
+  #       run: |
+  #         if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
+  #           echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT
+  #         else
+  #           echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT
+  #         fi
 
   test:
     name: ${{ matrix.tags }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
-    needs: [changes, define_nxf_versions]
+    needs: [changes]
     if: needs.changes.outputs.changes
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
+        NXF_VER:
+          - "latest-everything"
+          - "23.04"
         tags: ["${{ fromJson(needs.changes.outputs.tags) }}"]
         profile:
           - "docker"
@@ -180,3 +180,21 @@ jobs:
         if: always() # always run even if the previous step fails
         with:
           report_paths: test.xml
+
+  confirm-pass:
+    runs-on: ubuntu-latest
+    needs: [test]
+    if: always()
+    steps:
+      - name: All tests ok
+        if: ${{ success() || !contains(needs.*.result, 'failure') }}
+        run: exit 0
+      - name: One or more tests failed
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1
+
+      - name: debug-print
+        if: always()
+        run: |
+          echo "toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"

From 4cea4de07cbbb02c5d03974f59b5a19f06be3786 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 22 Jan 2024 20:48:49 +0100
Subject: [PATCH 716/852] update tests

---
 .../main.workflow_pipeline_completion.test    | 18 +++++++--------
 ...n.workflow_pipeline_initialisation.nf.test | 23 +++++++++----------
 2 files changed, 20 insertions(+), 21 deletions(-)

diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test
index a840f0ae..16f11e8f 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test
@@ -11,7 +11,7 @@ nextflow_workflow {
 
         when {
             params {
-                outdir = "$outputDir"
+                outdir = "tests/results"
             }
             workflow {
                 """
@@ -19,17 +19,17 @@ nextflow_workflow {
                 email           = null
                 email_on_fail   = null
                 plaintext_email = false
-                outdir          = "$params.outdir"
+                outdir          = "tests/results"
                 monochrome_logs = false
                 hook_url        = null
 
-                input [0] = input_type
-                input [1] = email
-                input [2] = email_on_fail
-                input [3] = plaintext_email
-                input [4] = outdir
-                input [5] = monochrome_logs
-                input [6] = hook_url
+                input[0] = input_type
+                input[1] = email
+                input[2] = email_on_fail
+                input[3] = plaintext_email
+                input[4] = outdir
+                input[5] = monochrome_logs
+                input[6] = hook_url
                 """
             }
         }
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
index fe00b6c9..035ecfd3 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
@@ -11,27 +11,26 @@ nextflow_workflow {
 
         when {
             params {
-                outdir = "$outputDir"
+                outdir = "tests/results"
             }
             workflow {
                 """
                 version             = false
                 help                = false
-                validate_params     = true
+                validate_params     = false
                 monochrome_logs     = false
                 outdir              = "$params.outdir"
-                input               = 'https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/testdata/v1.12.0/sra_ids_test.csv'
                 input_type          = 'sra'
-                ena_metadata_fields = 'null'
+                ena_metadata_fields = null
 
-                input [0] = version
-                input [1] = help
-                input [2] = validate_params
-                input [3] = monochrome_logs
-                input [4] = outdir
-                input [5] = input
-                input [6] = input_type
-                input [7] = ena_metadata_fields
+                input[0] = version
+                input[1] = help
+                input[2] = validate_params
+                input[3] = monochrome_logs
+                input[4] = outdir
+                input[5] = 'https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/testdata/v1.12.0/sra_ids_test.csv'
+                input[6] = input_type
+                input[7] = ena_metadata_fields
                 """
             }
         }

From bc256278d2224313abb96580b96c2a07bf6451a0 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 23 Jan 2024 14:48:11 +0000
Subject: [PATCH 717/852] Tag tidy based on review comments

---
 modules/nf-core/sratools/fasterqdump/tests/main.nf.test      | 1 -
 modules/nf-core/sratools/prefetch/tests/main.nf.test         | 1 -
 modules/nf-core/untar/tests/main.nf.test                     | 1 -
 .../tests/main.nf.test                                       | 2 +-
 .../utils_nextflow_pipeline/tests/main.workflow.nf.test      | 1 -
 .../nf-core/utils_nfvalidation_plugin/tests/main.nf.test     | 1 -
 tests/main.nf.test                                           | 2 --
 workflows/sra/tests/main.nf.test                             | 5 +----
 8 files changed, 2 insertions(+), 12 deletions(-)

diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
index 18f9b925..b3107336 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
@@ -3,7 +3,6 @@ nextflow_process {
     script "../main.nf"
     config "./nextflow.config"
     process "SRATOOLS_FASTERQDUMP"
-    
     tag "SRATOOLS_FASTERQDUMP"
 
     tag "UNTAR"
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test
index 0c210f9a..7319108c 100644
--- a/modules/nf-core/sratools/prefetch/tests/main.nf.test
+++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test
@@ -2,7 +2,6 @@ nextflow_process {
     name "Test Process SRATOOLS_PREFETCH"
     script "../main.nf"
     process "SRATOOLS_PREFETCH"
-
     tag "SRATOOLS_PREFETCH"
 
     test("sratools/prefetch") {
diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test
index e85ec082..0eb25d3c 100644
--- a/modules/nf-core/untar/tests/main.nf.test
+++ b/modules/nf-core/untar/tests/main.nf.test
@@ -3,7 +3,6 @@ nextflow_process {
     name "Test Process UNTAR"
     script "../main.nf"
     process "UNTAR"
-
     tag "UNTAR"
 
     test("test_untar") {
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
index b3d65c79..2f1d0835 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
@@ -3,11 +3,11 @@ nextflow_workflow {
     name "Test workflow: fastq_download_prefetch_fasterqdump_sratools/main.nf"
     script "../main.nf"
     workflow "FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS"
+    tag "FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS"
     
     tag "CUSTOM_SRATOOLSNCBISETTINGS"
     tag "SRATOOLS_PREFETCH"
     tag "SRATOOLS_FASTERQDUMP"
-    tag "SUBWORKFLOWS_FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS"
 
     test("Parameters: default") {
 
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
index 007606ef..3298fffe 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -4,7 +4,6 @@ nextflow_workflow {
     script "../main.nf"
     config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config"
     workflow "UTILS_NEXTFLOW_PIPELINE"
-
     tag "UTILS_NEXTFLOW_PIPELINE"
 
     test("Should run no inputs") {
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
index 47bfe461..b64a5106 100644
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
@@ -3,7 +3,6 @@ nextflow_workflow {
     name "Test Workflow UTILS_NFVALIDATION_PLUGIN"
     script "../main.nf"
     workflow "UTILS_NFVALIDATION_PLUGIN"
-
     tag "UTILS_NFVALIDATION_PLUGIN"
 
     test("Should run nothing") {
diff --git a/tests/main.nf.test b/tests/main.nf.test
index 3a88b84e..dc3662cd 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -4,8 +4,6 @@ nextflow_pipeline {
     script "../main.nf"
     tag "PIPELINE"
 
-    tag "SRA"
-
     test("Run with profile test") {
 
         when {
diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 3b452564..8fcd0e47 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -3,12 +3,9 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
-
-
-    // Subworkflows
     tag "SRA"
 
-    // Modules
+    // Dependencies
     tag "MULTIQC_MAPPINGS_CONFIG"
     tag "SRA_FASTQ_FTP"
     tag "SRA_IDS_TO_RUNINFO"

From cb4f0e6558cdf2e1435e71e8ef7e48d50b17a01a Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 26 Jan 2024 18:20:40 +0000
Subject: [PATCH 718/852] Update tags for utils_nfcore_fetchngs_pipeline
 subworkflow

---
 .../tests/main.function.nf.test                               | 4 +---
 .../tests/main.workflow_pipeline_completion.test              | 4 +---
 .../tests/main.workflow_pipeline_initialisation.nf.test       | 4 +---
 .../local/utils_nfcore_fetchngs_pipeline/tests/tags.yml       | 2 --
 4 files changed, 3 insertions(+), 11 deletions(-)
 delete mode 100644 subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/tags.yml

diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test
index 7b3ab592..5e5d3a62 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test
@@ -3,9 +3,7 @@ nextflow_function {
 
     name "Test Functions"
     script "subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf"
-    tag 'subworkflows'
-    tag 'utils_nfcore_fetchngs_pipeline'
-    tag 'subworkflows/utils_nfcore_fetchngs_pipeline'
+    tag "UTILS_NFCORE_FETCHNGS_PIPELINE"
 
     test("Function isSraId") {
 
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test
index 16f11e8f..a1814bf6 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test
@@ -3,9 +3,7 @@ nextflow_workflow {
     name "Test Workflow PIPELINE_COMPLETION"
     script "subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf"
     workflow "PIPELINE_COMPLETION"
-    tag 'subworkflows'
-    tag 'utils_nfcore_fetchngs_pipeline'
-    tag 'subworkflows/utils_nfcore_fetchngs_pipeline'
+    tag "PIPELINE_COMPLETION"
 
     test("Should run") {
 
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
index 035ecfd3..d8dc3963 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
@@ -3,9 +3,7 @@ nextflow_workflow {
     name "Test Workflow PIPELINE_INITIALISATION"
     script "subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf"
     workflow "PIPELINE_INITIALISATION"
-    tag 'subworkflows'
-    tag 'utils_nfcore_fetchngs_pipeline'
-    tag 'subworkflows/utils_nfcore_fetchngs_pipeline'
+    tag 'PIPELINE_INITIALISATION'
 
     test("Should run") {
 
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/tags.yml b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/tags.yml
deleted file mode 100644
index 944508d1..00000000
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nfcore_fetchngs_pipeline:
-  - subworkflows/local/utils_nfcore_fetchngs_pipeline/**

From 74fdcaab90fd1eec90d55fcf2aa197e77b7e1267 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 29 Jan 2024 17:00:23 +0000
Subject: [PATCH 719/852] Fixup for PR #253

---
 .github/workflows/ci.yml | 14 --------------
 CHANGELOG.md             |  1 +
 2 files changed, 1 insertion(+), 14 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 715800c8..12343148 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -97,20 +97,6 @@ jobs:
         run: |
           echo ${{ steps.list.outputs.tags }}
 
-  # define_nxf_versions:
-  #   name: Choose nextflow versions to test against depending on target branch
-  #   runs-on: ubuntu-latest
-  #   outputs:
-  #     matrix: ${{ steps.nxf_versions.outputs.matrix }}
-  #   steps:
-  #     - id: nxf_versions
-  #       run: |
-  #         if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
-  #           echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT
-  #         else
-  #           echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT
-  #         fi
-
   test:
     name: ${{ matrix.tags }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
     needs: [changes]
diff --git a/CHANGELOG.md b/CHANGELOG.md
index d512d75c..e1e9f8ee 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -27,6 +27,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #246](https://github.com/nf-core/fetchngs/pull/246) - Handle dark/light mode for logo in GitHub README properly
 - [PR #248](https://github.com/nf-core/fetchngs/pull/248) - Update pipeline level test data path to use mirror on s3
 - [PR #249](https://github.com/nf-core/fetchngs/pull/249) - Update modules which includes absolute paths for test data, making module level test compatible within the pipeline.
+- [PR #253](https://github.com/nf-core/fetchngs/pull/253) - Add implicit tags in nf-test files for simpler testing strategy
 
 ### Software dependencies
 

From a233dc0d091b678856b9a1b04cc4e47d46a6eec8 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 29 Jan 2024 17:02:08 +0000
Subject: [PATCH 720/852] Add Aspera CLI download support to pipeline

---
 CHANGELOG.md                                  | 10 +++
 CITATIONS.md                                  |  2 +
 README.md                                     |  6 +-
 conf/test_full.config                         |  4 +-
 modules/local/aspera_cli/environment.yml      |  7 ++
 modules/local/aspera_cli/main.nf              | 63 ++++++++++++++++
 modules/local/aspera_cli/nextflow.config      | 17 +++++
 modules/local/aspera_cli/tests/main.nf.test   | 37 ++++++++++
 .../local/aspera_cli/tests/main.nf.test.snap  | 71 +++++++++++++++++++
 nextflow.config                               |  1 +
 nextflow_schema.json                          |  6 ++
 workflows/sra/main.nf                         | 45 ++++++++----
 workflows/sra/nextflow.config                 |  1 +
 workflows/sra/tests/main.nf.test              |  2 +-
 .../sra_custom_ena_metadata_fields.nf.test    |  1 +
 .../sra_nf_core_pipeline_atacseq.nf.test      |  1 +
 .../tests/sra_nf_core_pipeline_rnaseq.nf.test |  1 +
 .../sra_nf_core_pipeline_taxprofiler.nf.test  |  1 +
 .../sra_nf_core_pipeline_viralrecon.nf.test   |  1 +
 19 files changed, 260 insertions(+), 17 deletions(-)
 create mode 100644 modules/local/aspera_cli/environment.yml
 create mode 100644 modules/local/aspera_cli/main.nf
 create mode 100644 modules/local/aspera_cli/nextflow.config
 create mode 100644 modules/local/aspera_cli/tests/main.nf.test
 create mode 100644 modules/local/aspera_cli/tests/main.nf.test.snap

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d512d75c..c35e92bc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -40,6 +40,16 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 >
 > **NB:** Dependency has been **removed** if new version information isn't present.
 
+### Parameters
+
+| Old parameter | New parameter          |
+| ------------- | ---------------------- |
+|               | `--force_ftp_download` |
+
+> **NB:** Parameter has been **updated** if both old and new parameter information is present.
+> **NB:** Parameter has been **added** if just the new parameter information is present.
+> **NB:** Parameter has been **removed** if new parameter information isn't present.
+
 ## [[1.11.0](https://github.com/nf-core/fetchngs/releases/tag/1.11.0)] - 2023-10-18
 
 ### Credits
diff --git a/CITATIONS.md b/CITATIONS.md
index 482d5600..a982bfd2 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -10,6 +10,8 @@
 
 ## Pipeline tools
 
+- [Aspera CLI](https://github.com/IBM/aspera-cli)
+
 - [Python](http://www.python.org)
 
 - [Requests](https://docs.python-requests.org/)
diff --git a/README.md b/README.md
index 56ba2cb0..2442527c 100644
--- a/README.md
+++ b/README.md
@@ -67,8 +67,10 @@ Via a single file of ids, provided one-per-line (see [example input file](https:
 1. Resolve database ids back to appropriate experiment-level ids and to be compatible with the [ENA API](https://ena-docs.readthedocs.io/en/latest/retrieval/programmatic-access.html)
 2. Fetch extensive id metadata via ENA API
 3. Download FastQ files:
-   - If direct download links are available from the ENA API, fetch in parallel via `curl` and perform `md5sum` check
-   - Otherwise use [`sra-tools`](https://github.com/ncbi/sra-tools) to download `.sra` files and convert them to FastQ
+   - If direct download links are available from the ENA API:
+     - Fetch in parallel via `aspera-cli` and perform `md5sum` check (default)
+     - Fetch in parallel via `wget` and perform `md5sum` check. Use `--force_ftp_download` to force this behaviour.
+   - Otherwise use [`sra-tools`](https://github.com/ncbi/sra-tools) to download `.sra` files and convert them to FastQ. Use `--force_sratools_download` to force this behaviour.
 4. Collate id metadata and paths to FastQ files in a single samplesheet
 
 ### Synapse ids
diff --git a/conf/test_full.config b/conf/test_full.config
index 9215d510..84595dfa 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -14,6 +14,6 @@ params {
     config_profile_name        = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'
 
-    // Input data for full size test
-    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/bb634bcfef520552e8314dfa3f8a764e1d62f7dc/testdata/v1.12.0/sra_ids_test_full.csv'
+    // File containing SRA ids from nf-core/rnaseq -profile test_full for full-sized test
+    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/100736c99d87667fb7c247c267bc8acfac647bed/testdata/v1.12.0/sra_ids_rnaseq_test_full.csv'
 }
diff --git a/modules/local/aspera_cli/environment.yml b/modules/local/aspera_cli/environment.yml
new file mode 100644
index 00000000..9fbc162f
--- /dev/null
+++ b/modules/local/aspera_cli/environment.yml
@@ -0,0 +1,7 @@
+name: aspera_cli
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::aspera-cli=4.14.0
diff --git a/modules/local/aspera_cli/main.nf b/modules/local/aspera_cli/main.nf
new file mode 100644
index 00000000..cf47b188
--- /dev/null
+++ b/modules/local/aspera_cli/main.nf
@@ -0,0 +1,63 @@
+process ASPERA_CLI {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/aspera-cli:4.14.0--hdfd78af_1' :
+        'biocontainers/aspera-cli:4.14.0--hdfd78af_1' }"
+
+    input:
+    tuple val(meta), val(fastq)
+    val user
+
+    output:
+    tuple val(meta), path("*fastq.gz"), emit: fastq
+    tuple val(meta), path("*md5")     , emit: md5
+    path "versions.yml"               , emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    if (meta.single_end) {
+        """
+        ascp \\
+            $args \\
+            -i \$CONDA_PREFIX/etc/aspera/aspera_bypass_dsa.pem \\
+            ${user}@${fastq[0]} \\
+            ${meta.id}.fastq.gz
+
+        echo "${meta.md5_1}  ${meta.id}.fastq.gz" > ${meta.id}.fastq.gz.md5
+        md5sum -c ${meta.id}.fastq.gz.md5
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            aspera_cli: \$(ascli --version)
+        END_VERSIONS
+        """
+    } else {
+        """
+        ascp \\
+            $args \\
+            -i \$CONDA_PREFIX/etc/aspera/aspera_bypass_dsa.pem \\
+            ${user}@${fastq[0]} \\
+            ${meta.id}_1.fastq.gz
+        
+        echo "${meta.md5_1}  ${meta.id}_1.fastq.gz" > ${meta.id}_1.fastq.gz.md5
+        md5sum -c ${meta.id}_1.fastq.gz.md5
+
+        ascp \\
+            $args \\
+            -i \$CONDA_PREFIX/etc/aspera/aspera_bypass_dsa.pem \\
+            ${user}@${fastq[1]} \\
+            ${meta.id}_2.fastq.gz
+
+        echo "${meta.md5_2}  ${meta.id}_2.fastq.gz" > ${meta.id}_2.fastq.gz.md5
+        md5sum -c ${meta.id}_2.fastq.gz.md5
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            aspera_cli: \$(ascli --version)
+        END_VERSIONS
+        """
+    }
+}
\ No newline at end of file
diff --git a/modules/local/aspera_cli/nextflow.config b/modules/local/aspera_cli/nextflow.config
new file mode 100644
index 00000000..fa2dbd90
--- /dev/null
+++ b/modules/local/aspera_cli/nextflow.config
@@ -0,0 +1,17 @@
+process {
+    withName: 'ASPERA_CLI' {
+        ext.args = '-QT -l 300m -P33001'
+        publishDir = [
+            [
+                path: { "${params.outdir}/fastq" },
+                mode: params.publish_dir_mode,
+                pattern: "*.fastq.gz"
+            ],
+            [
+                path: { "${params.outdir}/fastq/md5" },
+                mode: params.publish_dir_mode,
+                pattern: "*.md5"
+            ]
+        ]
+    }
+}
diff --git a/modules/local/aspera_cli/tests/main.nf.test b/modules/local/aspera_cli/tests/main.nf.test
new file mode 100644
index 00000000..d62dc94a
--- /dev/null
+++ b/modules/local/aspera_cli/tests/main.nf.test
@@ -0,0 +1,37 @@
+nextflow_process {
+
+    name "Test process: ASPERA_CLI"
+    script "../main.nf"
+    process "ASPERA_CLI"
+    
+    tag "ASPERA_CLI"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+
+            process {
+                """
+                input[0] = [
+                    [ id:'SRX9626017_SRR13191702', single_end:false, md5_1: '89c5be920021a035084d8aeb74f32df7', md5_2: '56271be38a80db78ef3bdfc5d9909b98' ], // meta map
+                    [
+                        'fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz',
+                        'fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz'
+                    ]
+                ]
+                input[1] = 'era-fasp'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/local/aspera_cli/tests/main.nf.test.snap b/modules/local/aspera_cli/tests/main.nf.test.snap
new file mode 100644
index 00000000..15497822
--- /dev/null
+++ b/modules/local/aspera_cli/tests/main.nf.test.snap
@@ -0,0 +1,71 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,baaaea61cba4294ec696fdfea1610848",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,8e43ad99049fabb6526a4b846da01c32"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
+                            "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
+                        ]
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,a51a1dfc6308d71058ddc12c46101dd3"
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,baaaea61cba4294ec696fdfea1610848",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,8e43ad99049fabb6526a4b846da01c32"
+                        ]
+                    ]
+                ],
+                "md5": [
+                    [
+                        {
+                            "id": "SRX9626017_SRR13191702",
+                            "single_end": false,
+                            "md5_1": "89c5be920021a035084d8aeb74f32df7",
+                            "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
+                        },
+                        [
+                            "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997",
+                            "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a51a1dfc6308d71058ddc12c46101dd3"
+                ]
+            }
+        ],
+        "timestamp": "2024-01-29T13:00:29.847293"
+    }
+}
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index b3c65b78..3aece1d7 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -17,6 +17,7 @@ params {
     ena_metadata_fields         = null
     sample_mapping_fields       = 'experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description'
     synapse_config              = null
+    force_ftp_download          = false
     force_sratools_download     = false
     skip_fastq_download         = false
     dbgap_key                   = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 31d9f17a..bdf37cd7 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -54,6 +54,12 @@
                     "help_text": "The default is 'auto' which can be used with nf-core/rnaseq v3.10 onwards to auto-detect strandedness during the pipeline execution.",
                     "default": "auto"
                 },
+                "force_ftp_download": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-tools",
+                    "description": "Force download FASTQ files via FTP instead of via the Aspera CLI.",
+                    "help_text": "If the Aspera CLI is not working on your infrastructure use this flag to force the pipeline to download data via FTP."
+                },
                 "force_sratools_download": {
                     "type": "boolean",
                     "fa_icon": "fas fa-tools",
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 62d8c577..80383085 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -8,6 +8,7 @@ include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_c
 include { SRA_FASTQ_FTP           } from '../../modules/local/sra_fastq_ftp'
 include { SRA_IDS_TO_RUNINFO      } from '../../modules/local/sra_ids_to_runinfo'
 include { SRA_RUNINFO_TO_FTP      } from '../../modules/local/sra_runinfo_to_ftp'
+include { ASPERA_CLI              } from '../../modules/local/aspera_cli'
 include { SRA_TO_SAMPLESHEET      } from '../../modules/local/sra_to_samplesheet'
 include { softwareVersionsToYAML  } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
 
@@ -54,10 +55,11 @@ workflow SRA {
         .out
         .tsv
         .splitCsv(header:true, sep:'\t')
-        .map{ meta ->
-            def meta_clone = meta.clone()
-            meta_clone.single_end = meta_clone.single_end.toBoolean()
-            return meta_clone
+        .map { 
+            meta ->
+                def meta_clone = meta.clone()
+                meta_clone.single_end = meta_clone.single_end.toBoolean()
+                return meta_clone
         }
         .unique()
         .set { ch_sra_metadata }
@@ -65,16 +67,36 @@ workflow SRA {
     if (!params.skip_fastq_download) {
 
         ch_sra_metadata
-            .map {
-                meta ->
-                    [ meta, [ meta.fastq_1, meta.fastq_2 ] ]
-            }
             .branch {
-                ftp: it[0].fastq_1  && !params.force_sratools_download
-                sra: !it[0].fastq_1 || params.force_sratools_download
+                meta ->                    
+                    def download_method = 'aspera'
+                    if (!meta.fastq_aspera || params.force_ftp_download) {
+                        if (meta.fastq_1) { 
+                            download_method = 'ftp'
+                        }
+                    }
+                    if ((!meta.fastq_aspera && !meta.fastq_1) || params.force_sratools_download) { 
+                        download_method = 'sratools' 
+                    }
+
+                    aspera: download_method == 'aspera'
+                        return [ meta, meta.fastq_aspera.tokenize(';').take(2) ]
+                    ftp: download_method == 'ftp'
+                        return [ meta, [ meta.fastq_1, meta.fastq_2 ] ]
+                    sratools: download_method == 'sratools'
+                        return [ meta, meta.run_accession ]
             }
             .set { ch_sra_reads }
 
+        //
+        // MODULE: If Aspera link is provided in run information then download FastQ directly via Aspera CLI and validate with md5sums
+        //
+        ASPERA_CLI (
+            ch_sra_reads.aspera,
+            'era-fasp'
+        )
+        ch_versions = ch_versions.mix(ASPERA_CLI.out.versions.first())
+
         //
         // MODULE: If FTP link is provided in run information then download FastQ directly via FTP and validate with md5sums
         //
@@ -87,7 +109,7 @@ workflow SRA {
         // SUBWORKFLOW: Download sequencing reads without FTP links using sra-tools.
         //
         FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS (
-            ch_sra_reads.sra.map { meta, reads -> [ meta, meta.run_accession ] },
+            ch_sra_reads.sratools,
             params.dbgap_key ? file(params.dbgap_key, checkIfExists: true) : []
         )
         ch_versions = ch_versions.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.versions.first())
@@ -157,7 +179,6 @@ workflow SRA {
     softwareVersionsToYAML(ch_versions)
         .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_fetchngs_software_mqc_versions.yml', sort: true, newLine: true)
 
-
     emit:
     samplesheet     = ch_samplesheet
     mappings        = ch_mappings
diff --git a/workflows/sra/nextflow.config b/workflows/sra/nextflow.config
index a48bcb73..56d7814c 100644
--- a/workflows/sra/nextflow.config
+++ b/workflows/sra/nextflow.config
@@ -1,4 +1,5 @@
 includeConfig "../../modules/local/multiqc_mappings_config/nextflow.config"
+includeConfig "../../modules/local/aspera_cli/nextflow.config"
 includeConfig "../../modules/local/sra_fastq_ftp/nextflow.config"
 includeConfig "../../modules/local/sra_ids_to_runinfo/nextflow.config"
 includeConfig "../../modules/local/sra_runinfo_to_ftp/nextflow.config"
diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 8fcd0e47..062d6886 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -7,12 +7,12 @@ nextflow_workflow {
 
     // Dependencies
     tag "MULTIQC_MAPPINGS_CONFIG"
+    tag "ASPERA_CLI"
     tag "SRA_FASTQ_FTP"
     tag "SRA_IDS_TO_RUNINFO"
     tag "SRA_RUNINFO_TO_FTP"
     tag "SRA_TO_SAMPLESHEET"
 
-
     test("Parameters: default") {
 
         when {
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index 0724b4fb..5fd4882b 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -9,6 +9,7 @@ nextflow_workflow {
 
     // Modules
     tag "MULTIQC_MAPPINGS_CONFIG"
+    tag "ASPERA_CLI"
     tag "SRA_FASTQ_FTP"
     tag "SRA_IDS_TO_RUNINFO"
     tag "SRA_RUNINFO_TO_FTP"
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index d792e09f..95069597 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -9,6 +9,7 @@ nextflow_workflow {
 
     // Modules
     tag "MULTIQC_MAPPINGS_CONFIG"
+    tag "ASPERA_CLI"
     tag "SRA_FASTQ_FTP"
     tag "SRA_IDS_TO_RUNINFO"
     tag "SRA_RUNINFO_TO_FTP"
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index 7f2603f6..99c7dbc5 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -9,6 +9,7 @@ nextflow_workflow {
 
     // Modules
     tag "MULTIQC_MAPPINGS_CONFIG"
+    tag "ASPERA_CLI"
     tag "SRA_FASTQ_FTP"
     tag "SRA_IDS_TO_RUNINFO"
     tag "SRA_RUNINFO_TO_FTP"
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index 7d4fcb23..d48a714e 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -9,6 +9,7 @@ nextflow_workflow {
 
     // Modules
     tag "MULTIQC_MAPPINGS_CONFIG"
+    tag "ASPERA_CLI"
     tag "SRA_FASTQ_FTP"
     tag "SRA_IDS_TO_RUNINFO"
     tag "SRA_RUNINFO_TO_FTP"
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index 89f8f370..f5802463 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -9,6 +9,7 @@ nextflow_workflow {
 
     // Modules
     tag "MULTIQC_MAPPINGS_CONFIG"
+    tag "ASPERA_CLI"
     tag "SRA_FASTQ_FTP"
     tag "SRA_IDS_TO_RUNINFO"
     tag "SRA_RUNINFO_TO_FTP"

From f58c5682a6c602befe660d06271811375a806d34 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 29 Jan 2024 17:09:05 +0000
Subject: [PATCH 721/852] Fix ECLint

---
 CHANGELOG.md                                | 1 +
 modules/local/aspera_cli/main.nf            | 2 +-
 modules/local/aspera_cli/tests/main.nf.test | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c35e92bc..fb853f96 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -27,6 +27,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #246](https://github.com/nf-core/fetchngs/pull/246) - Handle dark/light mode for logo in GitHub README properly
 - [PR #248](https://github.com/nf-core/fetchngs/pull/248) - Update pipeline level test data path to use mirror on s3
 - [PR #249](https://github.com/nf-core/fetchngs/pull/249) - Update modules which includes absolute paths for test data, making module level test compatible within the pipeline.
+- [PR #259](https://github.com/nf-core/fetchngs/pull/259) - Add Aspera CLI download support to pipeline ([#68](https://github.com/nf-core/fetchngs/issues/68))
 
 ### Software dependencies
 
diff --git a/modules/local/aspera_cli/main.nf b/modules/local/aspera_cli/main.nf
index cf47b188..412c618a 100644
--- a/modules/local/aspera_cli/main.nf
+++ b/modules/local/aspera_cli/main.nf
@@ -41,7 +41,7 @@ process ASPERA_CLI {
             -i \$CONDA_PREFIX/etc/aspera/aspera_bypass_dsa.pem \\
             ${user}@${fastq[0]} \\
             ${meta.id}_1.fastq.gz
-        
+
         echo "${meta.md5_1}  ${meta.id}_1.fastq.gz" > ${meta.id}_1.fastq.gz.md5
         md5sum -c ${meta.id}_1.fastq.gz.md5
 
diff --git a/modules/local/aspera_cli/tests/main.nf.test b/modules/local/aspera_cli/tests/main.nf.test
index d62dc94a..3858e2c3 100644
--- a/modules/local/aspera_cli/tests/main.nf.test
+++ b/modules/local/aspera_cli/tests/main.nf.test
@@ -3,7 +3,7 @@ nextflow_process {
     name "Test process: ASPERA_CLI"
     script "../main.nf"
     process "ASPERA_CLI"
-    
+
     tag "ASPERA_CLI"
 
     test("Should run without failures") {

From a78310f0080a3c8b1ad9777735998e3051301795 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 29 Jan 2024 17:22:03 +0000
Subject: [PATCH 722/852] CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e1e9f8ee..9d2e0a9a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -28,6 +28,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #248](https://github.com/nf-core/fetchngs/pull/248) - Update pipeline level test data path to use mirror on s3
 - [PR #249](https://github.com/nf-core/fetchngs/pull/249) - Update modules which includes absolute paths for test data, making module level test compatible within the pipeline.
 - [PR #253](https://github.com/nf-core/fetchngs/pull/253) - Add implicit tags in nf-test files for simpler testing strategy
+- [PR #258](https://github.com/nf-core/fetchngs/pull/258) - Fixes for [PR #253](https://github.com/nf-core/fetchngs/pull/253)
 
 ### Software dependencies
 

From 5f00ba81150a935a7c5d09ae4763e8e7b23575e2 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 29 Jan 2024 17:30:54 +0000
Subject: [PATCH 723/852] Mix Aspera CLI output channel with FTP and sratools
 reads

---
 workflows/sra/main.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 80383085..1e6c6e2f 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -115,9 +115,10 @@ workflow SRA {
         ch_versions = ch_versions.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.versions.first())
 
         // Isolate FASTQ channel which will be added to emit block
-        SRA_FASTQ_FTP
+        ASPERA_CLI
             .out
             .fastq
+            .mix(SRA_FASTQ_FTP.out.fastq)
             .mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads)
             .map {
                 meta, fastq ->

From d538a2aaa8a2ec5733124b298d221a864062c718 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 29 Jan 2024 17:31:57 +0000
Subject: [PATCH 724/852] Fix ECLint

---
 modules/local/aspera_cli/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/aspera_cli/main.nf b/modules/local/aspera_cli/main.nf
index 412c618a..de78a7b2 100644
--- a/modules/local/aspera_cli/main.nf
+++ b/modules/local/aspera_cli/main.nf
@@ -60,4 +60,4 @@ process ASPERA_CLI {
         END_VERSIONS
         """
     }
-}
\ No newline at end of file
+}

From 6cba93fdce634d4437e682f0179837ba3739fd16 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 29 Jan 2024 18:13:38 +0000
Subject: [PATCH 725/852] Fix pre-commit lint

---
 .devcontainer/devcontainer.json                      |  8 ++++----
 .github/workflows/download_pipeline.yml              |  2 +-
 .../local/multiqc_mappings_config/nextflow.config    |  2 +-
 modules/local/sra_ids_to_runinfo/nextflow.config     |  2 +-
 modules/local/sra_runinfo_to_ftp/nextflow.config     |  2 +-
 modules/local/synapse_get/nextflow.config            |  2 +-
 .../local/synapse_merge_samplesheet/nextflow.config  |  2 +-
 modules/local/synapse_show/nextflow.config           |  2 +-
 modules/local/synapse_to_samplesheet/nextflow.config |  2 +-
 .../nextflow.config                                  |  2 +-
 .../tests/main.nf.test                               |  2 +-
 .../tests/main.function.nf.test                      |  2 +-
 .../utils_nextflow_pipeline/tests/nextflow.config    |  2 +-
 .../tests/main.function.nf.test                      |  2 +-
 .../utils_nfcore_pipeline/tests/nextflow.config      |  2 +-
 .../utils_nfvalidation_plugin/tests/main.nf.test     |  2 +-
 workflows/sra/main.nf                                |  2 +-
 workflows/sra/nextflow.config                        |  2 +-
 .../sra/tests/sra_nf_core_pipeline_atacseq.nf.test   |  2 +-
 .../tests/sra_nf_core_pipeline_viralrecon.nf.test    |  2 +-
 workflows/sra/tests/sra_skip_fastq_download.nf.test  | 12 ++++++------
 workflows/synapse/nextflow.config                    |  2 +-
 22 files changed, 30 insertions(+), 30 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 4a9bc5c7..4ecfbfe3 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -18,11 +18,11 @@
                 "python.linting.flake8Path": "/opt/conda/bin/flake8",
                 "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
                 "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
-                "python.linting.pylintPath": "/opt/conda/bin/pylint",
+                "python.linting.pylintPath": "/opt/conda/bin/pylint"
             },
 
             // Add the IDs of extensions you want installed when the container is created.
-            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"],
-        },
-    },
+            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
+        }
+    }
 }
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 8611458a..8a330045 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -64,4 +64,4 @@ jobs:
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results 
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
diff --git a/modules/local/multiqc_mappings_config/nextflow.config b/modules/local/multiqc_mappings_config/nextflow.config
index e2382930..11c58341 100644
--- a/modules/local/multiqc_mappings_config/nextflow.config
+++ b/modules/local/multiqc_mappings_config/nextflow.config
@@ -6,4 +6,4 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/local/sra_ids_to_runinfo/nextflow.config b/modules/local/sra_ids_to_runinfo/nextflow.config
index 73da969a..9b9d0b16 100644
--- a/modules/local/sra_ids_to_runinfo/nextflow.config
+++ b/modules/local/sra_ids_to_runinfo/nextflow.config
@@ -5,4 +5,4 @@ process {
             enabled: false
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/local/sra_runinfo_to_ftp/nextflow.config b/modules/local/sra_runinfo_to_ftp/nextflow.config
index aee1848c..43263648 100644
--- a/modules/local/sra_runinfo_to_ftp/nextflow.config
+++ b/modules/local/sra_runinfo_to_ftp/nextflow.config
@@ -6,4 +6,4 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/local/synapse_get/nextflow.config b/modules/local/synapse_get/nextflow.config
index 869f80aa..9c42e741 100644
--- a/modules/local/synapse_get/nextflow.config
+++ b/modules/local/synapse_get/nextflow.config
@@ -13,4 +13,4 @@ process {
             ]
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/local/synapse_merge_samplesheet/nextflow.config b/modules/local/synapse_merge_samplesheet/nextflow.config
index 9befef9c..c94c53dd 100644
--- a/modules/local/synapse_merge_samplesheet/nextflow.config
+++ b/modules/local/synapse_merge_samplesheet/nextflow.config
@@ -6,4 +6,4 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/local/synapse_show/nextflow.config b/modules/local/synapse_show/nextflow.config
index a1864dfe..5b9167b3 100644
--- a/modules/local/synapse_show/nextflow.config
+++ b/modules/local/synapse_show/nextflow.config
@@ -6,4 +6,4 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/local/synapse_to_samplesheet/nextflow.config b/modules/local/synapse_to_samplesheet/nextflow.config
index b286c12c..83af86b6 100644
--- a/modules/local/synapse_to_samplesheet/nextflow.config
+++ b/modules/local/synapse_to_samplesheet/nextflow.config
@@ -5,4 +5,4 @@ process {
             enabled: false
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config
index b11c499f..de803a38 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config
@@ -1,2 +1,2 @@
 includeConfig '../../../modules/nf-core/sratools/prefetch/nextflow.config'
-includeConfig '../../../modules/nf-core/sratools/fasterqdump/nextflow.config'
\ No newline at end of file
+includeConfig '../../../modules/nf-core/sratools/fasterqdump/nextflow.config'
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
index 2f1d0835..9ff65074 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
@@ -4,7 +4,7 @@ nextflow_workflow {
     script "../main.nf"
     workflow "FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS"
     tag "FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS"
-    
+
     tag "CUSTOM_SRATOOLSNCBISETTINGS"
     tag "SRATOOLS_PREFETCH"
     tag "SRATOOLS_FASTERQDUMP"
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
index 8ed4310c..68718e4f 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
@@ -51,4 +51,4 @@ nextflow_function {
             )
         }
     }
-}
\ No newline at end of file
+}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
index 53574ffe..d0a926bf 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
@@ -6,4 +6,4 @@ manifest {
     nextflowVersion  = '!>=23.04.0'
     version         = '9.9.9'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
-}
\ No newline at end of file
+}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
index c176295d..f7ea05fc 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
@@ -111,4 +111,4 @@ nextflow_function {
             )
         }
     }
-}
\ No newline at end of file
+}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
index 53574ffe..d0a926bf 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
@@ -6,4 +6,4 @@ manifest {
     nextflowVersion  = '!>=23.04.0'
     version         = '9.9.9'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
-}
\ No newline at end of file
+}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
index 517ee54e..5784a33f 100644
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
@@ -197,4 +197,4 @@ nextflow_workflow {
             )
         }
     }
-}
\ No newline at end of file
+}
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 62d8c577..b119dcbe 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -119,7 +119,7 @@ workflow SRA {
         params.nf_core_rnaseq_strandedness ?: 'auto',
         params.sample_mapping_fields
     )
-  
+
     // Merge samplesheets and mapping files across all samples
     SRA_TO_SAMPLESHEET
         .out
diff --git a/workflows/sra/nextflow.config b/workflows/sra/nextflow.config
index a48bcb73..21b374c5 100644
--- a/workflows/sra/nextflow.config
+++ b/workflows/sra/nextflow.config
@@ -4,4 +4,4 @@ includeConfig "../../modules/local/sra_ids_to_runinfo/nextflow.config"
 includeConfig "../../modules/local/sra_runinfo_to_ftp/nextflow.config"
 includeConfig "../../modules/local/sra_to_samplesheet/nextflow.config"
 includeConfig "../../modules/nf-core/sratools/prefetch/nextflow.config"
-includeConfig "../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config"
\ No newline at end of file
+includeConfig "../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config"
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index d792e09f..509d89b0 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -3,7 +3,7 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
-    
+
     // Subworkflows
     tag "SRA"
 
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index 89f8f370..9e991a03 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -32,7 +32,7 @@ nextflow_workflow {
             assert workflow.success
 
             assertAll(
-                { 
+                {
                     with(workflow.out.samplesheet) {
                         assert path(get(0)).readLines().size() == 4
                         assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index b3fdd883..f9a79e15 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -32,25 +32,25 @@ nextflow_workflow {
             assert workflow.success
 
             assertAll(
-                { 
+                {
                     with(workflow.out.samplesheet) {
                         assert path(get(0)).readLines().size() == 4
                         assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
                         assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
                         assert path(get(0)).text.contains('Illumina HiSeq 2500')
-                    } 
+                    }
                 },
-                { 
+                {
                     with(workflow.out.mappings) {
                         assert path(get(0)).readLines().size() == 4
                         assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
                         assert path(get(0)).text.contains('Illumina HiSeq 2500')
-                    } 
+                    }
                 },
-                { 
+                {
                     with(workflow.out.sample_mappings) {
                         assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
-                    } 
+                    }
                 }
             )
         }
diff --git a/workflows/synapse/nextflow.config b/workflows/synapse/nextflow.config
index 01b71558..ad9c69ed 100644
--- a/workflows/synapse/nextflow.config
+++ b/workflows/synapse/nextflow.config
@@ -2,4 +2,4 @@ includeConfig "../../modules/local/synapse_get/nextflow.config"
 includeConfig "../../modules/local/synapse_to_samplesheet/nextflow.config"
 includeConfig "../../modules/local/synapse_list/nextflow.config"
 includeConfig "../../modules/local/synapse_merge_samplesheet/nextflow.config"
-includeConfig "../../modules/local/synapse_show/nextflow.config"
\ No newline at end of file
+includeConfig "../../modules/local/synapse_show/nextflow.config"

From 9d8b0f392aea60b5029909be55d3148c6146e50f Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 29 Jan 2024 19:21:23 +0000
Subject: [PATCH 726/852] Delete redundant tags.yml files

---
 subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml   | 2 --
 subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml     | 2 --
 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml | 2 --
 3 files changed, 6 deletions(-)
 delete mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
 delete mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
 delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml

diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
deleted file mode 100644
index f8476112..00000000
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nextflow_pipeline:
-  - subworkflows/nf-core/utils_nextflow_pipeline/**
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
deleted file mode 100644
index ac8523c9..00000000
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nfcore_pipeline:
-  - subworkflows/nf-core/utils_nfcore_pipeline/**
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
deleted file mode 100644
index 60b1cfff..00000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nfvalidation_plugin:
-  - subworkflows/nf-core/utils_nfvalidation_plugin/**

From 5ff5d2bcd18413c535b43772f00a2958232c421e Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 29 Jan 2024 19:39:08 +0000
Subject: [PATCH 727/852] Remove redundant tags from nf-core subworkflows

---
 .../utils_nextflow_pipeline/tests/main.function.nf.test    | 4 +---
 .../utils_nextflow_pipeline/tests/main.workflow.nf.test    | 4 +---
 .../utils_nfcore_pipeline/tests/main.function.nf.test      | 5 +----
 .../utils_nfcore_pipeline/tests/main.workflow.nf.test      | 5 +----
 .../nf-core/utils_nfvalidation_plugin/tests/main.nf.test   | 7 +------
 5 files changed, 5 insertions(+), 20 deletions(-)

diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
index 68718e4f..e49d617f 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
@@ -4,9 +4,7 @@ nextflow_function {
     name "Test Functions"
     script "subworkflows/nf-core/utils_nextflow_pipeline/main.nf"
     config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config"
-    tag 'subworkflows'
-    tag 'utils_nextflow_pipeline'
-    tag 'subworkflows/utils_nextflow_pipeline'
+    tag "UTILS_NEXTFLOW_PIPELINE"
 
     test("Test Function getWorkflowVersion") {
 
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
index f7c54bc6..b1b3a2c3 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -4,9 +4,7 @@ nextflow_workflow {
     script "../main.nf"
     config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config"
     workflow "UTILS_NEXTFLOW_PIPELINE"
-    tag 'subworkflows'
-    tag 'utils_nextflow_pipeline'
-    tag 'subworkflows/utils_nextflow_pipeline'
+    tag "UTILS_NEXTFLOW_PIPELINE"
 
     test("Should run no inputs") {
 
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
index f7ea05fc..74577b26 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
@@ -4,10 +4,7 @@ nextflow_function {
     name "Test Functions"
     script "../main.nf"
     config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
-    tag "subworkflows"
-    tag "subworkflows_nfcore"
-    tag "utils_nfcore_pipeline"
-    tag "subworkflows/utils_nfcore_pipeline"
+    tag "UTILS_NFCORE_PIPELINE"
 
     test("Test Function checkConfigProvided") {
 
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
index c5f7776a..cb7376c0 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
@@ -4,10 +4,7 @@ nextflow_workflow {
     script "../main.nf"
     config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
     workflow "UTILS_NFCORE_PIPELINE"
-    tag "subworkflows"
-    tag "subworkflows_nfcore"
-    tag "utils_nfcore_pipeline"
-    tag "subworkflows/utils_nfcore_pipeline"
+    tag "UTILS_NFCORE_PIPELINE"
 
     test("Should run without failures") {
 
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
index 5784a33f..b13e7e6e 100644
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
@@ -3,12 +3,7 @@ nextflow_workflow {
     name "Test Workflow UTILS_NFVALIDATION_PLUGIN"
     script "../main.nf"
     workflow "UTILS_NFVALIDATION_PLUGIN"
-    tag "subworkflows"
-    tag "subworkflows_nfcore"
-    tag "plugin/nf-validation"
-    tag "'plugin/nf-validation'"
-    tag "utils_nfvalidation_plugin"
-    tag "subworkflows/utils_nfvalidation_plugin"
+    tag "UTILS_NFVALIDATION_PLUGIN"
 
     test("Should run nothing") {
 

From 963dff2f4ac1790d6c6a710396d5c9d562451165 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 29 Jan 2024 19:48:03 +0000
Subject: [PATCH 728/852] Update CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d512d75c..ec2a25a1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -27,6 +27,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #246](https://github.com/nf-core/fetchngs/pull/246) - Handle dark/light mode for logo in GitHub README properly
 - [PR #248](https://github.com/nf-core/fetchngs/pull/248) - Update pipeline level test data path to use mirror on s3
 - [PR #249](https://github.com/nf-core/fetchngs/pull/249) - Update modules which includes absolute paths for test data, making module level test compatible within the pipeline.
+- [PR #257](https://github.com/nf-core/fetchngs/pull/257) - Template update for nf-core/tools v2.12
 
 ### Software dependencies
 

From 888597053131b9f60c0340f6b5dadc3cbc380af7 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 30 Jan 2024 10:09:18 +0000
Subject: [PATCH 729/852] Update usage docs

---
 docs/usage.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/docs/usage.md b/docs/usage.md
index 0cfb95d8..5c244223 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -66,6 +66,10 @@ You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g.
 
 From v1.9 of this pipeline the default `strandedness` in the output samplesheet will be set to `auto` when using `--nf_core_pipeline rnaseq`. This will only work with v3.10 onwards of nf-core/rnaseq which permits the auto-detection of strandedness during the pipeline execution. You can change this behaviour with the `--nf_core_rnaseq_strandedness` parameter which is set to `auto` by default.
 
+### Bypass Aspera data download
+
+If the appropriate download links are available, the pipeline uses the Aspera CLI by default to download FastQ files. If you are having issues and prefer to use FTP or sra-tools instead, you can use the [`--force_ftp_download`](https://nf-co.re/fetchngs/parameters#force_ftp_download) and [`--force_sratools_download`](https://nf-co.re/fetchngs/parameters#force_sratools_download) parameters, respectively.
+
 ### Bypass `FTP` data download
 
 If FTP connections are blocked on your network use the [`--force_sratools_download`](https://nf-co.re/fetchngs/parameters#force_sratools_download) parameter to force the pipeline to download data using sra-tools instead of the ENA FTP.

From 1f42b059a66ea22d163fb602b257125f1f25c464 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 30 Jan 2024 10:15:43 +0000
Subject: [PATCH 730/852] Fix pre-commit lint

---
 workflows/sra/main.nf | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 197cd658..6c657a68 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -55,7 +55,7 @@ workflow SRA {
         .out
         .tsv
         .splitCsv(header:true, sep:'\t')
-        .map { 
+        .map {
             meta ->
                 def meta_clone = meta.clone()
                 meta_clone.single_end = meta_clone.single_end.toBoolean()
@@ -68,15 +68,15 @@ workflow SRA {
 
         ch_sra_metadata
             .branch {
-                meta ->                    
+                meta ->
                     def download_method = 'aspera'
                     if (!meta.fastq_aspera || params.force_ftp_download) {
-                        if (meta.fastq_1) { 
+                        if (meta.fastq_1) {
                             download_method = 'ftp'
                         }
                     }
-                    if ((!meta.fastq_aspera && !meta.fastq_1) || params.force_sratools_download) { 
-                        download_method = 'sratools' 
+                    if ((!meta.fastq_aspera && !meta.fastq_1) || params.force_sratools_download) {
+                        download_method = 'sratools'
                     }
 
                     aspera: download_method == 'aspera'

From 84c206602a0f99a0120b0f867e4397b2bfb79600 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 30 Jan 2024 10:54:04 +0000
Subject: [PATCH 731/852] Add comment for contents of meta.fastq_aspera

---
 workflows/sra/main.nf | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 6c657a68..35ae18dc 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -70,6 +70,9 @@ workflow SRA {
             .branch {
                 meta ->
                     def download_method = 'aspera'
+                    // meta.fastq_aspera is a metadata string with ENA fasp links supported by Aspera
+                        // For single-end: 'fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz'
+                        // For paired-end: 'fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz'
                     if (!meta.fastq_aspera || params.force_ftp_download) {
                         if (meta.fastq_1) {
                             download_method = 'ftp'

From e33eef40f27689b7f768d1525122d4a33e3c288d Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 30 Jan 2024 11:48:03 +0000
Subject: [PATCH 732/852] Update usage docs for samples with more than 2 FastQ
 files

---
 docs/usage.md | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/docs/usage.md b/docs/usage.md
index 5c244223..42d134f3 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -66,6 +66,29 @@ You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g.
 
 From v1.9 of this pipeline the default `strandedness` in the output samplesheet will be set to `auto` when using `--nf_core_pipeline rnaseq`. This will only work with v3.10 onwards of nf-core/rnaseq which permits the auto-detection of strandedness during the pipeline execution. You can change this behaviour with the `--nf_core_rnaseq_strandedness` parameter which is set to `auto` by default.
 
+### Accessions with more than 2 FastQ files
+
+Using `SRR9320616` as an example, if we run the pipeline with default options to download via Aspera/FTP the ENA API indicates that this sample is associated with a single FastQ file:
+
+```
+run_accession	experiment_accession	sample_accession	secondary_sample_accession	study_accession	secondary_study_accession	submission_accession	run_alias	experiment_alias	sample_alias	study_alias	library_layout	library_selection	library_source	library_strategy	library_name	instrument_model	instrument_platform	base_count	read_count	tax_id	scientific_name	sample_title	experiment_title	study_title	sample_description	fastq_md5	fastq_bytes	fastq_ftp	fastq_galaxy	fastq_aspera
+SRR9320616	SRX6088086	SAMN12086751	SRS4989433	PRJNA549480	SRP201778	SRA900583	GSM3895942_r1	GSM3895942	GSM3895942	GSE132901	PAIRED	cDNA	TRANSCRIPTOMIC	RNA-Seq		Illumina HiSeq 2500	ILLUMINA	11857688850	120996825	10090	Mus musculus	Old 3 Kidney	Illumina HiSeq 2500 sequencing: GSM3895942: Old 3 Kidney Mus musculus RNA-Seq	A murine aging cell atlas reveals cell identity and tissue-specific trajectories of aging	Old 3 Kidney	98c939bbae1a1fcf9624905516485b67	7763114613	ftp.sra.ebi.ac.uk/vol1/fastq/SRR932/006/SRR9320616/SRR9320616.fastq.gz	ftp.sra.ebi.ac.uk/vol1/fastq/SRR932/006/SRR9320616/SRR9320616.fastq.gz	fasp.sra.ebi.ac.uk:/vol1/fastq/SRR932/006/SRR9320616/SRR9320616.fastq.gz
+```
+
+However, this sample actually has 2 additional FastQ files that are flagged as technical and can only be obtained by running sra-tools. This is particularly important for certain preps like 10x and others using UMI barcodes.
+
+```
+$ fasterq-dump --threads 6 --split-files --include-technical SRR9320616 --outfile SRR9320616.fastq --progress
+
+SRR9320616_1.fastq
+SRR9320616_2.fastq
+SRR9320616_3.fastq
+```
+
+This highlights that there is a discrepancy between the read data hosted on the ENA API and what can actually be fetched from sra-tools, where the latter seems to be the source of truth. If you anticipate that you may have more than 2 FastQ files per sample, it is recommended to use this pipeline with the `--force_sratools_download` parameter.
+
+See [issue #260](https://github.com/nf-core/fetchngs/issues/260) for more details.
+
 ### Bypass Aspera data download
 
 If the appropriate download links are available, the pipeline uses the Aspera CLI by default to download FastQ files. If you are having issues and prefer to use FTP or sra-tools instead, you can use the [`--force_ftp_download`](https://nf-co.re/fetchngs/parameters#force_ftp_download) and [`--force_sratools_download`](https://nf-co.re/fetchngs/parameters#force_sratools_download) parameters, respectively.

From b7979a30b1d50ad9ffa888258a0433134a0b2c01 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 30 Jan 2024 17:36:02 +0000
Subject: [PATCH 733/852] Revert sratools fasterqdump version to fix #221

---
 modules.json                                  |  3 +-
 .../sratools/fasterqdump/environment.yml      |  2 +-
 modules/nf-core/sratools/fasterqdump/main.nf  |  4 +-
 .../fasterqdump/sratools-fasterqdump.diff     | 63 +++++++++++++++++++
 4 files changed, 68 insertions(+), 4 deletions(-)
 create mode 100644 modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff

diff --git a/modules.json b/modules.json
index 1ddaa1fb..9190e3f5 100644
--- a/modules.json
+++ b/modules.json
@@ -13,7 +13,8 @@
                     "sratools/fasterqdump": {
                         "branch": "master",
                         "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620",
-                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
+                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"],
+                        "patch": "modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff"
                     },
                     "sratools/prefetch": {
                         "branch": "master",
diff --git a/modules/nf-core/sratools/fasterqdump/environment.yml b/modules/nf-core/sratools/fasterqdump/environment.yml
index 4011b691..dd0faa56 100644
--- a/modules/nf-core/sratools/fasterqdump/environment.yml
+++ b/modules/nf-core/sratools/fasterqdump/environment.yml
@@ -4,5 +4,5 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::sra-tools=3.0.8
+  - bioconda::sra-tools=2.11.0
   - conda-forge::pigz=2.6
diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf
index d4ddf268..e7cf157a 100644
--- a/modules/nf-core/sratools/fasterqdump/main.nf
+++ b/modules/nf-core/sratools/fasterqdump/main.nf
@@ -4,8 +4,8 @@ process SRATOOLS_FASTERQDUMP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:2f4a4c900edd6801ff0068c2b3048b4459d119eb-0' :
-        'biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:2f4a4c900edd6801ff0068c2b3048b4459d119eb-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' :
+        'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' }"
 
     input:
     tuple val(meta), path(sra)
diff --git a/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff b/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff
new file mode 100644
index 00000000..1fb8cbf4
--- /dev/null
+++ b/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff
@@ -0,0 +1,63 @@
+Changes in module 'nf-core/sratools/fasterqdump'
+--- modules/nf-core/sratools/fasterqdump/main.nf
++++ modules/nf-core/sratools/fasterqdump/main.nf
+@@ -4,8 +4,8 @@
+ 
+     conda "${moduleDir}/environment.yml"
+     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+-        'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:2f4a4c900edd6801ff0068c2b3048b4459d119eb-0' :
+-        'biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:2f4a4c900edd6801ff0068c2b3048b4459d119eb-0' }"
++        'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' :
++        'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' }"
+ 
+     input:
+     tuple val(meta), path(sra)
+
+--- /dev/null
++++ modules/nf-core/sratools/fasterqdump/nextflow.config
+@@ -0,0 +1,10 @@
++process {
++    withName: SRATOOLS_FASTERQDUMP {
++        ext.args = '--split-files --include-technical'
++        publishDir = [
++            path: { "${params.outdir}/fastq" },
++            mode: params.publish_dir_mode,
++            pattern: "*.fastq.gz"
++        ]
++    }
++}
+--- modules/nf-core/sratools/fasterqdump/environment.yml
++++ modules/nf-core/sratools/fasterqdump/environment.yml
+@@ -4,5 +4,5 @@
+   - bioconda
+   - defaults
+ dependencies:
+-  - bioconda::sra-tools=3.0.8
++  - bioconda::sra-tools=2.11.0
+   - conda-forge::pigz=2.6
+
+--- modules/nf-core/sratools/fasterqdump/tests/main.nf.test
++++ modules/nf-core/sratools/fasterqdump/tests/main.nf.test
+@@ -3,11 +3,9 @@
+     script "../main.nf"
+     config "./nextflow.config"
+     process "SRATOOLS_FASTERQDUMP"
+-    tag "modules"
+-    tag "modules_nfcore"
+-    tag "untar"
+-    tag "sratools"
+-    tag "sratools/fasterqdump"
++    tag "SRATOOLS_FASTERQDUMP"
++
++    tag "UNTAR"
+ 
+     test("Single-end") {
+ 
+
+--- modules/nf-core/sratools/fasterqdump/tests/tags.yml
++++ /dev/null
+@@ -1,2 +0,0 @@
+-sratools/fasterqdump:
+-  - modules/nf-core/sratools/fasterqdump/**
+
+************************************************************

From 7802ebc55aa05158f773e58608474901c183f6e9 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 30 Jan 2024 17:47:20 +0000
Subject: [PATCH 734/852] Update CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1476a599..a91320c1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -31,6 +31,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #257](https://github.com/nf-core/fetchngs/pull/257) - Template update for nf-core/tools v2.12
 - [PR #258](https://github.com/nf-core/fetchngs/pull/258) - Fixes for [PR #253](https://github.com/nf-core/fetchngs/pull/253)
 - [PR #259](https://github.com/nf-core/fetchngs/pull/259) - Add Aspera CLI download support to pipeline ([#68](https://github.com/nf-core/fetchngs/issues/68))
+- [PR #261](https://github.com/nf-core/fetchngs/pull/261) - Revert sratools fasterqdump version ([#221](https://github.com/nf-core/fetchngs/issues/221))
 
 ### Software dependencies
 

From 56a16a34e24843103d8b861eb8f6786ef5e05aac Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 30 Jan 2024 18:08:28 +0000
Subject: [PATCH 735/852] Update snapshots for new version of sratools

---
 .../fasterqdump/tests/main.nf.test.snap       | 12 +++++------
 .../tests/main.nf.test.snap                   | 20 +++++++++----------
 2 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
index e2cc2612..0e590311 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
+                    "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295"
                 ],
                 "reads": [
                     [
@@ -24,11 +24,11 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
+                    "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295"
                 ]
             }
         ],
-        "timestamp": "2024-01-09T12:55:00.629261"
+        "timestamp": "2024-01-30T18:02:53.958171"
     },
     "Paired-end": {
         "content": [
@@ -46,7 +46,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
+                    "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295"
                 ],
                 "reads": [
                     [
@@ -61,10 +61,10 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
+                    "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295"
                 ]
             }
         ],
-        "timestamp": "2024-01-09T12:55:34.40299"
+        "timestamp": "2024-01-30T18:03:20.841426"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
index 2123d3f7..63ba2e99 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
@@ -3,7 +3,7 @@
         "content": [
             19996
         ],
-        "timestamp": "2024-01-11T11:52:21.464438219"
+        "timestamp": "2024-01-30T18:05:15.684489"
     },
     "test_pe_reads_2_lines": {
         "content": [
@@ -16,29 +16,29 @@
                 "GTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACG"
             ]
         ],
-        "timestamp": "2024-01-11T11:52:21.437261931"
+        "timestamp": "2024-01-30T18:05:15.670447"
     },
     "test_pe_reads_2_size": {
         "content": [
             2011460
         ],
-        "timestamp": "2024-01-11T11:52:21.44875993"
+        "timestamp": "2024-01-30T18:05:15.675771"
     },
     "versions": {
         "content": [
             [
                 "versions.yml:md5,1a2218ff913fc33408bffccb081b5048",
-                "versions.yml:md5,98d78bba9f3da39a0b7db6e9c7dcc224",
-                "versions.yml:md5,9c558ff624585a6eee82a19c8c0136db"
+                "versions.yml:md5,2f3b3a13b36dabf13f09327613d5558d",
+                "versions.yml:md5,98d78bba9f3da39a0b7db6e9c7dcc224"
             ]
         ],
-        "timestamp": "2024-01-11T12:11:06.731937323"
+        "timestamp": "2024-01-30T18:05:15.692165"
     },
     "test_pe_reads_1_size": {
         "content": [
-            2011460
+            2013376
         ],
-        "timestamp": "2024-01-11T11:52:21.428267242"
+        "timestamp": "2024-01-30T18:05:15.666916"
     },
     "test_se_reads_lines": {
         "content": [
@@ -51,7 +51,7 @@
                 "ACGCAGGTGCCAGCAGCCGCGGTAATACGGAGGGAGCTAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGCTTTTCAAGTCAGGGGTGGAAATACCCGGGGCCGTCAACCCGACCG"
             ]
         ],
-        "timestamp": "2024-01-11T11:52:21.45496474"
+        "timestamp": "2024-01-30T18:05:15.679779"
     },
     "test_pe_reads_1_lines": {
         "content": [
@@ -64,6 +64,6 @@
                 "CGTACGAGCACGTCGCGAACCTGTAAAACAGGCAAACTGAGTTGGACGTGTGTTTTCTCGTTGAAACCAGGGACAAGGCTCTCCATCTTACCTTTCGGTCACACCCGGACGAAACCTAGATGTGCTGATGATCGGCTGCAACACGGACGAAACCGTAAGCAGCCTGCAGAAGATAGACGAGTTACTCGTGTCCTGTCAACGACAGTAATTAGTTATTAATTATACTGCGTGAGTGCAC"
             ]
         ],
-        "timestamp": "2024-01-11T11:52:21.400169604"
+        "timestamp": "2024-01-30T18:05:15.654112"
     }
 }
\ No newline at end of file

From a56d4fad3c469284ffc71300ce5b9f2cfab6d994 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Wed, 31 Jan 2024 10:04:56 +0000
Subject: [PATCH 736/852] Update nf-test to v0.8.4

---
 .github/workflows/ci.yml | 2 +-
 CHANGELOG.md             | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 12343148..1395c844 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -13,7 +13,7 @@ on:
 
 env:
   NXF_ANSI_LOG: false
-  NFT_VER: "0.8.3"
+  NFT_VER: "0.8.4"
   NFT_WORKDIR: "~"
   NFT_DIFF: "pdiff"
   NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1476a599..070a6364 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -31,6 +31,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #257](https://github.com/nf-core/fetchngs/pull/257) - Template update for nf-core/tools v2.12
 - [PR #258](https://github.com/nf-core/fetchngs/pull/258) - Fixes for [PR #253](https://github.com/nf-core/fetchngs/pull/253)
 - [PR #259](https://github.com/nf-core/fetchngs/pull/259) - Add Aspera CLI download support to pipeline ([#68](https://github.com/nf-core/fetchngs/issues/68))
+- [PR ###](https://github.com/nf-core/fetchngs/pull/) - Use nf-test version v0.8.4
 
 ### Software dependencies
 

From 9974e638a4515cb403bf19d508c0e3b8f899685f Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Wed, 31 Jan 2024 10:14:17 +0000
Subject: [PATCH 737/852] Remove implicit tags

---
 CHANGELOG.md                                                  | 2 +-
 modules/local/aspera_cli/tests/main.nf.test                   | 2 --
 modules/local/multiqc_mappings_config/tests/main.nf.test      | 2 --
 modules/local/sra_fastq_ftp/tests/main.nf.test                | 2 --
 modules/local/sra_ids_to_runinfo/tests/main.nf.test           | 2 --
 modules/local/sra_runinfo_to_ftp/tests/main.nf.test           | 2 --
 modules/local/sra_to_samplesheet/tests/main.nf.test           | 2 --
 .../nf-core/custom/sratoolsncbisettings/tests/main.nf.test    | 4 +---
 modules/nf-core/sratools/fasterqdump/tests/main.nf.test       | 1 -
 modules/nf-core/sratools/prefetch/tests/main.nf.test          | 1 -
 modules/nf-core/untar/tests/main.nf.test                      | 3 +--
 .../tests/main.workflow_pipeline_completion.test              | 1 -
 .../tests/main.workflow_pipeline_initialisation.nf.test       | 1 -
 .../tests/main.nf.test                                        | 1 -
 .../utils_nextflow_pipeline/tests/main.workflow.nf.test       | 1 -
 .../nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test | 1 -
 .../nf-core/utils_nfvalidation_plugin/tests/main.nf.test      | 1 -
 workflows/sra/tests/main.nf.test                              | 3 +--
 18 files changed, 4 insertions(+), 28 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 070a6364..a74c68b1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -31,7 +31,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #257](https://github.com/nf-core/fetchngs/pull/257) - Template update for nf-core/tools v2.12
 - [PR #258](https://github.com/nf-core/fetchngs/pull/258) - Fixes for [PR #253](https://github.com/nf-core/fetchngs/pull/253)
 - [PR #259](https://github.com/nf-core/fetchngs/pull/259) - Add Aspera CLI download support to pipeline ([#68](https://github.com/nf-core/fetchngs/issues/68))
-- [PR ###](https://github.com/nf-core/fetchngs/pull/) - Use nf-test version v0.8.4
+- [PR #262](https://github.com/nf-core/fetchngs/pull/262) - Use nf-test version v0.8.4
 
 ### Software dependencies
 
diff --git a/modules/local/aspera_cli/tests/main.nf.test b/modules/local/aspera_cli/tests/main.nf.test
index 3858e2c3..b2f5f1bd 100644
--- a/modules/local/aspera_cli/tests/main.nf.test
+++ b/modules/local/aspera_cli/tests/main.nf.test
@@ -4,8 +4,6 @@ nextflow_process {
     script "../main.nf"
     process "ASPERA_CLI"
 
-    tag "ASPERA_CLI"
-
     test("Should run without failures") {
 
         when {
diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test
index e782116e..106f3248 100644
--- a/modules/local/multiqc_mappings_config/tests/main.nf.test
+++ b/modules/local/multiqc_mappings_config/tests/main.nf.test
@@ -4,8 +4,6 @@ nextflow_process {
     script "../main.nf"
     process "MULTIQC_MAPPINGS_CONFIG"
 
-    tag "MULTIQC_MAPPINGS_CONFIG"
-
     test("Should run without failures") {
 
         when {
diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test
index 27329cd9..f58aaae2 100644
--- a/modules/local/sra_fastq_ftp/tests/main.nf.test
+++ b/modules/local/sra_fastq_ftp/tests/main.nf.test
@@ -4,8 +4,6 @@ nextflow_process {
     script "../main.nf"
     process "SRA_FASTQ_FTP"
 
-    tag "SRA_FASTQ_FTP"
-
     test("Should run without failures") {
 
         when {
diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test
index cc0d6de9..2e510ea1 100644
--- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test
+++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test
@@ -4,8 +4,6 @@ nextflow_process {
     script "../main.nf"
     process "SRA_IDS_TO_RUNINFO"
 
-    tag "SRA_IDS_TO_RUNINFO"
-
     test("Should run without failures") {
 
         when {
diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
index 1060b394..4b03249c 100644
--- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
+++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
@@ -4,8 +4,6 @@ nextflow_process {
     script "../main.nf"
     process "SRA_RUNINFO_TO_FTP"
 
-    tag "SRA_RUNINFO_TO_FTP"
-
     test("Should run without failures") {
 
         when {
diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test
index 999864b8..4458858e 100644
--- a/modules/local/sra_to_samplesheet/tests/main.nf.test
+++ b/modules/local/sra_to_samplesheet/tests/main.nf.test
@@ -4,8 +4,6 @@ nextflow_process {
     script "../main.nf"
     process "SRA_TO_SAMPLESHEET"
 
-    tag "SRA_TO_SAMPLESHEET"
-
     test("Should run without failures") {
 
         when {
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
index 6fde77c6..11899742 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
+++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
@@ -4,9 +4,7 @@ nextflow_process {
     script "../main.nf"
     process "CUSTOM_SRATOOLSNCBISETTINGS"
     config "modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config"
-
-    tag "CUSTOM_SRATOOLSNCBISETTINGS"
-
+    
     test("Should run without failures") {
 
         when {
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
index b3107336..c64f6fc1 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
@@ -3,7 +3,6 @@ nextflow_process {
     script "../main.nf"
     config "./nextflow.config"
     process "SRATOOLS_FASTERQDUMP"
-    tag "SRATOOLS_FASTERQDUMP"
 
     tag "UNTAR"
 
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test
index 7319108c..b0f5ffa2 100644
--- a/modules/nf-core/sratools/prefetch/tests/main.nf.test
+++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test
@@ -2,7 +2,6 @@ nextflow_process {
     name "Test Process SRATOOLS_PREFETCH"
     script "../main.nf"
     process "SRATOOLS_PREFETCH"
-    tag "SRATOOLS_PREFETCH"
 
     test("sratools/prefetch") {
 
diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test
index 0eb25d3c..05134043 100644
--- a/modules/nf-core/untar/tests/main.nf.test
+++ b/modules/nf-core/untar/tests/main.nf.test
@@ -3,8 +3,7 @@ nextflow_process {
     name "Test Process UNTAR"
     script "../main.nf"
     process "UNTAR"
-    tag "UNTAR"
-
+    
     test("test_untar") {
 
         when {
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test
index a1814bf6..cfbfab4c 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test
@@ -3,7 +3,6 @@ nextflow_workflow {
     name "Test Workflow PIPELINE_COMPLETION"
     script "subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf"
     workflow "PIPELINE_COMPLETION"
-    tag "PIPELINE_COMPLETION"
 
     test("Should run") {
 
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
index d8dc3963..611eaee7 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
@@ -3,7 +3,6 @@ nextflow_workflow {
     name "Test Workflow PIPELINE_INITIALISATION"
     script "subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf"
     workflow "PIPELINE_INITIALISATION"
-    tag 'PIPELINE_INITIALISATION'
 
     test("Should run") {
 
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
index 9ff65074..7293a792 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
@@ -3,7 +3,6 @@ nextflow_workflow {
     name "Test workflow: fastq_download_prefetch_fasterqdump_sratools/main.nf"
     script "../main.nf"
     workflow "FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS"
-    tag "FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS"
 
     tag "CUSTOM_SRATOOLSNCBISETTINGS"
     tag "SRATOOLS_PREFETCH"
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
index b1b3a2c3..94e7198c 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -4,7 +4,6 @@ nextflow_workflow {
     script "../main.nf"
     config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config"
     workflow "UTILS_NEXTFLOW_PIPELINE"
-    tag "UTILS_NEXTFLOW_PIPELINE"
 
     test("Should run no inputs") {
 
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
index cb7376c0..3df54055 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
@@ -4,7 +4,6 @@ nextflow_workflow {
     script "../main.nf"
     config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
     workflow "UTILS_NFCORE_PIPELINE"
-    tag "UTILS_NFCORE_PIPELINE"
 
     test("Should run without failures") {
 
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
index b13e7e6e..5649654e 100644
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
@@ -3,7 +3,6 @@ nextflow_workflow {
     name "Test Workflow UTILS_NFVALIDATION_PLUGIN"
     script "../main.nf"
     workflow "UTILS_NFVALIDATION_PLUGIN"
-    tag "UTILS_NFVALIDATION_PLUGIN"
 
     test("Should run nothing") {
 
diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 062d6886..7ad22a18 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -3,8 +3,7 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
-    tag "SRA"
-
+    
     // Dependencies
     tag "MULTIQC_MAPPINGS_CONFIG"
     tag "ASPERA_CLI"

From df2ee5b9dd7dc0dfa91eab1997c1ef99f19c06cb Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Wed, 31 Jan 2024 10:34:57 +0000
Subject: [PATCH 738/852] lint fix

---
 workflows/sra/tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 7ad22a18..c08f345a 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -3,7 +3,7 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
-    
+
     // Dependencies
     tag "MULTIQC_MAPPINGS_CONFIG"
     tag "ASPERA_CLI"

From 01ee6cc5a90a41d158383ac0466d0bee0b2a86ba Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Wed, 31 Jan 2024 11:09:11 +0000
Subject: [PATCH 739/852] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a74c68b1..c4ec2323 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -31,7 +31,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #257](https://github.com/nf-core/fetchngs/pull/257) - Template update for nf-core/tools v2.12
 - [PR #258](https://github.com/nf-core/fetchngs/pull/258) - Fixes for [PR #253](https://github.com/nf-core/fetchngs/pull/253)
 - [PR #259](https://github.com/nf-core/fetchngs/pull/259) - Add Aspera CLI download support to pipeline ([#68](https://github.com/nf-core/fetchngs/issues/68))
-- [PR #262](https://github.com/nf-core/fetchngs/pull/262) - Use nf-test version v0.8.4
+- [PR #262](https://github.com/nf-core/fetchngs/pull/262) - Use nf-test version v0.8.4 and remove implicit tags
 
 ### Software dependencies
 

From 3c31d5ef251a34e6daa1c8b650377f4a0a8038fa Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 31 Jan 2024 13:01:49 +0000
Subject: [PATCH 740/852] Rename utils_nfcore_fetchngs_pipeline subworkflow and
 fix tags

---
 ...completion.test => main.workflow_pipeline_completion.nf.test} | 1 +
 .../tests/main.workflow_pipeline_initialisation.nf.test          | 1 +
 2 files changed, 2 insertions(+)
 rename subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/{main.workflow_pipeline_completion.test => main.workflow_pipeline_completion.nf.test} (96%)

diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.nf.test
similarity index 96%
rename from subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test
rename to subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.nf.test
index cfbfab4c..b41fca23 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.nf.test
@@ -3,6 +3,7 @@ nextflow_workflow {
     name "Test Workflow PIPELINE_COMPLETION"
     script "subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf"
     workflow "PIPELINE_COMPLETION"
+    tag "UTILS_NFCORE_FETCHNGS_PIPELINE"
 
     test("Should run") {
 
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
index 611eaee7..3d107f3c 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
@@ -3,6 +3,7 @@ nextflow_workflow {
     name "Test Workflow PIPELINE_INITIALISATION"
     script "subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf"
     workflow "PIPELINE_INITIALISATION"
+    tag "UTILS_NFCORE_FETCHNGS_PIPELINE"
 
     test("Should run") {
 

From f7e2a11272a6a3334aebdf447b73d0275647f289 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 31 Jan 2024 21:04:09 +0000
Subject: [PATCH 741/852] Update workflow tags

---
 workflows/sra/tests/main.nf.test                      |  6 +++---
 .../sra/tests/sra_custom_ena_metadata_fields.nf.test  | 11 ++++-------
 .../sra/tests/sra_force_sratools_download.nf.test     | 10 ++++------
 .../sra/tests/sra_nf_core_pipeline_atacseq.nf.test    | 11 ++++-------
 .../sra/tests/sra_nf_core_pipeline_rnaseq.nf.test     | 11 ++++-------
 .../tests/sra_nf_core_pipeline_taxprofiler.nf.test    | 11 ++++-------
 .../sra/tests/sra_nf_core_pipeline_viralrecon.nf.test | 11 ++++-------
 workflows/sra/tests/sra_skip_fastq_download.nf.test   |  9 +++------
 8 files changed, 30 insertions(+), 50 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index c08f345a..69ad7f42 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -3,14 +3,14 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
+    tag "SRA_DEFAULT"
 
     // Dependencies
-    tag "MULTIQC_MAPPINGS_CONFIG"
-    tag "ASPERA_CLI"
-    tag "SRA_FASTQ_FTP"
     tag "SRA_IDS_TO_RUNINFO"
     tag "SRA_RUNINFO_TO_FTP"
+    tag "ASPERA_CLI"
     tag "SRA_TO_SAMPLESHEET"
+    tag "MULTIQC_MAPPINGS_CONFIG"
 
     test("Parameters: default") {
 
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index 5fd4882b..98d1432d 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -3,17 +3,14 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
+    tag "SRA_CUSTOM_ENA_METADATA_FIELDS"
 
-    // Subworkflows
-    tag "SRA"
-
-    // Modules
-    tag "MULTIQC_MAPPINGS_CONFIG"
-    tag "ASPERA_CLI"
-    tag "SRA_FASTQ_FTP"
+    // Dependencies
     tag "SRA_IDS_TO_RUNINFO"
     tag "SRA_RUNINFO_TO_FTP"
+    tag "SRA_FASTQ_FTP"
     tag "SRA_TO_SAMPLESHEET"
+    tag "MULTIQC_MAPPINGS_CONFIG"
 
     test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") {
 
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
index 2d01c694..62d499df 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -3,16 +3,14 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
+    tag "SRA_FORCE_SRATOOLS_DOWNLOAD"
 
-    // Subworkflows
-    tag "SRA"
-
-    // Modules
-    tag "MULTIQC_MAPPINGS_CONFIG"
-    tag "SRA_FASTQ_FTP"
+    // Dependencies
+    tag "FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS"
     tag "SRA_IDS_TO_RUNINFO"
     tag "SRA_RUNINFO_TO_FTP"
     tag "SRA_TO_SAMPLESHEET"
+    tag "MULTIQC_MAPPINGS_CONFIG"
 
     test("Parameters: --force_sratools_download") {
 
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index ce77baa2..26cac4b9 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -3,17 +3,14 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
+    tag "SRA_NF_CORE_PIPELINE_ATACSEQ"
 
-    // Subworkflows
-    tag "SRA"
-
-    // Modules
-    tag "MULTIQC_MAPPINGS_CONFIG"
-    tag "ASPERA_CLI"
-    tag "SRA_FASTQ_FTP"
+    // Dependencies
     tag "SRA_IDS_TO_RUNINFO"
     tag "SRA_RUNINFO_TO_FTP"
+    tag "ASPERA_CLI"
     tag "SRA_TO_SAMPLESHEET"
+    tag "MULTIQC_MAPPINGS_CONFIG"
 
     test("Parameters: --nf_core_pipeline atacseq") {
 
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index 99c7dbc5..b5a49dd4 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -3,17 +3,14 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
+    tag "SRA_NF_CORE_PIPELINE_RNASEQ"
 
-    // Subworkflows
-    tag "SRA"
-
-    // Modules
-    tag "MULTIQC_MAPPINGS_CONFIG"
-    tag "ASPERA_CLI"
-    tag "SRA_FASTQ_FTP"
+    // Dependencies
     tag "SRA_IDS_TO_RUNINFO"
     tag "SRA_RUNINFO_TO_FTP"
+    tag "ASPERA_CLI"
     tag "SRA_TO_SAMPLESHEET"
+    tag "MULTIQC_MAPPINGS_CONFIG"
 
     test("Parameters: --nf_core_pipeline rnaseq") {
 
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index d48a714e..0a92b446 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -3,17 +3,14 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
+    tag "SRA_NF_CORE_PIPELINE_TAXPROFILER"
 
-    // Subworkflows
-    tag "SRA"
-
-    // Modules
-    tag "MULTIQC_MAPPINGS_CONFIG"
-    tag "ASPERA_CLI"
-    tag "SRA_FASTQ_FTP"
+    // Dependencies
     tag "SRA_IDS_TO_RUNINFO"
     tag "SRA_RUNINFO_TO_FTP"
+    tag "ASPERA_CLI"
     tag "SRA_TO_SAMPLESHEET"
+    tag "MULTIQC_MAPPINGS_CONFIG"
 
     test("Parameters: --nf_core_pipeline taxprofiler") {
 
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index def5c3cf..f633e0d6 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -3,17 +3,14 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
+    tag "SRA_NF_CORE_PIPELINE_VIRALRECON"
 
-    // Subworkflows
-    tag "SRA"
-
-    // Modules
-    tag "MULTIQC_MAPPINGS_CONFIG"
-    tag "ASPERA_CLI"
-    tag "SRA_FASTQ_FTP"
+    // Dependencies
     tag "SRA_IDS_TO_RUNINFO"
     tag "SRA_RUNINFO_TO_FTP"
+    tag "ASPERA_CLI"
     tag "SRA_TO_SAMPLESHEET"
+    tag "MULTIQC_MAPPINGS_CONFIG"
 
     test("Parameters: --nf_core_pipeline viralrecon") {
 
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index f9a79e15..245dbb80 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -3,16 +3,13 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
+    tag "SRA_SKIP_FASTQ_DOWNLOAD"
 
-    // Subworkflows
-    tag "SRA"
-
-    // Modules
-    tag "MULTIQC_MAPPINGS_CONFIG"
-    tag "SRA_FASTQ_FTP"
+    // Dependencies
     tag "SRA_IDS_TO_RUNINFO"
     tag "SRA_RUNINFO_TO_FTP"
     tag "SRA_TO_SAMPLESHEET"
+    tag "MULTIQC_MAPPINGS_CONFIG"
 
     test("Parameters: --skip_fastq_download") {
 

From 46ec4f8b5a62524eb682b62aab0b643093d156c1 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 31 Jan 2024 21:12:42 +0000
Subject: [PATCH 742/852] Add test for --force_ftp_download

---
 .../sra/tests/sra_force_ftp_download.nf.test  |  36 +++
 .../tests/sra_force_ftp_download.nf.test.snap | 289 ++++++++++++++++++
 2 files changed, 325 insertions(+)
 create mode 100644 workflows/sra/tests/sra_force_ftp_download.nf.test
 create mode 100644 workflows/sra/tests/sra_force_ftp_download.nf.test.snap

diff --git a/workflows/sra/tests/sra_force_ftp_download.nf.test b/workflows/sra/tests/sra_force_ftp_download.nf.test
new file mode 100644
index 00000000..d66cc34a
--- /dev/null
+++ b/workflows/sra/tests/sra_force_ftp_download.nf.test
@@ -0,0 +1,36 @@
+nextflow_workflow {
+
+    name "Test workflow: sra/main.nf"
+    script "../main.nf"
+    workflow "SRA"
+    tag "SRA_FORCE_FTP_DOWNLOAD"
+
+    // Dependencies
+    tag "SRA_IDS_TO_RUNINFO"
+    tag "SRA_RUNINFO_TO_FTP"
+    tag "SRA_FASTQ_FTP"
+    tag "SRA_TO_SAMPLESHEET"
+    tag "MULTIQC_MAPPINGS_CONFIG"
+
+    test("Parameters: --force_ftp_download") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035")
+                """
+            }
+            params {
+                outdir = "results"
+                force_ftp_download = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/workflows/sra/tests/sra_force_ftp_download.nf.test.snap b/workflows/sra/tests/sra_force_ftp_download.nf.test.snap
new file mode 100644
index 00000000..1d92e034
--- /dev/null
+++ b/workflows/sra/tests/sra_force_ftp_download.nf.test.snap
@@ -0,0 +1,289 @@
+{
+    "Parameters: --force_ftp_download": {
+        "content": [
+            {
+                "0": [
+                    "samplesheet.csv:md5,f6bf5c012eef0296f12316e16544ea60"
+                ],
+                "1": [
+                    "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
+                ],
+                "2": [
+                    [
+                        "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768",
+                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
+                    ]
+                ],
+                "3": [
+                    {
+                        "base_count": "194930",
+                        "experiment_accession": "DRX026011",
+                        "experiment_alias": "DRX026011",
+                        "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
+                        "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,1c3a691ea99767f25de2492440a02cb7",
+                        "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,6fa02d3e52613cfe3464cc7a29f227d4",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                        "fastq_bytes": "60275;61610",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                        "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
+                        "id": "DRX026011_DRR028935",
+                        "instrument_model": "Illumina HiSeq 2500",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "PAIRED",
+                        "library_name": "day0_BbSQE-I",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
+                        "md5_2": "941c9998d746416dad53c94c480ddf30",
+                        "read_count": "965",
+                        "run_accession": "DRR028935",
+                        "run_alias": "DRR028935",
+                        "sample_accession": "SAMD00024405",
+                        "sample_alias": "SAMD00024405",
+                        "sample_description": "Liquid culture",
+                        "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
+                        "scientific_name": "Botryococcus braunii Showa",
+                        "secondary_sample_accession": "DRS019431",
+                        "secondary_study_accession": "DRP002616",
+                        "single_end": false,
+                        "study_accession": "PRJDB3420",
+                        "study_alias": "DRP002616",
+                        "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
+                        "submission_accession": "DRA002949",
+                        "tax_id": "1202541"
+                    },
+                    {
+                        "base_count": "1996273",
+                        "experiment_accession": "SRX6725035",
+                        "experiment_alias": "Emb289P1_bin131",
+                        "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
+                        "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,909e5d68f59d2f1c9315d4f8f6a2ef60",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                        "fastq_bytes": "605358",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                        "fastq_md5": "0b512d2dc31685983456bd56fd836544",
+                        "id": "SRX6725035_SRR9984183",
+                        "instrument_model": "Illumina HiSeq 2500",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "Emb289P1_bin131",
+                        "library_selection": "RANDOM",
+                        "library_source": "METAGENOMIC",
+                        "library_strategy": "WGS",
+                        "md5_1": "0b512d2dc31685983456bd56fd836544",
+                        "md5_2": "",
+                        "read_count": "58",
+                        "run_accession": "SRR9984183",
+                        "run_alias": "Emb289P1_bin131.fastq",
+                        "sample_accession": "SAMN12581720",
+                        "sample_alias": "Emb289P1_bin131",
+                        "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
+                        "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
+                        "scientific_name": "Defluviitaleaceae bacterium",
+                        "secondary_sample_accession": "SRS5277011",
+                        "secondary_study_accession": "SRP218535",
+                        "single_end": true,
+                        "study_accession": "PRJNA560329",
+                        "study_alias": "PRJNA560329",
+                        "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
+                        "submission_accession": "SRA942061",
+                        "tax_id": "2660712"
+                    },
+                    {
+                        "base_count": "35658",
+                        "experiment_accession": "ERX1234253",
+                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,98515d664854f1c96f55ac836fb671b9",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_bytes": "18077",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "id": "ERX1234253_ERR1160846",
+                        "instrument_model": "Illumina HiSeq 2500",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "10317.BLANK.93.3E.r22",
+                        "library_selection": "PCR",
+                        "library_source": "METAGENOMIC",
+                        "library_strategy": "AMPLICON",
+                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "md5_2": "",
+                        "read_count": "283",
+                        "run_accession": "ERR1160846",
+                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                        "sample_accession": "SAMEA3687214",
+                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                        "sample_description": "American Gut control",
+                        "sample_title": "10317.BLANK.93.3E.r22",
+                        "scientific_name": "metagenome",
+                        "secondary_sample_accession": "ERS994363",
+                        "secondary_study_accession": "ERP012803",
+                        "single_end": true,
+                        "study_accession": "PRJEB11419",
+                        "study_alias": "qiita_sid_10317",
+                        "study_title": "American Gut Project",
+                        "submission_accession": "ERA541392",
+                        "tax_id": "256318"
+                    }
+                ],
+                "4": [
+                    "versions.yml:md5,0bb049f166e93b3d9866ed7e4407c6c9",
+                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
+                    "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
+                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
+                ],
+                "mappings": [
+                    "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
+                ],
+                "sample_mappings": [
+                    [
+                        "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768",
+                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
+                    ]
+                ],
+                "samplesheet": [
+                    "samplesheet.csv:md5,f6bf5c012eef0296f12316e16544ea60"
+                ],
+                "sra_metadata": [
+                    {
+                        "base_count": "194930",
+                        "experiment_accession": "DRX026011",
+                        "experiment_alias": "DRX026011",
+                        "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
+                        "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,1c3a691ea99767f25de2492440a02cb7",
+                        "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,6fa02d3e52613cfe3464cc7a29f227d4",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                        "fastq_bytes": "60275;61610",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                        "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
+                        "id": "DRX026011_DRR028935",
+                        "instrument_model": "Illumina HiSeq 2500",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "PAIRED",
+                        "library_name": "day0_BbSQE-I",
+                        "library_selection": "cDNA",
+                        "library_source": "TRANSCRIPTOMIC",
+                        "library_strategy": "RNA-Seq",
+                        "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
+                        "md5_2": "941c9998d746416dad53c94c480ddf30",
+                        "read_count": "965",
+                        "run_accession": "DRR028935",
+                        "run_alias": "DRR028935",
+                        "sample_accession": "SAMD00024405",
+                        "sample_alias": "SAMD00024405",
+                        "sample_description": "Liquid culture",
+                        "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
+                        "scientific_name": "Botryococcus braunii Showa",
+                        "secondary_sample_accession": "DRS019431",
+                        "secondary_study_accession": "DRP002616",
+                        "single_end": false,
+                        "study_accession": "PRJDB3420",
+                        "study_alias": "DRP002616",
+                        "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
+                        "submission_accession": "DRA002949",
+                        "tax_id": "1202541"
+                    },
+                    {
+                        "base_count": "1996273",
+                        "experiment_accession": "SRX6725035",
+                        "experiment_alias": "Emb289P1_bin131",
+                        "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
+                        "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,909e5d68f59d2f1c9315d4f8f6a2ef60",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                        "fastq_bytes": "605358",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                        "fastq_md5": "0b512d2dc31685983456bd56fd836544",
+                        "id": "SRX6725035_SRR9984183",
+                        "instrument_model": "Illumina HiSeq 2500",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "Emb289P1_bin131",
+                        "library_selection": "RANDOM",
+                        "library_source": "METAGENOMIC",
+                        "library_strategy": "WGS",
+                        "md5_1": "0b512d2dc31685983456bd56fd836544",
+                        "md5_2": "",
+                        "read_count": "58",
+                        "run_accession": "SRR9984183",
+                        "run_alias": "Emb289P1_bin131.fastq",
+                        "sample_accession": "SAMN12581720",
+                        "sample_alias": "Emb289P1_bin131",
+                        "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
+                        "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
+                        "scientific_name": "Defluviitaleaceae bacterium",
+                        "secondary_sample_accession": "SRS5277011",
+                        "secondary_study_accession": "SRP218535",
+                        "single_end": true,
+                        "study_accession": "PRJNA560329",
+                        "study_alias": "PRJNA560329",
+                        "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
+                        "submission_accession": "SRA942061",
+                        "tax_id": "2660712"
+                    },
+                    {
+                        "base_count": "35658",
+                        "experiment_accession": "ERX1234253",
+                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,98515d664854f1c96f55ac836fb671b9",
+                        "fastq_2": "",
+                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_bytes": "18077",
+                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "id": "ERX1234253_ERR1160846",
+                        "instrument_model": "Illumina HiSeq 2500",
+                        "instrument_platform": "ILLUMINA",
+                        "library_layout": "SINGLE",
+                        "library_name": "10317.BLANK.93.3E.r22",
+                        "library_selection": "PCR",
+                        "library_source": "METAGENOMIC",
+                        "library_strategy": "AMPLICON",
+                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                        "md5_2": "",
+                        "read_count": "283",
+                        "run_accession": "ERR1160846",
+                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                        "sample_accession": "SAMEA3687214",
+                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                        "sample_description": "American Gut control",
+                        "sample_title": "10317.BLANK.93.3E.r22",
+                        "scientific_name": "metagenome",
+                        "secondary_sample_accession": "ERS994363",
+                        "secondary_study_accession": "ERP012803",
+                        "single_end": true,
+                        "study_accession": "PRJEB11419",
+                        "study_alias": "qiita_sid_10317",
+                        "study_title": "American Gut Project",
+                        "submission_accession": "ERA541392",
+                        "tax_id": "256318"
+                    }
+                ],
+                "versions": [
+                    "versions.yml:md5,0bb049f166e93b3d9866ed7e4407c6c9",
+                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
+                    "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
+                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-31T21:12:02.03283"
+    }
+}
\ No newline at end of file

From f5b0c58d0dae51f8c8d6bd519af3b4a856ea4b1a Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 31 Jan 2024 21:20:04 +0000
Subject: [PATCH 743/852] Remove snapshot and add custom checks

---
 .../sra/tests/sra_force_ftp_download.nf.test  |  26 +-
 .../tests/sra_force_ftp_download.nf.test.snap | 289 ------------------
 2 files changed, 23 insertions(+), 292 deletions(-)
 delete mode 100644 workflows/sra/tests/sra_force_ftp_download.nf.test.snap

diff --git a/workflows/sra/tests/sra_force_ftp_download.nf.test b/workflows/sra/tests/sra_force_ftp_download.nf.test
index d66cc34a..357bd180 100644
--- a/workflows/sra/tests/sra_force_ftp_download.nf.test
+++ b/workflows/sra/tests/sra_force_ftp_download.nf.test
@@ -21,15 +21,35 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "results"
+                outdir = "$outputDir"
                 force_ftp_download = true
             }
         }
 
         then {
+            assert workflow.success
+
             assertAll(
-                { assert workflow.success },
-                { assert snapshot(workflow.out).match() }
+                {
+                    with(workflow.out.samplesheet) {
+                        assert path(get(0)).readLines().size() == 4
+                        assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
+                        assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                        assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                    }
+                },
+                {
+                    with(workflow.out.mappings) {
+                        assert path(get(0)).readLines().size() == 4
+                        assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
+                        assert path(get(0)).text.contains('Illumina HiSeq 2500')
+                    }
+                },
+                {
+                    with(workflow.out.sample_mappings) {
+                        assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
+                    }
+                }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_force_ftp_download.nf.test.snap b/workflows/sra/tests/sra_force_ftp_download.nf.test.snap
deleted file mode 100644
index 1d92e034..00000000
--- a/workflows/sra/tests/sra_force_ftp_download.nf.test.snap
+++ /dev/null
@@ -1,289 +0,0 @@
-{
-    "Parameters: --force_ftp_download": {
-        "content": [
-            {
-                "0": [
-                    "samplesheet.csv:md5,f6bf5c012eef0296f12316e16544ea60"
-                ],
-                "1": [
-                    "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
-                ],
-                "2": [
-                    [
-                        "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768",
-                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
-                    ]
-                ],
-                "3": [
-                    {
-                        "base_count": "194930",
-                        "experiment_accession": "DRX026011",
-                        "experiment_alias": "DRX026011",
-                        "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
-                        "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,1c3a691ea99767f25de2492440a02cb7",
-                        "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,6fa02d3e52613cfe3464cc7a29f227d4",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_bytes": "60275;61610",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
-                        "id": "DRX026011_DRR028935",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "PAIRED",
-                        "library_name": "day0_BbSQE-I",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
-                        "md5_2": "941c9998d746416dad53c94c480ddf30",
-                        "read_count": "965",
-                        "run_accession": "DRR028935",
-                        "run_alias": "DRR028935",
-                        "sample_accession": "SAMD00024405",
-                        "sample_alias": "SAMD00024405",
-                        "sample_description": "Liquid culture",
-                        "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
-                        "scientific_name": "Botryococcus braunii Showa",
-                        "secondary_sample_accession": "DRS019431",
-                        "secondary_study_accession": "DRP002616",
-                        "single_end": false,
-                        "study_accession": "PRJDB3420",
-                        "study_alias": "DRP002616",
-                        "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
-                        "submission_accession": "DRA002949",
-                        "tax_id": "1202541"
-                    },
-                    {
-                        "base_count": "1996273",
-                        "experiment_accession": "SRX6725035",
-                        "experiment_alias": "Emb289P1_bin131",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
-                        "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,909e5d68f59d2f1c9315d4f8f6a2ef60",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_bytes": "605358",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_md5": "0b512d2dc31685983456bd56fd836544",
-                        "id": "SRX6725035_SRR9984183",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "Emb289P1_bin131",
-                        "library_selection": "RANDOM",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "WGS",
-                        "md5_1": "0b512d2dc31685983456bd56fd836544",
-                        "md5_2": "",
-                        "read_count": "58",
-                        "run_accession": "SRR9984183",
-                        "run_alias": "Emb289P1_bin131.fastq",
-                        "sample_accession": "SAMN12581720",
-                        "sample_alias": "Emb289P1_bin131",
-                        "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
-                        "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
-                        "scientific_name": "Defluviitaleaceae bacterium",
-                        "secondary_sample_accession": "SRS5277011",
-                        "secondary_study_accession": "SRP218535",
-                        "single_end": true,
-                        "study_accession": "PRJNA560329",
-                        "study_alias": "PRJNA560329",
-                        "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
-                        "submission_accession": "SRA942061",
-                        "tax_id": "2660712"
-                    },
-                    {
-                        "base_count": "35658",
-                        "experiment_accession": "ERX1234253",
-                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,98515d664854f1c96f55ac836fb671b9",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_bytes": "18077",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "10317.BLANK.93.3E.r22",
-                        "library_selection": "PCR",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "AMPLICON",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "read_count": "283",
-                        "run_accession": "ERR1160846",
-                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
-                        "sample_accession": "SAMEA3687214",
-                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
-                        "sample_description": "American Gut control",
-                        "sample_title": "10317.BLANK.93.3E.r22",
-                        "scientific_name": "metagenome",
-                        "secondary_sample_accession": "ERS994363",
-                        "secondary_study_accession": "ERP012803",
-                        "single_end": true,
-                        "study_accession": "PRJEB11419",
-                        "study_alias": "qiita_sid_10317",
-                        "study_title": "American Gut Project",
-                        "submission_accession": "ERA541392",
-                        "tax_id": "256318"
-                    }
-                ],
-                "4": [
-                    "versions.yml:md5,0bb049f166e93b3d9866ed7e4407c6c9",
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
-                ],
-                "mappings": [
-                    "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
-                ],
-                "sample_mappings": [
-                    [
-                        "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768",
-                        "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9"
-                    ]
-                ],
-                "samplesheet": [
-                    "samplesheet.csv:md5,f6bf5c012eef0296f12316e16544ea60"
-                ],
-                "sra_metadata": [
-                    {
-                        "base_count": "194930",
-                        "experiment_accession": "DRX026011",
-                        "experiment_alias": "DRX026011",
-                        "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
-                        "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,1c3a691ea99767f25de2492440a02cb7",
-                        "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,6fa02d3e52613cfe3464cc7a29f227d4",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_bytes": "60275;61610",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
-                        "id": "DRX026011_DRR028935",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "PAIRED",
-                        "library_name": "day0_BbSQE-I",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
-                        "md5_2": "941c9998d746416dad53c94c480ddf30",
-                        "read_count": "965",
-                        "run_accession": "DRR028935",
-                        "run_alias": "DRR028935",
-                        "sample_accession": "SAMD00024405",
-                        "sample_alias": "SAMD00024405",
-                        "sample_description": "Liquid culture",
-                        "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
-                        "scientific_name": "Botryococcus braunii Showa",
-                        "secondary_sample_accession": "DRS019431",
-                        "secondary_study_accession": "DRP002616",
-                        "single_end": false,
-                        "study_accession": "PRJDB3420",
-                        "study_alias": "DRP002616",
-                        "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
-                        "submission_accession": "DRA002949",
-                        "tax_id": "1202541"
-                    },
-                    {
-                        "base_count": "1996273",
-                        "experiment_accession": "SRX6725035",
-                        "experiment_alias": "Emb289P1_bin131",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
-                        "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,909e5d68f59d2f1c9315d4f8f6a2ef60",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_bytes": "605358",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_md5": "0b512d2dc31685983456bd56fd836544",
-                        "id": "SRX6725035_SRR9984183",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "Emb289P1_bin131",
-                        "library_selection": "RANDOM",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "WGS",
-                        "md5_1": "0b512d2dc31685983456bd56fd836544",
-                        "md5_2": "",
-                        "read_count": "58",
-                        "run_accession": "SRR9984183",
-                        "run_alias": "Emb289P1_bin131.fastq",
-                        "sample_accession": "SAMN12581720",
-                        "sample_alias": "Emb289P1_bin131",
-                        "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
-                        "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
-                        "scientific_name": "Defluviitaleaceae bacterium",
-                        "secondary_sample_accession": "SRS5277011",
-                        "secondary_study_accession": "SRP218535",
-                        "single_end": true,
-                        "study_accession": "PRJNA560329",
-                        "study_alias": "PRJNA560329",
-                        "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
-                        "submission_accession": "SRA942061",
-                        "tax_id": "2660712"
-                    },
-                    {
-                        "base_count": "35658",
-                        "experiment_accession": "ERX1234253",
-                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,98515d664854f1c96f55ac836fb671b9",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_bytes": "18077",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "10317.BLANK.93.3E.r22",
-                        "library_selection": "PCR",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "AMPLICON",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "read_count": "283",
-                        "run_accession": "ERR1160846",
-                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
-                        "sample_accession": "SAMEA3687214",
-                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
-                        "sample_description": "American Gut control",
-                        "sample_title": "10317.BLANK.93.3E.r22",
-                        "scientific_name": "metagenome",
-                        "secondary_sample_accession": "ERS994363",
-                        "secondary_study_accession": "ERP012803",
-                        "single_end": true,
-                        "study_accession": "PRJEB11419",
-                        "study_alias": "qiita_sid_10317",
-                        "study_title": "American Gut Project",
-                        "submission_accession": "ERA541392",
-                        "tax_id": "256318"
-                    }
-                ],
-                "versions": [
-                    "versions.yml:md5,0bb049f166e93b3d9866ed7e4407c6c9",
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-01-31T21:12:02.03283"
-    }
-}
\ No newline at end of file

From c0dbd9346665c875b0e446434893ed0ddde9376b Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 31 Jan 2024 21:48:34 +0000
Subject: [PATCH 744/852] Update custom/sratoolsncbisettings to only run when
 sra ids are provided

---
 modules/nf-core/custom/sratoolsncbisettings/main.nf            | 3 +++
 modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test | 3 ++-
 .../fastq_download_prefetch_fasterqdump_sratools/main.nf       | 2 +-
 .../tests/main.nf.test.snap                                    | 1 +
 4 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/custom/sratoolsncbisettings/main.nf b/modules/nf-core/custom/sratoolsncbisettings/main.nf
index ba9441c9..cf304500 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/main.nf
+++ b/modules/nf-core/custom/sratoolsncbisettings/main.nf
@@ -7,6 +7,9 @@ process CUSTOM_SRATOOLSNCBISETTINGS {
         'https://depot.galaxyproject.org/singularity/sra-tools:3.0.8--h9f5acd7_0' :
         'biocontainers/sra-tools:3.0.8--h9f5acd7_0' }"
 
+    input:
+    val sra_ids
+
     output:
     path('*.mkfg')     , emit: ncbi_settings
     path 'versions.yml', emit: versions
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
index 11899742..ae9db9b0 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
+++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
@@ -11,11 +11,12 @@ nextflow_process {
             params {
                 settings_path = '/tmp/.ncbi'
                 settings_file  = "${params.settings_path}/user-settings.mkfg"
-                outdir        = "$outputDir"
+                outdir         = "$outputDir"
             }
 
             process {
                 """
+                input[0] = ["SRX6725035"]
                 file(params.settings_path).mkdirs()
                 def settings = file(params.modules_testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
                 settings.copyTo(params.settings_file)
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf
index de31637e..0713892e 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf
@@ -17,7 +17,7 @@ workflow FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS {
     //
     // Detect existing NCBI user settings or create new ones.
     //
-    CUSTOM_SRATOOLSNCBISETTINGS()
+    CUSTOM_SRATOOLSNCBISETTINGS( ch_sra_ids )
     ch_ncbi_settings = CUSTOM_SRATOOLSNCBISETTINGS.out.ncbi_settings
     ch_versions = ch_versions.mix(CUSTOM_SRATOOLSNCBISETTINGS.out.versions)
 
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
index 63ba2e99..86252466 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
@@ -27,6 +27,7 @@
     "versions": {
         "content": [
             [
+                "versions.yml:md5,1a2218ff913fc33408bffccb081b5048",
                 "versions.yml:md5,1a2218ff913fc33408bffccb081b5048",
                 "versions.yml:md5,2f3b3a13b36dabf13f09327613d5558d",
                 "versions.yml:md5,98d78bba9f3da39a0b7db6e9c7dcc224"

From a70d97ee00a60b32db624f1027c83262a0b76554 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 1 Feb 2024 08:35:30 +0000
Subject: [PATCH 745/852] Install updated
 fastq_download_prefetch_fasterqdump_sratools subworkflow from nf-core/modules

---
 CHANGELOG.md                                  |  1 +
 modules.json                                  |  4 +-
 .../custom/sratoolsncbisettings/main.nf       |  2 +-
 .../sratoolsncbisettings/tests/main.nf.test   |  2 +-
 .../main.nf                                   |  2 +-
 .../tests/main.nf.test.snap                   | 43 +++++++++++++++----
 6 files changed, 41 insertions(+), 13 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 856667de..43c15bec 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -33,6 +33,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #259](https://github.com/nf-core/fetchngs/pull/259) - Add Aspera CLI download support to pipeline ([#68](https://github.com/nf-core/fetchngs/issues/68))
 - [PR #261](https://github.com/nf-core/fetchngs/pull/261) - Revert sratools fasterqdump version ([#221](https://github.com/nf-core/fetchngs/issues/221))
 - [PR #262](https://github.com/nf-core/fetchngs/pull/262) - Use nf-test version v0.8.4 and remove implicit tags
+- [PR #263](https://github.com/nf-core/fetchngs/pull/263) - Refine tags used for workflows
 
 ### Software dependencies
 
diff --git a/modules.json b/modules.json
index 9190e3f5..14bd461f 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
-                        "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620",
+                        "git_sha": "3aa09ac8899d7735cb5bc004da0ef5f35f9a7901",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/fasterqdump": {
@@ -32,7 +32,7 @@
                 "nf-core": {
                     "fastq_download_prefetch_fasterqdump_sratools": {
                         "branch": "master",
-                        "git_sha": "bdfd7bc8d2e5a93531e14bd94c4128d9a72a2435",
+                        "git_sha": "3aa09ac8899d7735cb5bc004da0ef5f35f9a7901",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {
diff --git a/modules/nf-core/custom/sratoolsncbisettings/main.nf b/modules/nf-core/custom/sratoolsncbisettings/main.nf
index cf304500..577117ed 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/main.nf
+++ b/modules/nf-core/custom/sratoolsncbisettings/main.nf
@@ -8,7 +8,7 @@ process CUSTOM_SRATOOLSNCBISETTINGS {
         'biocontainers/sra-tools:3.0.8--h9f5acd7_0' }"
 
     input:
-    val sra_ids
+    val ids
 
     output:
     path('*.mkfg')     , emit: ncbi_settings
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
index ae9db9b0..8cd0de8a 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
+++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
@@ -4,7 +4,7 @@ nextflow_process {
     script "../main.nf"
     process "CUSTOM_SRATOOLSNCBISETTINGS"
     config "modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config"
-    
+
     test("Should run without failures") {
 
         when {
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf
index 0713892e..fbeacf4a 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf
@@ -17,7 +17,7 @@ workflow FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS {
     //
     // Detect existing NCBI user settings or create new ones.
     //
-    CUSTOM_SRATOOLSNCBISETTINGS( ch_sra_ids )
+    CUSTOM_SRATOOLSNCBISETTINGS ( ch_sra_ids.collect() )
     ch_ncbi_settings = CUSTOM_SRATOOLSNCBISETTINGS.out.ncbi_settings
     ch_versions = ch_versions.mix(CUSTOM_SRATOOLSNCBISETTINGS.out.versions)
 
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
index 86252466..d64857ef 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
@@ -3,7 +3,11 @@
         "content": [
             19996
         ],
-        "timestamp": "2024-01-30T18:05:15.684489"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T08:34:54.56022"
     },
     "test_pe_reads_2_lines": {
         "content": [
@@ -16,30 +20,45 @@
                 "GTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACG"
             ]
         ],
-        "timestamp": "2024-01-30T18:05:15.670447"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T08:34:54.532626"
     },
     "test_pe_reads_2_size": {
         "content": [
             2011460
         ],
-        "timestamp": "2024-01-30T18:05:15.675771"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T08:34:54.542804"
     },
     "versions": {
         "content": [
             [
-                "versions.yml:md5,1a2218ff913fc33408bffccb081b5048",
                 "versions.yml:md5,1a2218ff913fc33408bffccb081b5048",
                 "versions.yml:md5,2f3b3a13b36dabf13f09327613d5558d",
                 "versions.yml:md5,98d78bba9f3da39a0b7db6e9c7dcc224"
             ]
         ],
-        "timestamp": "2024-01-30T18:05:15.692165"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T08:34:54.570734"
     },
     "test_pe_reads_1_size": {
         "content": [
             2013376
         ],
-        "timestamp": "2024-01-30T18:05:15.666916"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T08:34:54.525795"
     },
     "test_se_reads_lines": {
         "content": [
@@ -52,7 +71,11 @@
                 "ACGCAGGTGCCAGCAGCCGCGGTAATACGGAGGGAGCTAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGCTTTTCAAGTCAGGGGTGGAAATACCCGGGGCCGTCAACCCGACCG"
             ]
         ],
-        "timestamp": "2024-01-30T18:05:15.679779"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T08:34:54.550392"
     },
     "test_pe_reads_1_lines": {
         "content": [
@@ -65,6 +88,10 @@
                 "CGTACGAGCACGTCGCGAACCTGTAAAACAGGCAAACTGAGTTGGACGTGTGTTTTCTCGTTGAAACCAGGGACAAGGCTCTCCATCTTACCTTTCGGTCACACCCGGACGAAACCTAGATGTGCTGATGATCGGCTGCAACACGGACGAAACCGTAAGCAGCCTGCAGAAGATAGACGAGTTACTCGTGTCCTGTCAACGACAGTAATTAGTTATTAATTATACTGCGTGAGTGCAC"
             ]
         ],
-        "timestamp": "2024-01-30T18:05:15.654112"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-01T08:34:54.509486"
     }
 }
\ No newline at end of file

From 49b598b9e8dade03c08223a35e8b19713791090d Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 1 Feb 2024 10:01:43 +0000
Subject: [PATCH 746/852] Remove Synapse workflow from pipeline

---
 CHANGELOG.md | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 856667de..0c8c3a31 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unpublished Version / DEV]
 
+### :warning: Major enhancements
+
+- The Aspera CLI was recently added to [Bioconda](https://anaconda.org/bioconda/aspera-cli) and we have added it as another way of downloading FastQ files on top of the existing FTP and sra-tools support. In our limited benchmarks on all public Clouds we found ~50% speed-up in download times compared to FTP! We are not aware of any obvious downsides and have made this the default download method in the pipeline. You can however, revert to using FTP and sra-tools using the `--force_ftp_download` and `--force_sratools_download` parameters, respectively. We would love to have your feedback!
+- Support for Synapse ids has been dropped in this release. We haven't had any feedback from users whether it is being used or not. Users can run earlier versions of the pipeline if required.
+
 ### Credits
 
 Special thanks to the following for their contributions to the release:
@@ -48,9 +53,11 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 
 ### Parameters
 
-| Old parameter | New parameter          |
-| ------------- | ---------------------- |
-|               | `--force_ftp_download` |
+| Old parameter      | New parameter          |
+| ------------------ | ---------------------- |
+|                    | `--force_ftp_download` |
+| `--input_type`     |                        |
+| `--synapse_config` |                        |
 
 > **NB:** Parameter has been **updated** if both old and new parameter information is present.
 > **NB:** Parameter has been **added** if just the new parameter information is present.

From 4472842c87be594d3008b6ded001a587e05b4844 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 1 Feb 2024 10:02:46 +0000
Subject: [PATCH 747/852] Remove Synapse workflow from pipeline

---
 README.md                                     |   7 -
 assets/schema_input.json                      |   2 +-
 conf/test_synapse.config                      |  25 ----
 docs/output.md                                |  25 +---
 docs/usage.md                                 |  37 ++---
 main.nf                                       |  15 +-
 modules/local/synapse_get/main.nf             |  37 -----
 modules/local/synapse_get/nextflow.config     |  16 ---
 modules/local/synapse_list/main.nf            |  36 -----
 modules/local/synapse_list/nextflow.config    |  10 --
 .../local/synapse_merge_samplesheet/main.nf   |  28 ----
 .../synapse_merge_samplesheet/nextflow.config |   9 --
 modules/local/synapse_show/main.nf            |  36 -----
 modules/local/synapse_show/nextflow.config    |   9 --
 modules/local/synapse_to_samplesheet/main.nf  |  55 --------
 .../synapse_to_samplesheet/nextflow.config    |   8 --
 nextflow.config                               |  13 +-
 nextflow_schema.json                          |  13 --
 .../utils_nfcore_fetchngs_pipeline/main.nf    | 130 +-----------------
 .../tests/main.function.nf.test               |  19 ---
 .../main.workflow_pipeline_completion.test    |  14 +-
 ...n.workflow_pipeline_initialisation.nf.test |   4 +-
 workflows/synapse/main.nf                     | 125 -----------------
 workflows/synapse/nextflow.config             |   5 -
 24 files changed, 25 insertions(+), 653 deletions(-)
 delete mode 100644 conf/test_synapse.config
 delete mode 100644 modules/local/synapse_get/main.nf
 delete mode 100644 modules/local/synapse_get/nextflow.config
 delete mode 100644 modules/local/synapse_list/main.nf
 delete mode 100644 modules/local/synapse_list/nextflow.config
 delete mode 100644 modules/local/synapse_merge_samplesheet/main.nf
 delete mode 100644 modules/local/synapse_merge_samplesheet/nextflow.config
 delete mode 100644 modules/local/synapse_show/main.nf
 delete mode 100644 modules/local/synapse_show/nextflow.config
 delete mode 100644 modules/local/synapse_to_samplesheet/main.nf
 delete mode 100644 modules/local/synapse_to_samplesheet/nextflow.config
 delete mode 100644 workflows/synapse/main.nf
 delete mode 100644 workflows/synapse/nextflow.config

diff --git a/README.md b/README.md
index bf69b682..f652bd66 100644
--- a/README.md
+++ b/README.md
@@ -72,13 +72,6 @@ Via a single file of ids, provided one-per-line (see [example input file](https:
    - Otherwise use [`sra-tools`](https://github.com/ncbi/sra-tools) to download `.sra` files and convert them to FastQ. Use `--force_sratools_download` to force this behaviour.
 4. Collate id metadata and paths to FastQ files in a single samplesheet
 
-### Synapse ids
-
-1. Resolve Synapse directory ids to their corresponding FastQ files ids via the `synapse list` command.
-2. Retrieve FastQ file metadata including FastQ file names, md5sums, etags, annotations and other data provenance via the `synapse show` command.
-3. Download FastQ files in parallel via `synapse get`
-4. Collate paths to FastQ files in a single samplesheet
-
 ## Pipeline output
 
 The columns in the output samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines (see [usage docs](https://nf-co.re/fetchngs/usage#samplesheet-format)), these currently include:
diff --git a/assets/schema_input.json b/assets/schema_input.json
index 13044b1b..db9ffc00 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -9,7 +9,7 @@
         "properties": {
             "": {
                 "type": "string",
-                "pattern": "^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM])|(syn))(\\d+)$",
+                "pattern": "^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM]))(\\d+)$",
                 "errorMessage": "Please provide a valid SRA, ENA, DDBJ or GEO identifier"
             }
         }
diff --git a/conf/test_synapse.config b/conf/test_synapse.config
deleted file mode 100644
index 1ac1388a..00000000
--- a/conf/test_synapse.config
+++ /dev/null
@@ -1,25 +0,0 @@
-/*
-========================================================================================
-    Nextflow config file for running minimal tests
-========================================================================================
-    Defines input files and everything required to run a fast and simple pipeline test.
-
-    Use as follows:
-        nextflow run nf-core/fetchngs -profile test_synapse,<docker/singularity>
-
-----------------------------------------------------------------------------------------
-*/
-
-params {
-    config_profile_name        = 'Test profile using Synapse ids'
-    config_profile_description = 'Minimal test dataset to check pipeline function'
-
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
-    // Input data
-    input      = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/synapse_ids_test.csv'
-    input_type = 'synapse'
-}
diff --git a/docs/output.md b/docs/output.md
index aad48fe8..5a27bfca 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -8,9 +8,7 @@ This document describes the output produced by the pipeline. The directories lis
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data depending on the type of ids provided:
 
-- Download FastQ files and create samplesheet from:
-  1. [SRA / ENA / DDBJ / GEO ids](#sra--ena--ddbj--geo-ids)
-  2. [Synapse ids](#synapse-ids)
+- Download FastQ files and create samplesheet from [SRA / ENA / DDBJ / GEO ids](#sra--ena--ddbj--geo-ids)
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
 Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introduction) for a list of supported public repository identifiers and how to provide them to the pipeline.
@@ -36,27 +34,6 @@ Please see the [usage documentation](https://nf-co.re/fetchngs/usage#introductio
 
 The final sample information for all identifiers is obtained from the ENA which provides direct download links for FastQ files as well as their associated md5 sums. If download links exist, the files will be downloaded in parallel by FTP. Otherwise they are downloaded using sra-tools.
 
-### Synapse ids
-
-<details markdown="1">
-<summary>Output files</summary>
-
-- `fastq/`
-  - `*.fastq.gz`: Paired-end/single-end reads downloaded from Synapse.
-- `fastq/md5/`
-  - `*.md5`: Files containing `md5` sum for FastQ files downloaded from the Synapse platform.
-- `samplesheet/`
-  - `samplesheet.csv`: Auto-created samplesheet with collated metadata and paths to downloaded FastQ files.
-- `metadata/`
-  - `*.metadata.txt`: Original metadata file generated using the `synapse show` command.
-  - `*.list.txt`: Original output of the `synapse list` command, containing the Synapse ids, file version numbers, file names, and other file-specific data for the Synapse directory ID provided.
-
-</details>
-
-FastQ files and corresponding sample information for `Synapse` identifiers are downloaded in parallel directly from the [Synapse](https://www.synapse.org/#) platform. A [configuration file](http://python-docs.synapse.org/build/html/Credentials.html#use-synapseconfig) containing valid login credentials is required for Synapse downloads.
-
-The final sample information for the FastQ files downloaded from `Synapse` is obtained from the file name itself. The file names are parsed according to the glob pattern `*{1,2}*`. This returns the sample name, presumed to be the longest possible string matching the glob pattern, with the fewest number of wildcard insertions. Further information on sample name parsing can be found in the [usage documentation](https://nf-co.re/fetchngs/usage#introduction).
-
 ### Pipeline information
 
 <details markdown="1">
diff --git a/docs/usage.md b/docs/usage.md
index 42d134f3..06ff7802 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -8,15 +8,15 @@
 
 The pipeline has been set-up to automatically download and process the raw FastQ files from both public and private repositories. Identifiers can be provided in a file, one-per-line via the `--input` parameter. Currently, the following types of example identifiers are supported:
 
-| `SRA`        | `ENA`        | `DDBJ`       | `GEO`      | `Synapse`   |
-| ------------ | ------------ | ------------ | ---------- | ----------- |
-| SRR11605097  | ERR4007730   | DRR171822    | GSM4432381 | syn26240435 |
-| SRX8171613   | ERX4009132   | DRX162434    | GSE147507  |             |
-| SRS6531847   | ERS4399630   | DRS090921    |            |             |
-| SAMN14689442 | SAMEA6638373 | SAMD00114846 |            |             |
-| SRP256957    | ERP120836    | DRP004793    |            |             |
-| SRA1068758   | ERA2420837   | DRA008156    |            |             |
-| PRJNA625551  | PRJEB37513   | PRJDB4176    |            |             |
+| `SRA`        | `ENA`        | `DDBJ`       | `GEO`      |
+| ------------ | ------------ | ------------ | ---------- |
+| SRR11605097  | ERR4007730   | DRR171822    | GSM4432381 |
+| SRX8171613   | ERX4009132   | DRX162434    | GSE147507  |
+| SRS6531847   | ERS4399630   | DRS090921    |            |
+| SAMN14689442 | SAMEA6638373 | SAMD00114846 |            |
+| SRP256957    | ERP120836    | DRP004793    |            |
+| SRA1068758   | ERA2420837   | DRA008156    |            |
+| PRJNA625551  | PRJEB37513   | PRJDB4176    |            |
 
 ### SRR / ERR / DRR ids
 
@@ -34,25 +34,6 @@ If you have a GEO accession (found in the data availability section of published
 
 This downloads a text file called `SRR_Acc_List.txt` that can be directly provided to the pipeline once renamed with a .csv extension e.g. `--input SRR_Acc_List.csv`.
 
-### Synapse ids
-
-[Synapse](https://www.synapse.org/#) is a collaborative research platform created by [Sage Bionetworks](https://sagebionetworks.org/). Its aim is to promote reproducible research and responsible data sharing throughout the biomedical community. To download data from `Synapse`, the Synapse id of the _directory_ containing all files to be downloaded should be provided. The Synapse id should be an eleven-characters beginning with `syn`.
-
-This Synapse id will then be resolved to the Synapse id of the corresponding FastQ files contained within the directory. The individual FastQ files are then downloaded in parellel using the `synapse get` command. All Synapse metadata, annotations and data provenance are also downloaded using the `synapse show` command, and are outputted to a separate metadata file. By default, only the md5sums, file sizes, etags, Synapse ids, file names, and file versions are shown.
-
-In order to download data from Synapse, an account must be created and a user configuration file provided via the parameter `--synapse_config`. For more information about Synapse configuration, please see the [Synapse client configuration](https://help.synapse.org/docs/Client-Configuration.1985446156.html) documentation.
-
-The final sample information for the FastQ files used for samplesheet generation is obtained from the file name itself. The file names are parsed according to the glob pattern `*{1,2}*`, which returns the sample name, presumed to be the longest possible string matching the glob pattern, with the fewest number of wildcard insertions.
-
-<details markdown="1">
-<summary>Supported File Names</summary>
-
-- Files named `SRR493366_1.fastq` and `SRR493366_2.fastq` will have a sample name of `SRR493366`
-- Files named `SRR_493_367_1.fastq` and `SRR_493_367_2.fastq` will have a sample name of `SRR_493_367`
-- Files named `filename12_1.fastq` and `filename12_2.fastq` will have a sample name of `filename12`
-
-</details>
-
 ### Samplesheet format
 
 As a bonus, the columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include:
diff --git a/main.nf b/main.nf
index d3779d16..b5b499d5 100644
--- a/main.nf
+++ b/main.nf
@@ -17,8 +17,7 @@ nextflow.enable.dsl = 2
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-if (params.input_type == 'sra')     include { SRA     } from './workflows/sra'
-if (params.input_type == 'synapse') include { SYNAPSE } from './workflows/synapse'
+include { SRA } from './workflows/sra'
 
 //
 // WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided
@@ -33,15 +32,7 @@ workflow NFCORE_FETCHNGS {
     //
     // WORKFLOW: Download FastQ files for SRA / ENA / GEO / DDBJ ids
     //
-    if (params.input_type == 'sra') {
-        SRA ( ids )
-
-    //
-    // WORKFLOW: Download FastQ files for Synapse ids
-    //
-    } else if (params.input_type == 'synapse') {
-        SYNAPSE ( ids )
-    }
+    SRA ( ids )
 
 }
 
@@ -69,7 +60,6 @@ workflow {
         params.monochrome_logs,
         params.outdir,
         params.input,
-        params.input_type,
         params.ena_metadata_fields
     )
 
@@ -84,7 +74,6 @@ workflow {
     // SUBWORKFLOW: Run completion tasks
     //
     PIPELINE_COMPLETION (
-        params.input_type,
         params.email,
         params.email_on_fail,
         params.plaintext_email,
diff --git a/modules/local/synapse_get/main.nf b/modules/local/synapse_get/main.nf
deleted file mode 100644
index c8a6d7a4..00000000
--- a/modules/local/synapse_get/main.nf
+++ /dev/null
@@ -1,37 +0,0 @@
-
-process SYNAPSE_GET {
-    tag "$meta.id"
-    label 'process_low'
-    label 'error_retry'
-
-    conda "bioconda::synapseclient=2.7.1"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/synapseclient:2.7.1--pyh7cba7a3_0' :
-        'biocontainers/synapseclient:2.7.1--pyh7cba7a3_0' }"
-
-    input:
-    val meta
-    path config
-
-    output:
-    tuple val(meta), path("*.fastq.gz"), emit: fastq
-    tuple val(meta), path("*md5")      , emit: md5
-    path "versions.yml"                , emit: versions
-
-    script:
-    def args = task.ext.args ?: ''
-    """
-    synapse \\
-        -c $config \\
-        get \\
-        $args \\
-        $meta.id
-
-    echo "${meta.md5} \t ${meta.name}" > ${meta.id}.md5
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        synapse: \$(synapse --version | sed -e "s/Synapse Client //g")
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/synapse_get/nextflow.config b/modules/local/synapse_get/nextflow.config
deleted file mode 100644
index 9c42e741..00000000
--- a/modules/local/synapse_get/nextflow.config
+++ /dev/null
@@ -1,16 +0,0 @@
-process {
-    withName: 'SYNAPSE_GET' {
-        publishDir = [
-            [
-                path: { "${params.outdir}/fastq" },
-                mode: params.publish_dir_mode,
-                pattern: "*.fastq.gz"
-            ],
-            [
-                path: { "${params.outdir}/fastq/md5" },
-                mode: params.publish_dir_mode,
-                pattern: "*.md5"
-            ]
-        ]
-    }
-}
diff --git a/modules/local/synapse_list/main.nf b/modules/local/synapse_list/main.nf
deleted file mode 100644
index 0c03f8b2..00000000
--- a/modules/local/synapse_list/main.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-
-process SYNAPSE_LIST {
-    tag "$id"
-    label 'process_low'
-
-    conda "bioconda::synapseclient=2.7.1"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/synapseclient:2.7.1--pyh7cba7a3_0' :
-        'biocontainers/synapseclient:2.7.1--pyh7cba7a3_0' }"
-
-    input:
-    val id
-    path config
-
-    output:
-    path "*.txt"       , emit: txt
-    path "versions.yml", emit: versions
-
-    script:
-    def args  = task.ext.args  ?: ''
-    def args2 = task.ext.args2 ?: ''
-    """
-    synapse \\
-        -c $config \\
-        list \\
-        $args \\
-        $id \\
-        $args2 \\
-        > ${id}.list.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        syanpse: \$(synapse --version | sed -e "s/Synapse Client //g")
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/synapse_list/nextflow.config b/modules/local/synapse_list/nextflow.config
deleted file mode 100644
index 15124234..00000000
--- a/modules/local/synapse_list/nextflow.config
+++ /dev/null
@@ -1,10 +0,0 @@
-process {
-    withName: SYNAPSE_LIST {
-        ext.args = '--long'
-        publishDir = [
-            path: { "${params.outdir}/metadata" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-}
diff --git a/modules/local/synapse_merge_samplesheet/main.nf b/modules/local/synapse_merge_samplesheet/main.nf
deleted file mode 100644
index 4cb2abc3..00000000
--- a/modules/local/synapse_merge_samplesheet/main.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-
-process SYNAPSE_MERGE_SAMPLESHEET {
-
-    conda "conda-forge::sed=4.7"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'nf-core/ubuntu:20.04' }"
-
-    input:
-    path ('samplesheets/*')
-
-    output:
-    path "samplesheet.csv", emit: samplesheet
-    path "versions.yml"   , emit: versions
-
-    script:
-    """
-    head -n 1 `ls ./samplesheets/* | head -n 1` > samplesheet.csv
-    for fileid in `ls ./samplesheets/*`; do
-        awk 'NR>1' \$fileid >> samplesheet.csv
-    done
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/synapse_merge_samplesheet/nextflow.config b/modules/local/synapse_merge_samplesheet/nextflow.config
deleted file mode 100644
index c94c53dd..00000000
--- a/modules/local/synapse_merge_samplesheet/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-    withName: SYNAPSE_MERGE_SAMPLESHEET {
-        publishDir = [
-            path: { "${params.outdir}/samplesheet" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-}
diff --git a/modules/local/synapse_show/main.nf b/modules/local/synapse_show/main.nf
deleted file mode 100644
index e1f756a5..00000000
--- a/modules/local/synapse_show/main.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-
-process SYNAPSE_SHOW {
-    tag "$id"
-    label 'process_low'
-
-    conda "bioconda::synapseclient=2.7.1"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/synapseclient:2.7.1--pyh7cba7a3_0' :
-        'biocontainers/synapseclient:2.7.1--pyh7cba7a3_0' }"
-
-    input:
-    val id
-    path config
-
-    output:
-    path "*.txt"       , emit: metadata
-    path "versions.yml", emit: versions
-
-    script:
-    def args  = task.ext.args  ?: ''
-    def args2 = task.ext.args2 ?: ''
-    """
-    synapse \\
-        -c $config \\
-        show \\
-        $args \\
-        $id \\
-        $args2 \\
-        > ${id}.metadata.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        synapse: \$(synapse --version | sed -e "s/Synapse Client //g")
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/synapse_show/nextflow.config b/modules/local/synapse_show/nextflow.config
deleted file mode 100644
index 5b9167b3..00000000
--- a/modules/local/synapse_show/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-    withName: 'SYNAPSE_SHOW' {
-        publishDir = [
-            path: { "${params.outdir}/metadata" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-}
diff --git a/modules/local/synapse_to_samplesheet/main.nf b/modules/local/synapse_to_samplesheet/main.nf
deleted file mode 100644
index 393203de..00000000
--- a/modules/local/synapse_to_samplesheet/main.nf
+++ /dev/null
@@ -1,55 +0,0 @@
-
-process SYNAPSE_TO_SAMPLESHEET {
-    tag "$meta.id"
-
-    executor 'local'
-    memory 100.MB
-
-    input:
-    tuple val(meta), path(fastq)
-    val pipeline
-    val strandedness
-
-    output:
-    tuple val(meta), path("*.csv"), emit: samplesheet
-
-    exec:
-
-    //  Remove custom keys
-    def meta_map = meta.clone()
-    meta_map.remove("id")
-
-    def fastq_1 = "${params.outdir}/fastq/${fastq}"
-    def fastq_2 = ''
-    if (fastq instanceof List && fastq.size() == 2) {
-        fastq_1 = "${params.outdir}/fastq/${fastq[0]}"
-        fastq_2 = "${params.outdir}/fastq/${fastq[1]}"
-    }
-
-    // Add relevant fields to the beginning of the map
-    pipeline_map = [
-        sample  : "${meta.id}",
-        fastq_1 : fastq_1,
-        fastq_2 : fastq_2
-    ]
-
-    // Add nf-core pipeline specific entries
-    if (pipeline) {
-        if (pipeline == 'rnaseq') {
-            pipeline_map << [ strandedness: strandedness ]
-        } else if (pipeline == 'atacseq') {
-            pipeline_map << [ replicate: 1 ]
-        } else if (pipeline == 'taxprofiler') {
-            pipeline_map << [ fasta: '' ]
-        }
-    }
-    pipeline_map << meta_map
-
-    // Create a samplesheet
-    samplesheet  = pipeline_map.keySet().collect{ '"' + it + '"'}.join(",") + '\n'
-    samplesheet += pipeline_map.values().collect{ '"' + it + '"'}.join(",")
-
-    // Write samplesheet to file
-    def samplesheet_file = task.workDir.resolve("${meta.id}.samplesheet.csv")
-    samplesheet_file.text = samplesheet
-}
diff --git a/modules/local/synapse_to_samplesheet/nextflow.config b/modules/local/synapse_to_samplesheet/nextflow.config
deleted file mode 100644
index 83af86b6..00000000
--- a/modules/local/synapse_to_samplesheet/nextflow.config
+++ /dev/null
@@ -1,8 +0,0 @@
-process {
-    withName: SYNAPSE_TO_SAMPLESHEET {
-        publishDir = [
-            path: { "${params.outdir}/samplesheet" },
-            enabled: false
-        ]
-    }
-}
diff --git a/nextflow.config b/nextflow.config
index 593f9ad0..c9b67f04 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -11,12 +11,10 @@ params {
 
     // Input options
     input                       = null
-    input_type                  = 'sra'
     nf_core_pipeline            = null
     nf_core_rnaseq_strandedness = 'auto'
     ena_metadata_fields         = null
     sample_mapping_fields       = 'experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description'
-    synapse_config              = null
     force_ftp_download          = false
     force_sratools_download     = false
     skip_fastq_download         = false
@@ -67,11 +65,7 @@ try {
 }
 
 // Workflow specific configs
-if (params.input_type == 'sra') {
-    includeConfig './workflows/sra/nextflow.config'
-} else if (params.input_type == 'synapse') {
-    includeConfig './workflows/synapse/nextflow.config'
-}
+includeConfig './workflows/sra/nextflow.config'
 
 // Load nf-core/fetchngs custom profiles from different institutions.
 // Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs!
@@ -173,9 +167,8 @@ profiles {
         executor.cpus          = 4
         executor.memory        = 8.GB
     }
-    test         { includeConfig 'conf/test.config'         }
-    test_synapse { includeConfig 'conf/test_synapse.config' }
-    test_full    { includeConfig 'conf/test_full.config'    }
+    test         { includeConfig 'conf/test.config'      }
+    test_full    { includeConfig 'conf/test_full.config' }
 }
 
 // Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
diff --git a/nextflow_schema.json b/nextflow_schema.json
index bdf37cd7..77ae6673 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -22,13 +22,6 @@
                     "fa_icon": "fas fa-file-excel",
                     "description": "File containing SRA/ENA/GEO/DDBJ identifiers one per line to download their associated metadata and FastQ files."
                 },
-                "input_type": {
-                    "type": "string",
-                    "default": "sra",
-                    "description": "Specifies the type of identifier provided via `--input` - available options are 'sra' and 'synapse'.",
-                    "fa_icon": "fas fa-keyboard",
-                    "enum": ["sra", "synapse"]
-                },
                 "ena_metadata_fields": {
                     "type": "string",
                     "fa_icon": "fas fa-columns",
@@ -90,12 +83,6 @@
                     "fa_icon": "fas fa-envelope",
                     "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
                     "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
-                },
-                "synapse_config": {
-                    "type": "string",
-                    "description": "Path to Synapse configuration file",
-                    "fa_icon": "fas fa-users-cog",
-                    "hidden": true
                 }
             }
         },
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
index 821344d0..7b46200f 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
@@ -35,7 +35,6 @@ workflow PIPELINE_INITIALISATION {
     monochrome_logs     // boolean: Do not use coloured log outputs
     outdir              //  string: The output directory where the results will be saved
     input               //  string: File containing SRA/ENA/GEO/DDBJ identifiers one per line to download their associated metadata and FastQ files
-    input_type          //  string: Specifies the type of identifier provided via `--input` - available options are 'sra' and 'synapse'
     ena_metadata_fields //  string: Comma-separated list of ENA metadata fields to fetch before downloading data
 
     main:
@@ -74,18 +73,10 @@ workflow PIPELINE_INITIALISATION {
     // Auto-detect input id type
     //
     ch_input = file(input)
-    def inferred_input_type = ''
     if (isSraId(ch_input)) {
-        inferred_input_type = 'sra'
         sraCheckENAMetadataFields(ena_metadata_fields)
-    } else if (isSynapseId(ch_input)) {
-        inferred_input_type = 'synapse'
     } else {
-        error('Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!')
-    }
-
-    if (input_type != inferred_input_type) {
-        error("Ids auto-detected as ${inferred_input_type}. Please provide '--input_type ${inferred_input_type}' as a parameter to the pipeline!")
+        error('Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ ids!')
     }
 
     // Read in ids from --input file
@@ -109,7 +100,6 @@ workflow PIPELINE_INITIALISATION {
 workflow PIPELINE_COMPLETION {
 
     take:
-    input_type      //  string: 'sra' or 'synapse'
     email           //  string: email address
     email_on_fail   //  string: email address sent on pipeline failure
     plaintext_email // boolean: Send plain-text email instead of HTML
@@ -135,11 +125,7 @@ workflow PIPELINE_COMPLETION {
             imNotification(summary_params, hook_url)
         }
 
-        if (input_type == 'sra') {
-            sraCurateSamplesheetWarn()
-        } else if (input_type == 'synapse') {
-            synapseCurateSamplesheetWarn()
-        }
+        sraCurateSamplesheetWarn()
     }
 }
 
@@ -175,32 +161,6 @@ def isSraId(input) {
     return is_sra
 }
 
-//
-// Check if input ids are from the Synapse platform
-//
-def isSynapseId(input) {
-    def is_synapse = false
-    def total_ids = 0
-    def no_match_ids = []
-    def pattern = /^syn\d{8}$/
-    input.eachLine { line ->
-        total_ids += 1
-        if (!(line =~ pattern)) {
-            no_match_ids << line
-        }
-    }
-
-    def num_match = total_ids - no_match_ids.size()
-    if (num_match > 0) {
-        if (num_match == total_ids) {
-            is_synapse = true
-        } else {
-            error("Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / GEO / DDBJ or Synapse ids!")
-        }
-    }
-    return is_synapse
-}
-
 //
 // Check and validate parameters
 //
@@ -226,89 +186,3 @@ def sraCurateSamplesheetWarn() {
         "  running nf-core/other pipelines.\n" +
         "==================================================================================="
 }
-
-//
-// Convert metadata obtained from the 'synapse show' command to a Groovy map
-//
-def synapseShowToMap(synapse_file) {
-    def meta = [:]
-    def category = ''
-    synapse_file.eachLine { line ->
-        def entries = [null, null]
-        if (!line.startsWith(' ') && !line.trim().isEmpty()) {
-            category = line.tokenize(':')[0]
-        } else {
-            entries = line.trim().tokenize('=')
-        }
-        meta["${category}|${entries[0]}"] = entries[1]
-    }
-    meta.id = meta['properties|id']
-    meta.name = meta['properties|name']
-    meta.md5 = meta['File|md5']
-    return meta.findAll{ it.value != null }
-}
-
-//
-// Print a warning after pipeline has completed
-//
-def synapseCurateSamplesheetWarn() {
-    log.warn "=============================================================================\n" +
-        "  Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" +
-        "  Where applicable, default values will be used for sample-specific metadata\n" +
-        "  such as strandedness, controls etc as this information is not provided\n" +
-        "  in a standardised manner when uploading data to Synapse.\n" +
-        "==================================================================================="
-}
-
-//
-// Obtain Sample ID from File Name
-//
-def synapseSampleNameFromFastQ(input_file, pattern) {
-
-    def sampleids = ""
-
-    def filePattern = pattern.toString()
-    int p = filePattern.lastIndexOf('/')
-        if( p != -1 )
-            filePattern = filePattern.substring(p+1)
-
-    input_file.each {
-        String fileName = input_file.getFileName().toString()
-
-        String indexOfWildcards = filePattern.findIndexOf { it=='*' || it=='?' }
-        String indexOfBrackets = filePattern.findIndexOf { it=='{' || it=='[' }
-        if( indexOfWildcards==-1 && indexOfBrackets==-1 ) {
-            if( fileName == filePattern )
-                return actual.getSimpleName()
-            throw new IllegalArgumentException("Not a valid file pair globbing pattern: pattern=$filePattern file=$fileName")
-        }
-
-        int groupCount = 0
-        for( int i=0; i<filePattern.size(); i++ ) {
-            def ch = filePattern[i]
-            if( ch=='?' || ch=='*' )
-                groupCount++
-            else if( ch=='{' || ch=='[' )
-                break
-        }
-
-        def regex = filePattern
-                .replace('.','\\.')
-                .replace('*','(.*)')
-                .replace('?','(.?)')
-                .replace('{','(?:')
-                .replace('}',')')
-                .replace(',','|')
-
-        def matcher = (fileName =~ /$regex/)
-        if( matcher.matches() ) {
-            int c=Math.min(groupCount, matcher.groupCount())
-            int end = c ? matcher.end(c) : ( indexOfBrackets != -1 ? indexOfBrackets : fileName.size() )
-            def prefix = fileName.substring(0,end)
-            while(prefix.endsWith('-') || prefix.endsWith('_') || prefix.endsWith('.') )
-                prefix=prefix[0..-2]
-            sampleids = prefix
-        }
-    }
-    return sampleids
-}
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test
index 5e5d3a62..85c16bf9 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test
@@ -74,23 +74,4 @@ nextflow_function {
         }
     }
 
-    test("Function isSynapseId") {
-
-        function "isSynapseId"
-
-        when {
-            function {
-                """
-                input[0] = 'syn26240435'
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert snapshot(function.result).match() }
-            )
-        }
-    }
 }
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test
index cfbfab4c..669ac29f 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test
@@ -12,7 +12,6 @@ nextflow_workflow {
             }
             workflow {
                 """
-                input_type      = 'sra'
                 email           = null
                 email_on_fail   = null
                 plaintext_email = false
@@ -20,13 +19,12 @@ nextflow_workflow {
                 monochrome_logs = false
                 hook_url        = null
 
-                input[0] = input_type
-                input[1] = email
-                input[2] = email_on_fail
-                input[3] = plaintext_email
-                input[4] = outdir
-                input[5] = monochrome_logs
-                input[6] = hook_url
+                input[0] = email
+                input[1] = email_on_fail
+                input[2] = plaintext_email
+                input[3] = outdir
+                input[4] = monochrome_logs
+                input[5] = hook_url
                 """
             }
         }
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
index 611eaee7..62103e77 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
@@ -17,7 +17,6 @@ nextflow_workflow {
                 validate_params     = false
                 monochrome_logs     = false
                 outdir              = "$params.outdir"
-                input_type          = 'sra'
                 ena_metadata_fields = null
 
                 input[0] = version
@@ -26,8 +25,7 @@ nextflow_workflow {
                 input[3] = monochrome_logs
                 input[4] = outdir
                 input[5] = 'https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/testdata/v1.12.0/sra_ids_test.csv'
-                input[6] = input_type
-                input[7] = ena_metadata_fields
+                input[6] = ena_metadata_fields
                 """
             }
         }
diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf
deleted file mode 100644
index 38071b60..00000000
--- a/workflows/synapse/main.nf
+++ /dev/null
@@ -1,125 +0,0 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    IMPORT LOCAL MODULES/SUBWORKFLOWS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-include { SYNAPSE_LIST              } from '../../modules/local/synapse_list'
-include { SYNAPSE_SHOW              } from '../../modules/local/synapse_show'
-include { SYNAPSE_GET               } from '../../modules/local/synapse_get'
-include { SYNAPSE_TO_SAMPLESHEET    } from '../../modules/local/synapse_to_samplesheet'
-include { SYNAPSE_MERGE_SAMPLESHEET } from '../../modules/local/synapse_merge_samplesheet'
-include { softwareVersionsToYAML    } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    RUN MAIN WORKFLOW
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-workflow SYNAPSE {
-
-    take:
-    ids               // channel: [ ids ]
-    ch_synapse_config // channel: [ synapse_config ]
-
-    main:
-    ch_versions = Channel.empty()
-
-    //
-    // MODULE: Expand synapse ids for individual FastQ files
-    //
-    SYNAPSE_LIST (
-        ids,
-        ch_synapse_config
-    )
-    ch_versions = ch_versions.mix(SYNAPSE_LIST.out.versions.first())
-
-    // Create channel for FastQ synapse ids
-    SYNAPSE_LIST
-        .out
-        .txt
-        .splitCsv(header:false, sep:' ')
-        .map { it[0] }
-        .unique()
-        .set { ch_samples }
-
-    //
-    // MODULE: Download metadata for each synapse id
-    //
-    SYNAPSE_SHOW (
-        ch_samples,
-        ch_synapse_config
-    )
-    ch_versions = ch_versions.mix(SYNAPSE_SHOW.out.versions.first())
-
-    // Get metadata into channels
-    SYNAPSE_SHOW
-        .out
-        .metadata
-        .map { it -> WorkflowMain.synapseShowToMap(it) }
-        .set { ch_samples_meta }
-
-    //
-    // MODULE: Download FastQs by synapse id
-    //
-    SYNAPSE_GET (
-        ch_samples_meta,
-        ch_synapse_config
-    )
-    ch_versions = ch_versions.mix(SYNAPSE_GET.out.versions.first())
-
-    // Combine channels for PE/SE FastQs: [ [ id:SRR6357070, synapse_ids:syn26240474;syn26240477 ], [ fastq_1, fastq_2 ] ]
-    SYNAPSE_GET
-        .out
-        .fastq
-        .map { meta, fastq -> [ WorkflowMain.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), fastq ] }
-        .groupTuple(sort: { it -> it.baseName })
-        .set { ch_fastq }
-
-    SYNAPSE_GET
-        .out
-        .fastq
-        .map { meta, fastq -> [ WorkflowMain.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), meta.id ] }
-        .groupTuple()
-        .join(ch_fastq)
-        .map { id, synids, fastq ->
-            def meta = [ id:id, synapse_ids:synids.join(';') ]
-            [ meta, fastq ]
-        }
-        .set { ch_fastq }
-
-    //
-    // MODULE: Create samplesheet per sample
-    //
-    SYNAPSE_TO_SAMPLESHEET (
-        ch_fastq,
-        params.nf_core_pipeline ?: '',
-        params.nf_core_rnaseq_strandedness ?: 'auto'
-    )
-
-    //
-    // MODULE: Merge samplesheets
-    //
-    SYNAPSE_MERGE_SAMPLESHEET (
-        SYNAPSE_TO_SAMPLESHEET.out.samplesheet.collect{ it[1] }
-    )
-    ch_versions = ch_versions.mix(SYNAPSE_MERGE_SAMPLESHEET.out.versions)
-
-    //
-    // Collate and save software versions
-    //
-    softwareVersionsToYAML(ch_versions)
-        .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_fetchngs_software_mqc_versions.yml', sort: true, newLine: true)
-
-    emit:
-    fastq       = ch_fastq
-    samplesheet = SYNAPSE_MERGE_SAMPLESHEET.out.samplesheet
-    versions    = ch_versions.unique()
-}
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    THE END
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
diff --git a/workflows/synapse/nextflow.config b/workflows/synapse/nextflow.config
deleted file mode 100644
index ad9c69ed..00000000
--- a/workflows/synapse/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-includeConfig "../../modules/local/synapse_get/nextflow.config"
-includeConfig "../../modules/local/synapse_to_samplesheet/nextflow.config"
-includeConfig "../../modules/local/synapse_list/nextflow.config"
-includeConfig "../../modules/local/synapse_merge_samplesheet/nextflow.config"
-includeConfig "../../modules/local/synapse_show/nextflow.config"

From cd4b6bf98336db21c84c52cb1303a0da5405a5f6 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 1 Feb 2024 10:45:33 +0000
Subject: [PATCH 748/852] Update CHANGELOG

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b0061622..b54f463c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - The Aspera CLI was recently added to [Bioconda](https://anaconda.org/bioconda/aspera-cli) and we have added it as another way of downloading FastQ files on top of the existing FTP and sra-tools support. In our limited benchmarks on all public Clouds we found ~50% speed-up in download times compared to FTP! We are not aware of any obvious downsides and have made this the default download method in the pipeline. You can however, revert to using FTP and sra-tools using the `--force_ftp_download` and `--force_sratools_download` parameters, respectively. We would love to have your feedback!
 - Support for Synapse ids has been dropped in this release. We haven't had any feedback from users whether it is being used or not. Users can run earlier versions of the pipeline if required.
+- We have significantly refactored and standardised the way we are using nf-test within this pipeline. This pipeline is now the current, best-practice implementation for nf-test usage on nf-core. We required a number of features to be added to nf-test and a huge shoutout to [Lukas Forer](https://github.com/lukfor) for entertaining our requests and implementing them within upstream :heart:!
 
 ### Credits
 
@@ -17,6 +18,7 @@ Special thanks to the following for their contributions to the release:
 - [Adam Talbot](https://github.com/adamrtalbot)
 - [Alexandru Mizeranschi](https://github.com/nicolae06)
 - [Alexander Blaessle](https://github.com/alexblaessle)
+- [Lukas Forer](https://github.com/lukfor)
 - [Maxime Garcia](https://github.com/maxulysse)
 - [Sebastian Uhrig](https://github.com/suhrig)
 

From 76b5fd9ebb0473b9da93bf54d59212504bfd7441 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 1 Feb 2024 10:47:23 +0000
Subject: [PATCH 749/852] Bump pipeline version to 1.12.0

---
 CHANGELOG.md    | 2 +-
 nextflow.config | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b54f463c..3807610a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unpublished Version / DEV]
+## [[1.12.0](https://github.com/nf-core/fetchngs/releases/tag/1.12.0)] - 2024-02-02
 
 ### :warning: Major enhancements
 
diff --git a/nextflow.config b/nextflow.config
index c9b67f04..fad805bf 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -226,7 +226,7 @@ manifest {
     description     = """Pipeline to fetch metadata and raw FastQ files from public databases"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.12.0dev'
+    version         = '1.12.0'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
 

From 3e825cca662854cde363876444a2d404f8bd43c9 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 1 Feb 2024 11:15:48 +0000
Subject: [PATCH 750/852] Update CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3807610a..750abeff 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -41,6 +41,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #261](https://github.com/nf-core/fetchngs/pull/261) - Revert sratools fasterqdump version ([#221](https://github.com/nf-core/fetchngs/issues/221))
 - [PR #262](https://github.com/nf-core/fetchngs/pull/262) - Use nf-test version v0.8.4 and remove implicit tags
 - [PR #263](https://github.com/nf-core/fetchngs/pull/263) - Refine tags used for workflows
+- [PR #264](https://github.com/nf-core/fetchngs/pull/264) - Remove synapse workflow from pipeline
 
 ### Software dependencies
 

From 80a898389d1fe3f83d2335817fb43aefd1f018cf Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 1 Feb 2024 17:41:42 +0000
Subject: [PATCH 751/852] Use +profile in CI to add test to
 docker/conda/singularity profile

Changes:
 - Uses "+" syntax from nf-test to add a the test profile to pre-existing profile
 - No other changes yet, keeping the PR small
 - We can replace parts of the test config after this is implemented
---
 .github/workflows/ci.yml | 2 +-
 CHANGELOG.md             | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1395c844..2d4387a8 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -148,7 +148,7 @@ jobs:
 
       - name: Run nf-test
         run: |
-          nf-test test --verbose --tag ${{ matrix.tags }} --profile "${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
+          nf-test test --verbose --tag ${{ matrix.tags }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
 
       - uses: pcolby/tap-summary@v1
         with:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 750abeff..ff44ad66 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -42,6 +42,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #262](https://github.com/nf-core/fetchngs/pull/262) - Use nf-test version v0.8.4 and remove implicit tags
 - [PR #263](https://github.com/nf-core/fetchngs/pull/263) - Refine tags used for workflows
 - [PR #264](https://github.com/nf-core/fetchngs/pull/264) - Remove synapse workflow from pipeline
+- [PR #265](https://github.com/nf-core/fetchngs/pull/265) - Use "+" syntax for profiles to accumulate profiles in nf-test
 
 ### Software dependencies
 

From 6ae6f14045de0dc3d21c7696e13806809fcbb7c2 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 1 Feb 2024 18:11:35 +0000
Subject: [PATCH 752/852] Make gitignore match template

---
 .gitignore   | 14 +++++++-------
 .nf-core.yml |  2 +-
 CHANGELOG.md |  1 +
 3 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/.gitignore b/.gitignore
index ef809d7c..3e70ad89 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,12 +1,12 @@
-*.pyc
-.DS_Store
 .nextflow*
-.nf-test.log
+work/
 data/
+results/
+.DS_Store
+testing/
+testing*
+*.pyc
+.nf-test.log
 nf-test
 .nf-test*
-results/
 test.xml
-testing*
-testing/
-work/
diff --git a/.nf-core.yml b/.nf-core.yml
index 707d5cd8..705cd855 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -7,5 +7,5 @@ lint:
     - lib/Utils.groovy
     - lib/WorkflowMain.groovy
   files_unchanged:
-    - .gitignore
+    - '.gitignore'
     - assets/sendmail_template.txt
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 750abeff..093039f3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -42,6 +42,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #262](https://github.com/nf-core/fetchngs/pull/262) - Use nf-test version v0.8.4 and remove implicit tags
 - [PR #263](https://github.com/nf-core/fetchngs/pull/263) - Refine tags used for workflows
 - [PR #264](https://github.com/nf-core/fetchngs/pull/264) - Remove synapse workflow from pipeline
+- [PR #266](https://github.com/nf-core/fetchngs/pull/266) - Make .gitignore match template
 
 ### Software dependencies
 

From cf07cad9a335092e3e63800a50f63eae3f4630cd Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 1 Feb 2024 18:13:25 +0000
Subject: [PATCH 753/852] revert .nf-core.yml

---
 .nf-core.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index 705cd855..707d5cd8 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -7,5 +7,5 @@ lint:
     - lib/Utils.groovy
     - lib/WorkflowMain.groovy
   files_unchanged:
-    - '.gitignore'
+    - .gitignore
     - assets/sendmail_template.txt

From 93e997a76a18a402a1470f2867528650ffd36e83 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Fri, 2 Feb 2024 11:22:01 +0100
Subject: [PATCH 754/852] Update README.md

restore badges
---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index f652bd66..9419fa1a 100644
--- a/README.md
+++ b/README.md
@@ -4,6 +4,7 @@
     <img alt="nf-core/fetchngs" src="docs/images/nf-core-fetchngs_logo_light.png">
   </picture>
 </h1>
+
 [![GitHub Actions CI Status](https://github.com/nf-core/fetchngs/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/fetchngs/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/nf-core/fetchngs/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/fetchngs/actions?query=workflow%3A%22nf-core+linting%22)
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/fetchngs/results)

From b35e947990b59f400c1140620456a1f513c402ba Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 2 Feb 2024 11:13:19 +0000
Subject: [PATCH 755/852] Add Mermaid diagram

---
 CHANGELOG.md |  1 +
 README.md    | 30 ++++++++++++++++++++++++++++++
 2 files changed, 31 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0f2d0620..495ab427 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -44,6 +44,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #264](https://github.com/nf-core/fetchngs/pull/264) - Remove synapse workflow from pipeline
 - [PR #265](https://github.com/nf-core/fetchngs/pull/265) - Use "+" syntax for profiles to accumulate profiles in nf-test
 - [PR #266](https://github.com/nf-core/fetchngs/pull/266) - Make .gitignore match template
+- [PR #267](https://github.com/nf-core/fetchngs/pull/267) - Add mermaid diagram
 
 ### Software dependencies
 
diff --git a/README.md b/README.md
index 9419fa1a..b35e583e 100644
--- a/README.md
+++ b/README.md
@@ -23,6 +23,36 @@
 
 **nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from both public and private databases. At present, the pipeline supports SRA / ENA / DDBJ / GEO / Synapse ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)).
 
+```mermaid
+flowchart LR
+    IDS("`Input 
+    File`") --> SRA & GEO & ENA & DDBJ
+    subgraph SG_DBIDS[Database IDs]
+      SRA("SRA")
+      GEO("GEO")
+      ENA("ENA")
+      DDBJ("DDBJ")
+    end
+    subgraph SG_METADATA[Download Metadata]
+      SRA & GEO & ENA & DDBJ --> META("`Get 
+      Metadata`")
+      META --> LINKS("`Get 
+      Download
+      Links`")
+    end
+    subgraph SG_FETCH_FASTQ[Download FastQ]
+      LINKS --> |default| ASPERA("Aspera")
+      LINKS --> |--force_ftp_download| FTP("FTP")
+      LINKS --> |--force_sra_tools_download| SRATOOLS("sra-tools")
+    end
+    subgraph SG_FASTQ[Pipeline Outputs]
+      ASPERA & FTP & SRATOOLS --> FASTQ("FastQ")
+      FASTQ --> SAMPLESHEET("Samplesheet")
+    end
+    LINKS --> |--skip_fastq_download| SAMPLESHEET
+    
+```
+
 ## Usage
 
 > [!NOTE]

From e5daf3af2c62bfd45be8df2282b4baf3d3301a0f Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 2 Feb 2024 11:14:33 +0000
Subject: [PATCH 756/852] Correct CHANGELOG

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 495ab427..35c7a01d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -44,7 +44,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #264](https://github.com/nf-core/fetchngs/pull/264) - Remove synapse workflow from pipeline
 - [PR #265](https://github.com/nf-core/fetchngs/pull/265) - Use "+" syntax for profiles to accumulate profiles in nf-test
 - [PR #266](https://github.com/nf-core/fetchngs/pull/266) - Make .gitignore match template
-- [PR #267](https://github.com/nf-core/fetchngs/pull/267) - Add mermaid diagram
+- [PR #268](https://github.com/nf-core/fetchngs/pull/268) - Add mermaid diagram
 
 ### Software dependencies
 

From fb324b84851de952c65111a5e4ceb83dbc39f793 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 2 Feb 2024 11:15:42 +0000
Subject: [PATCH 757/852] Change theme to Forest

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index b35e583e..90a147ac 100644
--- a/README.md
+++ b/README.md
@@ -24,6 +24,7 @@
 **nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from both public and private databases. At present, the pipeline supports SRA / ENA / DDBJ / GEO / Synapse ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)).
 
 ```mermaid
+%%{init: {'theme': 'forest' } }%%
 flowchart LR
     IDS("`Input 
     File`") --> SRA & GEO & ENA & DDBJ

From bece63439b7e290a6dac3c50fb07440e599aceec Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 2 Feb 2024 11:19:23 +0000
Subject: [PATCH 758/852] Trying some themes

---
 README.md | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 90a147ac..523c9c01 100644
--- a/README.md
+++ b/README.md
@@ -24,7 +24,20 @@
 **nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from both public and private databases. At present, the pipeline supports SRA / ENA / DDBJ / GEO / Synapse ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)).
 
 ```mermaid
-%%{init: {'theme': 'forest' } }%%
+%%{
+  init: {
+    "theme": "forest",
+    "fontFamily": "monospace",
+    "logLevel": "info",
+    "flowchart": {
+      "htmlLabels": true,
+      "curve": "linear"
+    },
+    "sequence": {
+      "mirrorActors": true
+    }
+  }
+}%%
 flowchart LR
     IDS("`Input 
     File`") --> SRA & GEO & ENA & DDBJ
@@ -42,7 +55,7 @@ flowchart LR
       Links`")
     end
     subgraph SG_FETCH_FASTQ[Download FastQ]
-      LINKS --> |default| ASPERA("Aspera")
+      LINKS --> |"(default)"| ASPERA("Aspera")
       LINKS --> |--force_ftp_download| FTP("FTP")
       LINKS --> |--force_sra_tools_download| SRATOOLS("sra-tools")
     end

From 26ba7580deb1837b2bd4d2d26c8da4e6070b6e83 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 2 Feb 2024 11:21:20 +0000
Subject: [PATCH 759/852] Remove backticks|

---
 README.md | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 523c9c01..c7e9d5a0 100644
--- a/README.md
+++ b/README.md
@@ -39,8 +39,8 @@
   }
 }%%
 flowchart LR
-    IDS("`Input 
-    File`") --> SRA & GEO & ENA & DDBJ
+    IDS("Input 
+    File") --> SRA & GEO & ENA & DDBJ
     subgraph SG_DBIDS[Database IDs]
       SRA("SRA")
       GEO("GEO")
@@ -48,11 +48,11 @@ flowchart LR
       DDBJ("DDBJ")
     end
     subgraph SG_METADATA[Download Metadata]
-      SRA & GEO & ENA & DDBJ --> META("`Get 
-      Metadata`")
-      META --> LINKS("`Get 
+      SRA & GEO & ENA & DDBJ --> META("Get 
+      Metadata")
+      META --> LINKS("Get 
       Download
-      Links`")
+      Links")
     end
     subgraph SG_FETCH_FASTQ[Download FastQ]
       LINKS --> |"(default)"| ASPERA("Aspera")

From 7b69bce638030188e06d62f8b1c6085285e4c552 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 2 Feb 2024 11:22:02 +0000
Subject: [PATCH 760/852] Remove some theme stuff

---
 README.md | 2 --
 1 file changed, 2 deletions(-)

diff --git a/README.md b/README.md
index c7e9d5a0..188fc3f4 100644
--- a/README.md
+++ b/README.md
@@ -27,11 +27,9 @@
 %%{
   init: {
     "theme": "forest",
-    "fontFamily": "monospace",
     "logLevel": "info",
     "flowchart": {
       "htmlLabels": true,
-      "curve": "linear"
     },
     "sequence": {
       "mirrorActors": true

From 0e18e7ee20910dd4fed20c6f01a2ebb7362fe77b Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 2 Feb 2024 11:26:01 +0000
Subject: [PATCH 761/852] pulling more stuff out of the mermaid

---
 README.md | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/README.md b/README.md
index 188fc3f4..847fe3ee 100644
--- a/README.md
+++ b/README.md
@@ -27,13 +27,7 @@
 %%{
   init: {
     "theme": "forest",
-    "logLevel": "info",
-    "flowchart": {
-      "htmlLabels": true,
-    },
-    "sequence": {
-      "mirrorActors": true
-    }
+    "logLevel": "info"
   }
 }%%
 flowchart LR

From f94c742c6395bf0041c2f16430d74d0c530407a4 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 2 Feb 2024 11:38:59 +0000
Subject: [PATCH 762/852] Approximate nf-core theme (attempt 1)

---
 README.md | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 847fe3ee..095f8e45 100644
--- a/README.md
+++ b/README.md
@@ -26,8 +26,14 @@
 ```mermaid
 %%{
   init: {
-    "theme": "forest",
-    "logLevel": "info"
+    'theme': 'base',
+    'themeVariables': {
+      'fontFamily': "maven pro bold",
+      'primaryColor': '#24B064',
+      'primaryTextColor': '#fff',
+      'secondaryColor': '#006100',
+      'tertiaryColor': '#fff'
+    }
   }
 }%%
 flowchart LR

From ddf7e3c8da8155e0d370212ad9ea29cca533316e Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 2 Feb 2024 12:13:51 +0000
Subject: [PATCH 763/852] Style updates to Mermaid

---
 README.md | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 095f8e45..23fbd2a0 100644
--- a/README.md
+++ b/README.md
@@ -28,10 +28,13 @@
   init: {
     'theme': 'base',
     'themeVariables': {
-      'fontFamily': "maven pro bold",
+      'fontFamily': "maven",
       'primaryColor': '#24B064',
       'primaryTextColor': '#fff',
-      'secondaryColor': '#006100',
+      'secondaryTextColor': '#000000',
+      'secondaryColor': '#BCDDB6',
+      'edgeLabelBackground': '#C8C8C8',
+      'noteTextColor': '#050505',
       'tertiaryColor': '#fff'
     }
   }

From 64a40cf54b39455322d6a0a0728c7cb9c9eef49a Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 2 Feb 2024 16:01:42 +0000
Subject: [PATCH 764/852] Remove theme stuff because it doesn't work on Github
 Dark mode

---
 README.md | 15 ---------------
 1 file changed, 15 deletions(-)

diff --git a/README.md b/README.md
index 23fbd2a0..8b6d253b 100644
--- a/README.md
+++ b/README.md
@@ -24,21 +24,6 @@
 **nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from both public and private databases. At present, the pipeline supports SRA / ENA / DDBJ / GEO / Synapse ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)).
 
 ```mermaid
-%%{
-  init: {
-    'theme': 'base',
-    'themeVariables': {
-      'fontFamily': "maven",
-      'primaryColor': '#24B064',
-      'primaryTextColor': '#fff',
-      'secondaryTextColor': '#000000',
-      'secondaryColor': '#BCDDB6',
-      'edgeLabelBackground': '#C8C8C8',
-      'noteTextColor': '#050505',
-      'tertiaryColor': '#fff'
-    }
-  }
-}%%
 flowchart LR
     IDS("Input 
     File") --> SRA & GEO & ENA & DDBJ

From 342a331c5b09b4250831ec4d9ff60460457f5794 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 12 Feb 2024 17:41:20 +0000
Subject: [PATCH 765/852] Parse nf-test file directly for finding target
 objects

Add new method for detecting file changes by parsing nf-test files directly using python
Can stand in until nf-test list has new features
---
 .github/python/find_changed_files.py | 140 +++++++++++++++++++++++++++
 .github/workflows/ci.yml             |  40 +++++---
 2 files changed, 165 insertions(+), 15 deletions(-)
 create mode 100644 .github/python/find_changed_files.py

diff --git a/.github/python/find_changed_files.py b/.github/python/find_changed_files.py
new file mode 100644
index 00000000..91241c0d
--- /dev/null
+++ b/.github/python/find_changed_files.py
@@ -0,0 +1,140 @@
+#!/usr/bin/env python
+
+## This script is used to generate scan *.nf.test files for function/process/workflow name and return as a JSON list
+# It is functionally similar to nf-test list but fills a gap until feature https://github.com/askimed/nf-test/issues/196 is added
+
+import argparse
+import json
+import logging
+import re
+import yaml
+
+from pathlib import Path
+
+
+def parse_args() -> argparse.Namespace:
+    """
+    Parse command line arguments and return an ArgumentParser object.
+
+    Returns:
+        argparse.ArgumentParser: The ArgumentParser object with the parsed arguments.
+    """
+    parser = argparse.ArgumentParser(
+        description="Scan *.nf.test files for function/process/workflow name and return as a JSON list"
+    )
+    parser.add_argument(
+        "paths", nargs="*", default=["."], help="List of directories or files to scan"
+    )
+    parser.add_argument(
+        "-l",
+        "--log-level",
+        choices=["DEBUG", "INFO", "WARNING", "ERROR"],
+        default="INFO",
+        help="Logging level",
+    )
+    parser.add_argument(
+        "-t",
+        "--types",
+        nargs="+",
+        choices=["function", "process", "workflow", "pipeline"],
+        default=["function", "process", "workflow", "pipeline"],
+        help="Types of tests to include.",
+    )
+    return parser.parse_args()
+
+
+def find_files(paths: list[str]) -> list[Path]:
+    """
+    Find all files matching pattern *.nf.test recursively from a list of paths.
+
+    Args:
+        paths (list): List of directories or files to scan.
+
+    Returns:
+        list: List of files matching the pattern *.nf.test.
+    """
+    return [test_file for path in paths for test_file in Path(path).rglob("*.nf.test")]
+
+
+def process_files(files: list[Path]) -> list[str]:
+    """
+    Process the files and return lines that begin with 'workflow', 'process', or 'function' and have a single string afterwards.
+
+    Args:
+        files (list): List of files to process.
+
+    Returns:
+        list: List of lines that match the criteria.
+    """
+    result = []
+    for file in files:
+        with open(file, "r") as f:
+            lines = f.readlines()
+            for line in lines:
+                line = line.strip()
+                if line.startswith(("workflow", "process", "function")):
+                    words = line.split()
+                    if len(words) == 2 and re.match(r'^".*"$', words[1]):
+                        result.append(line)
+    return result
+
+
+def generate(
+    lines: list[str], types: list[str] = ["function", "process", "workflow", "pipeline"]
+) -> dict[str, list[str]]:
+    """
+    Generate a dictionary of function, process, workflow, and pipeline lists from the lines.
+
+    Args:
+        lines (list): List of lines to process.
+        types (list): List of types to include.
+
+    Returns:
+        dict: Dictionary with function, process, workflow, and pipeline lists.
+    """
+    result: dict[str, list[str]] = {
+        "function": [],
+        "process": [],
+        "workflow": [],
+        "pipeline": [],
+    }
+    for line in lines:
+        words = line.split()
+        if len(words) == 2:
+            keyword = words[0]
+            name = words[1].strip("'\"")  # Strip both single and double quotes
+            if keyword in types:
+                result[keyword].append(name)
+    return result
+
+
+def read_yaml_file(file_path: str) -> dict:
+    """
+    Read a YAML file and return its contents as a dictionary.
+
+    Args:
+        file_path (str): The path to the YAML file.
+
+    Returns:
+        dict: The contents of the YAML file as a dictionary.
+    """
+    with open(file_path, "r") as f:
+        data = yaml.safe_load(f)
+    return data
+
+
+if __name__ == "__main__":
+
+    # Utility stuff
+    args = parse_args()
+    logging.basicConfig(level=args.log_level)
+
+    files = find_files(args.paths)
+    lines = process_files(files)
+    result = generate(lines, args.types)
+
+    # Flatten dict to list of results
+    # Mmm ugly. Yet glorious.
+    result_flat = list(set().union(*result.values()))
+    # Print to stdout
+    print(json.dumps(result_flat))
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2d4387a8..241a4bf3 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -30,23 +30,33 @@ jobs:
       changes: ${{ steps.changed_files.outputs.any_modified }}
       tags: ${{ steps.list.outputs.tags }}
     steps:
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
-
-      - name: Cache nf-test installation
-        id: cache-software
-        uses: actions/cache@v3
+      - uses: actions/setup-python@v4
         with:
-          path: |
-            /usr/local/bin/nf-test
-            /home/runner/.nf-test/nf-test.jar
-          key: ${{ runner.os }}-${{ env.NFT_VER }}-nftest
+          python-version: "3.11"
+          architecture: "x64"
 
-      - name: Install nf-test
-        if: steps.cache-software.outputs.cache-hit != 'true'
+      - name: Install pdiff to see diff between nf-test snapshots
         run: |
-          wget -qO- https://code.askimed.com/install/nf-test | bash
-          sudo mv nf-test /usr/local/bin/
+          python -m pip install --upgrade pip
+          pip install pdiff
+
+      # - name: Install Nextflow
+      #   uses: nf-core/setup-nextflow@v1
+
+      # - name: Cache nf-test installation
+      #   id: cache-software
+      #   uses: actions/cache@v3
+      #   with:
+      #     path: |
+      #       /usr/local/bin/nf-test
+      #       /home/runner/.nf-test/nf-test.jar
+      #     key: ${{ runner.os }}-${{ env.NFT_VER }}-nftest
+
+      # - name: Install nf-test
+      #   if: steps.cache-software.outputs.cache-hit != 'true'
+      #   run: |
+      #     wget -qO- https://code.askimed.com/install/nf-test | bash
+      #     sudo mv nf-test /usr/local/bin/
 
       - uses: actions/checkout@v3
         with:
@@ -91,7 +101,7 @@ jobs:
       - name: nf-test list tags
         id: list
         if: ${{ steps.changed_files.outputs.any_modified }}
-        run: echo tags=$(nf-test list --silent --tags --format json ${{ steps.changed_files.outputs.all_changed_files }} ${{ steps.changed_files.outputs.changed_keys }}) >> $GITHUB_OUTPUT
+        run: echo tags=$(python .github/python/find_changed_files.py ${{ steps.changed_files.outputs.all_changed_files }} ${{ steps.changed_files.outputs.changed_keys }}) >> $GITHUB_OUTPUT
 
       - name: debug2
         run: |

From 4eee0e39ff080c0df18d6f132b6e37ff3294b6f0 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 12 Feb 2024 18:18:49 +0000
Subject: [PATCH 766/852] remove pyyaml

---
 .github/python/find_changed_files.py | 16 ----------------
 .github/workflows/ci.yml             |  5 -----
 2 files changed, 21 deletions(-)

diff --git a/.github/python/find_changed_files.py b/.github/python/find_changed_files.py
index 91241c0d..39e04676 100644
--- a/.github/python/find_changed_files.py
+++ b/.github/python/find_changed_files.py
@@ -7,7 +7,6 @@
 import json
 import logging
 import re
-import yaml
 
 from pathlib import Path
 
@@ -108,21 +107,6 @@ def generate(
     return result
 
 
-def read_yaml_file(file_path: str) -> dict:
-    """
-    Read a YAML file and return its contents as a dictionary.
-
-    Args:
-        file_path (str): The path to the YAML file.
-
-    Returns:
-        dict: The contents of the YAML file as a dictionary.
-    """
-    with open(file_path, "r") as f:
-        data = yaml.safe_load(f)
-    return data
-
-
 if __name__ == "__main__":
 
     # Utility stuff
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 241a4bf3..6f64125e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -35,11 +35,6 @@ jobs:
           python-version: "3.11"
           architecture: "x64"
 
-      - name: Install pdiff to see diff between nf-test snapshots
-        run: |
-          python -m pip install --upgrade pip
-          pip install pdiff
-
       # - name: Install Nextflow
       #   uses: nf-core/setup-nextflow@v1
 

From ae50c4b242511333318c4d9a7e985efa21e6a589 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 13 Feb 2024 11:03:27 +0000
Subject: [PATCH 767/852] Update to improve filtering of output

Changes:
 - find_changed_files.py now supports filtering to only process, workflow or function
 - still struggling for Pipeline tag support
---
 .github/python/find_changed_files.py | 38 +++++++++++++++-------------
 .github/workflows/ci.yml             | 18 -------------
 2 files changed, 21 insertions(+), 35 deletions(-)

diff --git a/.github/python/find_changed_files.py b/.github/python/find_changed_files.py
index 39e04676..485b61c7 100644
--- a/.github/python/find_changed_files.py
+++ b/.github/python/find_changed_files.py
@@ -8,6 +8,7 @@
 import logging
 import re
 
+from itertools import chain
 from pathlib import Path
 
 
@@ -22,7 +23,11 @@ def parse_args() -> argparse.Namespace:
         description="Scan *.nf.test files for function/process/workflow name and return as a JSON list"
     )
     parser.add_argument(
-        "paths", nargs="*", default=["."], help="List of directories or files to scan"
+        "-p",
+        "--paths",
+        nargs="+",
+        default=["."],
+        help="List of directories or files to scan",
     )
     parser.add_argument(
         "-l",
@@ -35,8 +40,8 @@ def parse_args() -> argparse.Namespace:
         "-t",
         "--types",
         nargs="+",
-        choices=["function", "process", "workflow", "pipeline"],
-        default=["function", "process", "workflow", "pipeline"],
+        choices=["function", "process", "workflow"],
+        default=["function", "process", "workflow"],
         help="Types of tests to include.",
     )
     return parser.parse_args()
@@ -79,24 +84,19 @@ def process_files(files: list[Path]) -> list[str]:
 
 
 def generate(
-    lines: list[str], types: list[str] = ["function", "process", "workflow", "pipeline"]
+    lines: list[str], types: list[str] = ["function", "process", "workflow"]
 ) -> dict[str, list[str]]:
     """
-    Generate a dictionary of function, process, workflow, and pipeline lists from the lines.
+    Generate a dictionary of function, process and workflow lists from the lines.
 
     Args:
         lines (list): List of lines to process.
         types (list): List of types to include.
 
     Returns:
-        dict: Dictionary with function, process, workflow, and pipeline lists.
+        dict: Dictionary with function, process and workflow lists.
     """
-    result: dict[str, list[str]] = {
-        "function": [],
-        "process": [],
-        "workflow": [],
-        "pipeline": [],
-    }
+    result: dict[str, list[str]] = {"function": [], "process": [], "workflow": []}
     for line in lines:
         words = line.split()
         if len(words) == 2:
@@ -113,12 +113,16 @@ def generate(
     args = parse_args()
     logging.basicConfig(level=args.log_level)
 
+    # Parse nf-test files for targets of tests
     files = find_files(args.paths)
     lines = process_files(files)
-    result = generate(lines, args.types)
+    result = generate(lines)
+
+    # Get only relevant results (specified by -t)
+    # Unique using a set
+    target_results = list(
+        {item for sublist in map(result.get, args.types) for item in sublist}
+    )
 
-    # Flatten dict to list of results
-    # Mmm ugly. Yet glorious.
-    result_flat = list(set().union(*result.values()))
     # Print to stdout
-    print(json.dumps(result_flat))
+    print(json.dumps(target_results))
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6f64125e..314e8868 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -35,24 +35,6 @@ jobs:
           python-version: "3.11"
           architecture: "x64"
 
-      # - name: Install Nextflow
-      #   uses: nf-core/setup-nextflow@v1
-
-      # - name: Cache nf-test installation
-      #   id: cache-software
-      #   uses: actions/cache@v3
-      #   with:
-      #     path: |
-      #       /usr/local/bin/nf-test
-      #       /home/runner/.nf-test/nf-test.jar
-      #     key: ${{ runner.os }}-${{ env.NFT_VER }}-nftest
-
-      # - name: Install nf-test
-      #   if: steps.cache-software.outputs.cache-hit != 'true'
-      #   run: |
-      #     wget -qO- https://code.askimed.com/install/nf-test | bash
-      #     sudo mv nf-test /usr/local/bin/
-
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0

From a33d3698b535ba45c85ca75404f5346d4156ddf8 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 13 Feb 2024 11:25:27 +0000
Subject: [PATCH 768/852] find_changed_files handles PIPELINE tags

---
 .github/python/find_changed_files.py | 34 ++++++++++++++++++++++++----
 .github/workflows/ci.yml             |  6 ++++-
 2 files changed, 34 insertions(+), 6 deletions(-)

diff --git a/.github/python/find_changed_files.py b/.github/python/find_changed_files.py
index 485b61c7..6dc73449 100644
--- a/.github/python/find_changed_files.py
+++ b/.github/python/find_changed_files.py
@@ -40,8 +40,8 @@ def parse_args() -> argparse.Namespace:
         "-t",
         "--types",
         nargs="+",
-        choices=["function", "process", "workflow"],
-        default=["function", "process", "workflow"],
+        choices=["function", "process", "workflow", "pipeline"],
+        default=["function", "process", "workflow", "pipeline"],
         help="Types of tests to include.",
     )
     return parser.parse_args()
@@ -57,7 +57,18 @@ def find_files(paths: list[str]) -> list[Path]:
     Returns:
         list: List of files matching the pattern *.nf.test.
     """
-    return [test_file for path in paths for test_file in Path(path).rglob("*.nf.test")]
+    # this is a bit clunky
+    result = []
+    for path in paths:
+        path_obj = Path(path)
+        # If Path is the exact nf-test file add to list:
+        if path_obj.match("*.nf.test"):
+            result.append(path_obj)
+        # Else recursively search for nf-test files:
+        else:
+            for file in path_obj.rglob("*.nf.test"):
+                result.append(file)
+    return result
 
 
 def process_files(files: list[Path]) -> list[str]:
@@ -73,6 +84,7 @@ def process_files(files: list[Path]) -> list[str]:
     result = []
     for file in files:
         with open(file, "r") as f:
+            is_pipeline_test = True
             lines = f.readlines()
             for line in lines:
                 line = line.strip()
@@ -80,11 +92,18 @@ def process_files(files: list[Path]) -> list[str]:
                     words = line.split()
                     if len(words) == 2 and re.match(r'^".*"$', words[1]):
                         result.append(line)
+                        is_pipeline_test = False
+
+            # If no results included workflow, process or function
+            # Add a dummy result to fill the 'pipeline' category
+            if is_pipeline_test:
+                result.append("pipeline 'PIPELINE'")
+
     return result
 
 
 def generate(
-    lines: list[str], types: list[str] = ["function", "process", "workflow"]
+    lines: list[str], types: list[str] = ["function", "process", "workflow", "pipeline"]
 ) -> dict[str, list[str]]:
     """
     Generate a dictionary of function, process and workflow lists from the lines.
@@ -96,7 +115,12 @@ def generate(
     Returns:
         dict: Dictionary with function, process and workflow lists.
     """
-    result: dict[str, list[str]] = {"function": [], "process": [], "workflow": []}
+    result: dict[str, list[str]] = {
+        "function": [],
+        "process": [],
+        "workflow": [],
+        "pipeline": [],
+    }
     for line in lines:
         words = line.split()
         if len(words) == 2:
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 314e8868..d2ddf312 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -78,7 +78,11 @@ jobs:
       - name: nf-test list tags
         id: list
         if: ${{ steps.changed_files.outputs.any_modified }}
-        run: echo tags=$(python .github/python/find_changed_files.py ${{ steps.changed_files.outputs.all_changed_files }} ${{ steps.changed_files.outputs.changed_keys }}) >> $GITHUB_OUTPUT
+        run: echo tags=$(python \
+          .github/python/find_changed_files.py \
+          -t pipeline workflow process \
+          -p ${{ steps.changed_files.outputs.all_changed_files }} ${{ steps.changed_files.outputs.changed_keys }} \
+          ) >> $GITHUB_OUTPUT
 
       - name: debug2
         run: |

From e4db6185c866a305eb93b1b924bebcd80a7fc78a Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 13 Feb 2024 11:27:58 +0000
Subject: [PATCH 769/852] Tidy GHA command using line wrappings

---
 .github/workflows/ci.yml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d2ddf312..1ec7c811 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -78,10 +78,11 @@ jobs:
       - name: nf-test list tags
         id: list
         if: ${{ steps.changed_files.outputs.any_modified }}
-        run: echo tags=$(python \
-          .github/python/find_changed_files.py \
-          -t pipeline workflow process \
-          -p ${{ steps.changed_files.outputs.all_changed_files }} ${{ steps.changed_files.outputs.changed_keys }} \
+        run: >
+          echo tags=$(python
+            .github/python/find_changed_files.py
+            -t pipeline workflow process
+            -p ${{ steps.changed_files.outputs.all_changed_files }} ${{ steps.changed_files.outputs.changed_keys }}
           ) >> $GITHUB_OUTPUT
 
       - name: debug2

From a8d2c2f0bf3554907e81895f54c1b103e5d4702c Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 13 Feb 2024 11:29:32 +0000
Subject: [PATCH 770/852] Tidy GHA command using line wrappings

---
 .github/workflows/ci.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1ec7c811..5697b76a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -78,11 +78,11 @@ jobs:
       - name: nf-test list tags
         id: list
         if: ${{ steps.changed_files.outputs.any_modified }}
-        run: >
-          echo tags=$(python
-            .github/python/find_changed_files.py
-            -t pipeline workflow process
-            -p ${{ steps.changed_files.outputs.all_changed_files }} ${{ steps.changed_files.outputs.changed_keys }}
+        run: |
+          echo tags=$(python \
+            .github/python/find_changed_files.py \
+            -t pipeline workflow process \
+            -p ${{ steps.changed_files.outputs.all_changed_files }} ${{ steps.changed_files.outputs.changed_keys }} \
           ) >> $GITHUB_OUTPUT
 
       - name: debug2

From c5a3e7d2b8b1e3d210a03a6c6a3b8c9ca7b43fe0 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 13 Feb 2024 12:16:43 +0000
Subject: [PATCH 771/852] Upate utility subworkflows

---
 modules.json                                  |  2 +-
 .../nf-core/utils_nfcore_pipeline/main.nf     | 50 ++++++++++++++++++-
 .../nf-core/utils_nfcore_pipeline/meta.yml    |  6 ++-
 .../tests/main.function.nf.test               | 25 +++++++++-
 .../tests/main.function.nf.test.snap          |  4 ++
 .../tests/main.workflow.nf.test               | 12 +++++
 .../utils_nfcore_pipeline/tests/tags.yml      |  2 +
 7 files changed, 96 insertions(+), 5 deletions(-)
 create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml

diff --git a/modules.json b/modules.json
index 14bd461f..71a3e25c 100644
--- a/modules.json
+++ b/modules.json
@@ -42,7 +42,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
+                        "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 2b7ec3df..a8b55d6f 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -13,8 +13,12 @@ import nextflow.extension.FilesEx
 
 workflow UTILS_NFCORE_PIPELINE {
 
+    take:
+    nextflow_cli_args
+
     main:
     valid_config = checkConfigProvided()
+    checkProfileProvided(nextflow_cli_args)
 
     emit:
     valid_config
@@ -43,6 +47,20 @@ def checkConfigProvided() {
     return valid_config
 }
 
+//
+// Exit pipeline if --profile contains spaces
+//
+def checkProfileProvided(nextflow_cli_args) {
+    if (workflow.profile.endsWith(',')) {
+        error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" +
+            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+    }
+    if (nextflow_cli_args[0]) {
+        log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" +
+            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+    }
+}
+
 //
 // Citation string for pipeline
 //
@@ -101,6 +119,7 @@ def softwareVersionsToYAML(ch_versions) {
     return ch_versions
                 .unique()
                 .map { processVersionsFromYAML(it) }
+                .unique()
                 .mix(Channel.of(workflowVersionToYAML()))
 }
 
@@ -227,10 +246,33 @@ def logColours(monochrome_logs=true) {
     return colorcodes
 }
 
+//
+// Attach the multiqc report to email
+//
+def attachMultiqcReport(multiqc_report) {
+    def mqc_report = null
+    try {
+        if (workflow.success) {
+            mqc_report = multiqc_report.getVal()
+            if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
+                if (mqc_report.size() > 1) {
+                    log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
+                }
+                mqc_report = mqc_report[0]
+            }
+        }
+    } catch (all) {
+        if (multiqc_report) {
+            log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
+        }
+    }
+    return mqc_report
+}
+
 //
 // Construct and send completion email
 //
-def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true) {
+def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) {
 
     // Set up the e-mail variables
     def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
@@ -268,6 +310,9 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     email_fields['projectDir']   = workflow.projectDir
     email_fields['summary']      = summary << misc_fields
 
+    // On success try attach the multiqc report
+    def mqc_report = attachMultiqcReport(multiqc_report)
+
     // Check if we are only sending emails on failure
     def email_address = email
     if (!email && email_on_fail && !workflow.success) {
@@ -286,7 +331,8 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     def email_html    = html_template.toString()
 
     // Render the sendmail template
-    def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}" ]
+    def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
+    def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
     def sf                     = new File("${workflow.projectDir}/assets/sendmail_template.txt")
     def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
     def sendmail_html          = sendmail_template.toString()
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml
index dd1462b2..d08d2434 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml
@@ -7,7 +7,11 @@ keywords:
   - initialise
   - version
 components: []
-input: []
+input:
+  - nextflow_cli_args:
+      type: list
+      description: |
+        Nextflow CLI positional arguments
 output:
   - success:
       type: boolean
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
index 74577b26..1dc317f8 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
@@ -4,7 +4,10 @@ nextflow_function {
     name "Test Functions"
     script "../main.nf"
     config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
-    tag "UTILS_NFCORE_PIPELINE"
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "utils_nfcore_pipeline"
+    tag "subworkflows/utils_nfcore_pipeline"
 
     test("Test Function checkConfigProvided") {
 
@@ -18,6 +21,26 @@ nextflow_function {
         }
     }
 
+    test("Test Function checkProfileProvided") {
+
+        function "checkProfileProvided"
+
+        when {
+            function {
+                """
+                input[0] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
     test("Test Function workflowCitation") {
 
         function "workflowCitation"
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
index afb9ab4d..10f948e6 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
@@ -1,4 +1,8 @@
 {
+    "Test Function checkProfileProvided": {
+        "content": null,
+        "timestamp": "2024-02-09T15:43:55.145717"
+    },
     "Test Function checkConfigProvided": {
         "content": [
             true
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
index 3df54055..8940d32d 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
@@ -4,9 +4,21 @@ nextflow_workflow {
     script "../main.nf"
     config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
     workflow "UTILS_NFCORE_PIPELINE"
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "utils_nfcore_pipeline"
+    tag "subworkflows/utils_nfcore_pipeline"
 
     test("Should run without failures") {
 
+        when {
+            workflow {
+                """
+                input[0] = []
+                """
+            }
+        }
+
         then {
             assertAll(
                 { assert workflow.success },
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
new file mode 100644
index 00000000..ac8523c9
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/utils_nfcore_pipeline:
+  - subworkflows/nf-core/utils_nfcore_pipeline/**

From 9c567e418fd1cdcc855397766069a4e475893ed5 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 13 Feb 2024 12:49:59 +0000
Subject: [PATCH 772/852] Add argument to UTILS_NFCORE_PIPELINE

---
 assets/methods_description_template.yml                   | 2 --
 subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf | 2 +-
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
index 49a0a9fd..469f4a46 100644
--- a/assets/methods_description_template.yml
+++ b/assets/methods_description_template.yml
@@ -3,8 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "nf-core/fetchngs Methods Description"
 section_href: "https://github.com/nf-core/fetchngs"
 plot_type: "html"
-## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
-## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>
   <p>Data was processed using nf-core/fetchngs v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
index 7b46200f..18660e50 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
@@ -67,7 +67,7 @@ workflow PIPELINE_INITIALISATION {
     //
     // Check config provided to the pipeline
     //
-    UTILS_NFCORE_PIPELINE ()
+    UTILS_NFCORE_PIPELINE ( args )
 
     //
     // Auto-detect input id type

From 302694cfe6674a2a49809d4fd3cd128447cc08e1 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Wed, 14 Feb 2024 13:37:33 +0000
Subject: [PATCH 773/852] CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0f2d0620..498168cc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -44,6 +44,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #264](https://github.com/nf-core/fetchngs/pull/264) - Remove synapse workflow from pipeline
 - [PR #265](https://github.com/nf-core/fetchngs/pull/265) - Use "+" syntax for profiles to accumulate profiles in nf-test
 - [PR #266](https://github.com/nf-core/fetchngs/pull/266) - Make .gitignore match template
+- [PR #273](https://github.com/nf-core/fetchngs/pull/273) - Update subworkflows
 
 ### Software dependencies
 

From fdf576fd3a3e2b27e079faf2cb35a23c729deeff Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Fri, 16 Feb 2024 12:16:39 -0600
Subject: [PATCH 774/852] chore: Emiller88 => edmundmiller

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 498168cc..653da944 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -77,7 +77,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 Special thanks to the following for their contributions to the release:
 
 - [Adam Talbot](https://github.com/adamrtalbot)
-- [Edmund Miller](https://github.com/Emiller88)
+- [Edmund Miller](https://github.com/edmundmiller)
 - [Esha Joshi](https://github.com/ejseqera)
 - [Harshil Patel](https://github.com/drpatelh)
 - [Lukas Forer](https://github.com/lukfor)

From ba7d804d3251dc8f9af0edc6f92dffbbe4cfda96 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Sun, 18 Feb 2024 11:56:26 +0000
Subject: [PATCH 775/852] [automated] Fix linting with Prettier

---
 README.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 8b6d253b..31831022 100644
--- a/README.md
+++ b/README.md
@@ -25,7 +25,7 @@
 
 ```mermaid
 flowchart LR
-    IDS("Input 
+    IDS("Input
     File") --> SRA & GEO & ENA & DDBJ
     subgraph SG_DBIDS[Database IDs]
       SRA("SRA")
@@ -34,9 +34,9 @@ flowchart LR
       DDBJ("DDBJ")
     end
     subgraph SG_METADATA[Download Metadata]
-      SRA & GEO & ENA & DDBJ --> META("Get 
+      SRA & GEO & ENA & DDBJ --> META("Get
       Metadata")
-      META --> LINKS("Get 
+      META --> LINKS("Get
       Download
       Links")
     end
@@ -50,7 +50,7 @@ flowchart LR
       FASTQ --> SAMPLESHEET("Samplesheet")
     end
     LINKS --> |--skip_fastq_download| SAMPLESHEET
-    
+
 ```
 
 ## Usage

From bd09ad07a7e08410e15aea5b84b4a6c629764f54 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 18 Feb 2024 12:28:43 +0000
Subject: [PATCH 776/852] Rename --force_ftp_download to
 --force_aspera_download to make FTP default again

---
 CHANGELOG.md          | 12 ++++++------
 README.md             |  4 ++--
 docs/usage.md         |  8 ++------
 nextflow.config       |  2 +-
 nextflow_schema.json  |  6 +++---
 workflows/sra/main.nf | 34 ++++++++++++++++------------------
 6 files changed, 30 insertions(+), 36 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 653da944..ba9ee43b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### :warning: Major enhancements
 
-- The Aspera CLI was recently added to [Bioconda](https://anaconda.org/bioconda/aspera-cli) and we have added it as another way of downloading FastQ files on top of the existing FTP and sra-tools support. In our limited benchmarks on all public Clouds we found ~50% speed-up in download times compared to FTP! We are not aware of any obvious downsides and have made this the default download method in the pipeline. You can however, revert to using FTP and sra-tools using the `--force_ftp_download` and `--force_sratools_download` parameters, respectively. We would love to have your feedback!
+- The Aspera CLI was recently added to [Bioconda](https://anaconda.org/bioconda/aspera-cli) and we have added it as another way of downloading FastQ files on top of the existing FTP and sra-tools support. In our limited benchmarks on all public Clouds we found ~50% speed-up in download times compared to FTP! FTP downloads will still be the default download method but you can however, choose to use sra-tools or Aspera using the `--force_sratools_download` or `--force_aspera_download` parameters, respectively. We would love to have your feedback!
 - Support for Synapse ids has been dropped in this release. We haven't had any feedback from users whether it is being used or not. Users can run earlier versions of the pipeline if required.
 - We have significantly refactored and standardised the way we are using nf-test within this pipeline. This pipeline is now the current, best-practice implementation for nf-test usage on nf-core. We required a number of features to be added to nf-test and a huge shoutout to [Lukas Forer](https://github.com/lukfor) for entertaining our requests and implementing them within upstream :heart:!
 
@@ -60,11 +60,11 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 
 ### Parameters
 
-| Old parameter      | New parameter          |
-| ------------------ | ---------------------- |
-|                    | `--force_ftp_download` |
-| `--input_type`     |                        |
-| `--synapse_config` |                        |
+| Old parameter      | New parameter             |
+| ------------------ | ------------------------- |
+|                    | `--force_aspera_download` |
+| `--input_type`     |                           |
+| `--synapse_config` |                           |
 
 > **NB:** Parameter has been **updated** if both old and new parameter information is present.
 > **NB:** Parameter has been **added** if just the new parameter information is present.
diff --git a/README.md b/README.md
index 9419fa1a..ef748159 100644
--- a/README.md
+++ b/README.md
@@ -68,8 +68,8 @@ Via a single file of ids, provided one-per-line (see [example input file](https:
 2. Fetch extensive id metadata via ENA API
 3. Download FastQ files:
    - If direct download links are available from the ENA API:
-     - Fetch in parallel via `aspera-cli` and perform `md5sum` check (default)
-     - Fetch in parallel via `wget` and perform `md5sum` check. Use `--force_ftp_download` to force this behaviour.
+     - Fetch in parallel via `wget` and perform `md5sum` check (default).
+     - Fetch in parallel via `aspera-cli` and perform `md5sum` check. Use `--force_aspera_download` to force this behaviour.
    - Otherwise use [`sra-tools`](https://github.com/ncbi/sra-tools) to download `.sra` files and convert them to FastQ. Use `--force_sratools_download` to force this behaviour.
 4. Collate id metadata and paths to FastQ files in a single samplesheet
 
diff --git a/docs/usage.md b/docs/usage.md
index 06ff7802..756a62a3 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -70,13 +70,9 @@ This highlights that there is a discrepancy between the read data hosted on the
 
 See [issue #260](https://github.com/nf-core/fetchngs/issues/260) for more details.
 
-### Bypass Aspera data download
+### Primary options for downloading data
 
-If the appropriate download links are available, the pipeline uses the Aspera CLI by default to download FastQ files. If you are having issues and prefer to use FTP or sra-tools instead, you can use the [`--force_ftp_download`](https://nf-co.re/fetchngs/parameters#force_ftp_download) and [`--force_sratools_download`](https://nf-co.re/fetchngs/parameters#force_sratools_download) parameters, respectively.
-
-### Bypass `FTP` data download
-
-If FTP connections are blocked on your network use the [`--force_sratools_download`](https://nf-co.re/fetchngs/parameters#force_sratools_download) parameter to force the pipeline to download data using sra-tools instead of the ENA FTP.
+If the appropriate download links are available, the pipeline uses FTP by default to download FastQ files. If you are having issues and prefer to use sra-tools or Aspera instead, you can use the [`--force_sratools_download`](https://nf-co.re/fetchngs/parameters#force_sratools_download) or [`--force_aspera_download`](https://nf-co.re/fetchngs/parameters#force_aspera_download) parameters, respectively.
 
 ### Downloading dbGAP data with JWT
 
diff --git a/nextflow.config b/nextflow.config
index fad805bf..c6658f4a 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -15,7 +15,7 @@ params {
     nf_core_rnaseq_strandedness = 'auto'
     ena_metadata_fields         = null
     sample_mapping_fields       = 'experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description'
-    force_ftp_download          = false
+    force_aspera_download       = false
     force_sratools_download     = false
     skip_fastq_download         = false
     dbgap_key                   = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 77ae6673..5ad7a50d 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -47,11 +47,11 @@
                     "help_text": "The default is 'auto' which can be used with nf-core/rnaseq v3.10 onwards to auto-detect strandedness during the pipeline execution.",
                     "default": "auto"
                 },
-                "force_ftp_download": {
+                "force_aspera_download": {
                     "type": "boolean",
                     "fa_icon": "fas fa-tools",
-                    "description": "Force download FASTQ files via FTP instead of via the Aspera CLI.",
-                    "help_text": "If the Aspera CLI is not working on your infrastructure use this flag to force the pipeline to download data via FTP."
+                    "description": "Force download FASTQ files via Aspera CLI instead of via FTP.",
+                    "help_text": "If FTP downloads are not working on your infrastructure use this flag to force the pipeline to download data via the Aspera CLI."
                 },
                 "force_sratools_download": {
                     "type": "boolean",
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 35ae18dc..61906273 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -69,37 +69,26 @@ workflow SRA {
         ch_sra_metadata
             .branch {
                 meta ->
-                    def download_method = 'aspera'
+                    def download_method = 'ftp'
                     // meta.fastq_aspera is a metadata string with ENA fasp links supported by Aspera
                         // For single-end: 'fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz'
                         // For paired-end: 'fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz'
-                    if (!meta.fastq_aspera || params.force_ftp_download) {
-                        if (meta.fastq_1) {
-                            download_method = 'ftp'
-                        }
+                    if (meta.fastq_aspera && params.force_aspera_download) {
+                        download_method = 'aspera'
                     }
                     if ((!meta.fastq_aspera && !meta.fastq_1) || params.force_sratools_download) {
                         download_method = 'sratools'
                     }
 
-                    aspera: download_method == 'aspera'
-                        return [ meta, meta.fastq_aspera.tokenize(';').take(2) ]
                     ftp: download_method == 'ftp'
                         return [ meta, [ meta.fastq_1, meta.fastq_2 ] ]
                     sratools: download_method == 'sratools'
                         return [ meta, meta.run_accession ]
+                    aspera: download_method == 'aspera'
+                        return [ meta, meta.fastq_aspera.tokenize(';').take(2) ]
             }
             .set { ch_sra_reads }
 
-        //
-        // MODULE: If Aspera link is provided in run information then download FastQ directly via Aspera CLI and validate with md5sums
-        //
-        ASPERA_CLI (
-            ch_sra_reads.aspera,
-            'era-fasp'
-        )
-        ch_versions = ch_versions.mix(ASPERA_CLI.out.versions.first())
-
         //
         // MODULE: If FTP link is provided in run information then download FastQ directly via FTP and validate with md5sums
         //
@@ -117,12 +106,21 @@ workflow SRA {
         )
         ch_versions = ch_versions.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.versions.first())
 
+        //
+        // MODULE: If Aspera link is provided in run information then download FastQ directly via Aspera CLI and validate with md5sums
+        //
+        ASPERA_CLI (
+            ch_sra_reads.aspera,
+            'era-fasp'
+        )
+        ch_versions = ch_versions.mix(ASPERA_CLI.out.versions.first())
+
         // Isolate FASTQ channel which will be added to emit block
-        ASPERA_CLI
+        SRA_FASTQ_FTP
             .out
             .fastq
-            .mix(SRA_FASTQ_FTP.out.fastq)
             .mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads)
+            .mix(ASPERA_CLI.out.fastq)
             .map {
                 meta, fastq ->
                     def reads = fastq instanceof List ? fastq.flatten() : [ fastq ]

From 047f81fee0907da3c2459944291e0d9509fddfbd Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 18 Feb 2024 12:30:12 +0000
Subject: [PATCH 777/852] Update workflow tags and tests to change default
 behaviour to FTP download

---
 workflows/sra/tests/main.nf.test                            | 2 +-
 ...p_download.nf.test => sra_force_aspera_download.nf.test} | 6 +++---
 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test    | 2 +-
 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test     | 2 +-
 .../sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test      | 2 +-
 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test | 2 +-
 6 files changed, 8 insertions(+), 8 deletions(-)
 rename workflows/sra/tests/{sra_force_ftp_download.nf.test => sra_force_aspera_download.nf.test} (93%)

diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 69ad7f42..dddc5275 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -8,7 +8,7 @@ nextflow_workflow {
     // Dependencies
     tag "SRA_IDS_TO_RUNINFO"
     tag "SRA_RUNINFO_TO_FTP"
-    tag "ASPERA_CLI"
+    tag "SRA_FASTQ_FTP"
     tag "SRA_TO_SAMPLESHEET"
     tag "MULTIQC_MAPPINGS_CONFIG"
 
diff --git a/workflows/sra/tests/sra_force_ftp_download.nf.test b/workflows/sra/tests/sra_force_aspera_download.nf.test
similarity index 93%
rename from workflows/sra/tests/sra_force_ftp_download.nf.test
rename to workflows/sra/tests/sra_force_aspera_download.nf.test
index 357bd180..af0911bd 100644
--- a/workflows/sra/tests/sra_force_ftp_download.nf.test
+++ b/workflows/sra/tests/sra_force_aspera_download.nf.test
@@ -8,11 +8,11 @@ nextflow_workflow {
     // Dependencies
     tag "SRA_IDS_TO_RUNINFO"
     tag "SRA_RUNINFO_TO_FTP"
-    tag "SRA_FASTQ_FTP"
+    tag "ASPERA_CLI"
     tag "SRA_TO_SAMPLESHEET"
     tag "MULTIQC_MAPPINGS_CONFIG"
 
-    test("Parameters: --force_ftp_download") {
+    test("Parameters: --force_aspera_download") {
 
         when {
             workflow {
@@ -22,7 +22,7 @@ nextflow_workflow {
             }
             params {
                 outdir = "$outputDir"
-                force_ftp_download = true
+                force_aspera_download = true
             }
         }
 
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index 26cac4b9..522ab75b 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -8,7 +8,7 @@ nextflow_workflow {
     // Dependencies
     tag "SRA_IDS_TO_RUNINFO"
     tag "SRA_RUNINFO_TO_FTP"
-    tag "ASPERA_CLI"
+    tag "SRA_FASTQ_FTP"
     tag "SRA_TO_SAMPLESHEET"
     tag "MULTIQC_MAPPINGS_CONFIG"
 
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index b5a49dd4..f6f1b560 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -8,7 +8,7 @@ nextflow_workflow {
     // Dependencies
     tag "SRA_IDS_TO_RUNINFO"
     tag "SRA_RUNINFO_TO_FTP"
-    tag "ASPERA_CLI"
+    tag "SRA_FASTQ_FTP"
     tag "SRA_TO_SAMPLESHEET"
     tag "MULTIQC_MAPPINGS_CONFIG"
 
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index 0a92b446..b9373b57 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -8,7 +8,7 @@ nextflow_workflow {
     // Dependencies
     tag "SRA_IDS_TO_RUNINFO"
     tag "SRA_RUNINFO_TO_FTP"
-    tag "ASPERA_CLI"
+    tag "SRA_FASTQ_FTP"
     tag "SRA_TO_SAMPLESHEET"
     tag "MULTIQC_MAPPINGS_CONFIG"
 
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index f633e0d6..4985b9d0 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -8,7 +8,7 @@ nextflow_workflow {
     // Dependencies
     tag "SRA_IDS_TO_RUNINFO"
     tag "SRA_RUNINFO_TO_FTP"
-    tag "ASPERA_CLI"
+    tag "SRA_FASTQ_FTP"
     tag "SRA_TO_SAMPLESHEET"
     tag "MULTIQC_MAPPINGS_CONFIG"
 

From c2827a00007387397e83350493f427d898d5c3d3 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Mon, 19 Feb 2024 10:01:19 +0100
Subject: [PATCH 778/852] Apply suggestions from code review

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 31831022..05a8f2b5 100644
--- a/README.md
+++ b/README.md
@@ -41,8 +41,8 @@ flowchart LR
       Links")
     end
     subgraph SG_FETCH_FASTQ[Download FastQ]
-      LINKS --> |"(default)"| ASPERA("Aspera")
-      LINKS --> |--force_ftp_download| FTP("FTP")
+      LINKS --> |"(default)"| FTP("FTP")
+      LINKS --> |--force_aspera_download| ASPERA("Aspera")
       LINKS --> |--force_sra_tools_download| SRATOOLS("sra-tools")
     end
     subgraph SG_FASTQ[Pipeline Outputs]

From f4e3a1f036f14135576b726cf9e08b9927707cf4 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 19 Feb 2024 09:54:39 +0000
Subject: [PATCH 779/852] confirm-pass will pass if no tests are triggered

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 5697b76a..86c6b5bc 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -165,7 +165,7 @@ jobs:
     if: always()
     steps:
       - name: All tests ok
-        if: ${{ success() || !contains(needs.*.result, 'failure') }}
+        if: ${{ !contains(needs.*.result, 'failure') }}
         run: exit 0
       - name: One or more tests failed
         if: ${{ contains(needs.*.result, 'failure') }}

From 61ee0cba845581789ce15043977a1d168faea3b8 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 19 Feb 2024 12:10:01 +0000
Subject: [PATCH 780/852] Replace --force_* parameters with --download_method

---
 CHANGELOG.md                                  | 14 +++++++-----
 README.md                                     |  6 ++---
 docs/usage.md                                 |  4 ++--
 nextflow.config                               |  3 +--
 nextflow_schema.json                          | 22 ++++++++-----------
 workflows/sra/main.nf                         |  8 +++----
 ...est => sra_download_method_aspera.nf.test} |  6 ++---
 ...t => sra_download_method_sratools.nf.test} |  6 ++---
 8 files changed, 33 insertions(+), 36 deletions(-)
 rename workflows/sra/tests/{sra_force_aspera_download.nf.test => sra_download_method_aspera.nf.test} (93%)
 rename workflows/sra/tests/{sra_force_sratools_download.nf.test => sra_download_method_sratools.nf.test} (93%)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ba9ee43b..68a8174d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,7 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### :warning: Major enhancements
 
-- The Aspera CLI was recently added to [Bioconda](https://anaconda.org/bioconda/aspera-cli) and we have added it as another way of downloading FastQ files on top of the existing FTP and sra-tools support. In our limited benchmarks on all public Clouds we found ~50% speed-up in download times compared to FTP! FTP downloads will still be the default download method but you can however, choose to use sra-tools or Aspera using the `--force_sratools_download` or `--force_aspera_download` parameters, respectively. We would love to have your feedback!
+- The Aspera CLI was recently added to [Bioconda](https://anaconda.org/bioconda/aspera-cli) and we have added it as another way of downloading FastQ files in addition to the existing FTP and sra-tools support. In our limited benchmarks on all public Clouds we found ~50% speed-up in download times compared to FTP! FTP downloads will still be the default download method (i.e. `--download_method ftp`) but you can choose to use sra-tools or Aspera using `--download_method sratools` or `--download_method aspera`, respectively. We would love to have your feedback!
+- The `--force_sratools_download` parameter has been deprecated in favour of using `--download_method <method>` to explicitly specify the download method; available options are `ftp`, `sratools` or `aspera`.
 - Support for Synapse ids has been dropped in this release. We haven't had any feedback from users whether it is being used or not. Users can run earlier versions of the pipeline if required.
 - We have significantly refactored and standardised the way we are using nf-test within this pipeline. This pipeline is now the current, best-practice implementation for nf-test usage on nf-core. We required a number of features to be added to nf-test and a huge shoutout to [Lukas Forer](https://github.com/lukfor) for entertaining our requests and implementing them within upstream :heart:!
 
@@ -60,11 +61,12 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 
 ### Parameters
 
-| Old parameter      | New parameter             |
-| ------------------ | ------------------------- |
-|                    | `--force_aspera_download` |
-| `--input_type`     |                           |
-| `--synapse_config` |                           |
+| Old parameter               | New parameter       |
+| --------------------------- | ------------------- |
+|                             | `--download_method` |
+| `--input_type`              |                     |
+| `--force_sratools_download` |                     |
+| `--synapse_config`          |                     |
 
 > **NB:** Parameter has been **updated** if both old and new parameter information is present.
 > **NB:** Parameter has been **added** if just the new parameter information is present.
diff --git a/README.md b/README.md
index ef748159..58fa86f4 100644
--- a/README.md
+++ b/README.md
@@ -68,9 +68,9 @@ Via a single file of ids, provided one-per-line (see [example input file](https:
 2. Fetch extensive id metadata via ENA API
 3. Download FastQ files:
    - If direct download links are available from the ENA API:
-     - Fetch in parallel via `wget` and perform `md5sum` check (default).
-     - Fetch in parallel via `aspera-cli` and perform `md5sum` check. Use `--force_aspera_download` to force this behaviour.
-   - Otherwise use [`sra-tools`](https://github.com/ncbi/sra-tools) to download `.sra` files and convert them to FastQ. Use `--force_sratools_download` to force this behaviour.
+     - Fetch in parallel via `wget` and perform `md5sum` check (`--download_method ftp`; default).
+     - Fetch in parallel via `aspera-cli` and perform `md5sum` check. Use `--download_method aspera` to force this behaviour.
+   - Otherwise use [`sra-tools`](https://github.com/ncbi/sra-tools) to download `.sra` files and convert them to FastQ. Use `--download_method sratools` to force this behaviour.
 4. Collate id metadata and paths to FastQ files in a single samplesheet
 
 ## Pipeline output
diff --git a/docs/usage.md b/docs/usage.md
index 756a62a3..2bc9a125 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -66,13 +66,13 @@ SRR9320616_2.fastq
 SRR9320616_3.fastq
 ```
 
-This highlights that there is a discrepancy between the read data hosted on the ENA API and what can actually be fetched from sra-tools, where the latter seems to be the source of truth. If you anticipate that you may have more than 2 FastQ files per sample, it is recommended to use this pipeline with the `--force_sratools_download` parameter.
+This highlights that there is a discrepancy between the read data hosted on the ENA API and what can actually be fetched from sra-tools, where the latter seems to be the source of truth. If you anticipate that you may have more than 2 FastQ files per sample, it is recommended to use this pipeline with the `--download_method sratools` parameter.
 
 See [issue #260](https://github.com/nf-core/fetchngs/issues/260) for more details.
 
 ### Primary options for downloading data
 
-If the appropriate download links are available, the pipeline uses FTP by default to download FastQ files. If you are having issues and prefer to use sra-tools or Aspera instead, you can use the [`--force_sratools_download`](https://nf-co.re/fetchngs/parameters#force_sratools_download) or [`--force_aspera_download`](https://nf-co.re/fetchngs/parameters#force_aspera_download) parameters, respectively.
+If the appropriate download links are available, the pipeline uses FTP by default to download FastQ files by setting the `--download_method ftp` parameter. If you are having issues and prefer to use sra-tools or Aspera instead, you can set the [`--download_method`](https://nf-co.re/fetchngs/parameters#download_method) parameter to `--download_method sratools` or `--download_method aspera`, respectively.
 
 ### Downloading dbGAP data with JWT
 
diff --git a/nextflow.config b/nextflow.config
index c6658f4a..40333478 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -15,8 +15,7 @@ params {
     nf_core_rnaseq_strandedness = 'auto'
     ena_metadata_fields         = null
     sample_mapping_fields       = 'experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description'
-    force_aspera_download       = false
-    force_sratools_download     = false
+    download_method             = 'ftp'
     skip_fastq_download         = false
     dbgap_key                   = null
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 5ad7a50d..e870974a 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -30,7 +30,7 @@
                 },
                 "sample_mapping_fields": {
                     "type": "string",
-                    "fa_icon": "fas fa-globe-americas",
+                    "fa_icon": "fas fa-columns",
                     "description": "Comma-separated list of ENA metadata fields used to create a separate 'id_mappings.csv' and 'multiqc_config.yml' with selected fields that can be used to rename samples in general and in MultiQC.",
                     "default": "experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description"
                 },
@@ -42,22 +42,18 @@
                 },
                 "nf_core_rnaseq_strandedness": {
                     "type": "string",
-                    "fa_icon": "fas fa-car",
+                    "fa_icon": "fas fa-dna",
                     "description": "Value for 'strandedness' entry added to samplesheet created when using '--nf_core_pipeline rnaseq'.",
                     "help_text": "The default is 'auto' which can be used with nf-core/rnaseq v3.10 onwards to auto-detect strandedness during the pipeline execution.",
                     "default": "auto"
                 },
-                "force_aspera_download": {
-                    "type": "boolean",
-                    "fa_icon": "fas fa-tools",
-                    "description": "Force download FASTQ files via Aspera CLI instead of via FTP.",
-                    "help_text": "If FTP downloads are not working on your infrastructure use this flag to force the pipeline to download data via the Aspera CLI."
-                },
-                "force_sratools_download": {
-                    "type": "boolean",
-                    "fa_icon": "fas fa-tools",
-                    "description": "Force download FASTQ files via sra-tools instead of via the ENA FTP.",
-                    "help_text": "If FTP connections are blocked on your network use this flag to force the pipeline to download data using sra-tools instead of the ENA FTP."
+                "download_method": {
+                    "type": "string",
+                    "default": "ftp",
+                    "fa_icon": "fas fa-download",
+                    "enum": ["aspera", "ftp", "sratools"],
+                    "description": "Method to download FastQ files. Available options are 'aspera', 'ftp' or 'sratools'. Default is 'ftp'.",
+                    "help_text": "FTP and Aspera CLI download FastQ files directly from the ENA FTP whereas sratools uses sra-tools to download *.sra files and convert to FastQ."
                 },
                 "skip_fastq_download": {
                     "type": "boolean",
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
index 61906273..0c8cac0c 100644
--- a/workflows/sra/main.nf
+++ b/workflows/sra/main.nf
@@ -73,19 +73,19 @@ workflow SRA {
                     // meta.fastq_aspera is a metadata string with ENA fasp links supported by Aspera
                         // For single-end: 'fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz'
                         // For paired-end: 'fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz'
-                    if (meta.fastq_aspera && params.force_aspera_download) {
+                    if (meta.fastq_aspera && params.download_method == 'aspera') {
                         download_method = 'aspera'
                     }
-                    if ((!meta.fastq_aspera && !meta.fastq_1) || params.force_sratools_download) {
+                    if ((!meta.fastq_aspera && !meta.fastq_1) || params.download_method == 'sratools') {
                         download_method = 'sratools'
                     }
 
+                    aspera: download_method == 'aspera'
+                        return [ meta, meta.fastq_aspera.tokenize(';').take(2) ]
                     ftp: download_method == 'ftp'
                         return [ meta, [ meta.fastq_1, meta.fastq_2 ] ]
                     sratools: download_method == 'sratools'
                         return [ meta, meta.run_accession ]
-                    aspera: download_method == 'aspera'
-                        return [ meta, meta.fastq_aspera.tokenize(';').take(2) ]
             }
             .set { ch_sra_reads }
 
diff --git a/workflows/sra/tests/sra_force_aspera_download.nf.test b/workflows/sra/tests/sra_download_method_aspera.nf.test
similarity index 93%
rename from workflows/sra/tests/sra_force_aspera_download.nf.test
rename to workflows/sra/tests/sra_download_method_aspera.nf.test
index af0911bd..d36f9095 100644
--- a/workflows/sra/tests/sra_force_aspera_download.nf.test
+++ b/workflows/sra/tests/sra_download_method_aspera.nf.test
@@ -3,7 +3,7 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
-    tag "SRA_FORCE_FTP_DOWNLOAD"
+    tag "SRA_DOWNLOAD_METHOD_ASPERA"
 
     // Dependencies
     tag "SRA_IDS_TO_RUNINFO"
@@ -12,7 +12,7 @@ nextflow_workflow {
     tag "SRA_TO_SAMPLESHEET"
     tag "MULTIQC_MAPPINGS_CONFIG"
 
-    test("Parameters: --force_aspera_download") {
+    test("Parameters: --download_method aspera") {
 
         when {
             workflow {
@@ -22,7 +22,7 @@ nextflow_workflow {
             }
             params {
                 outdir = "$outputDir"
-                force_aspera_download = true
+                download_method = 'aspera'
             }
         }
 
diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_download_method_sratools.nf.test
similarity index 93%
rename from workflows/sra/tests/sra_force_sratools_download.nf.test
rename to workflows/sra/tests/sra_download_method_sratools.nf.test
index 62d499df..05613f1e 100644
--- a/workflows/sra/tests/sra_force_sratools_download.nf.test
+++ b/workflows/sra/tests/sra_download_method_sratools.nf.test
@@ -3,7 +3,7 @@ nextflow_workflow {
     name "Test workflow: sra/main.nf"
     script "../main.nf"
     workflow "SRA"
-    tag "SRA_FORCE_SRATOOLS_DOWNLOAD"
+    tag "SRA_DOWNLOAD_METHOD_SRATOOLS"
 
     // Dependencies
     tag "FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS"
@@ -12,7 +12,7 @@ nextflow_workflow {
     tag "SRA_TO_SAMPLESHEET"
     tag "MULTIQC_MAPPINGS_CONFIG"
 
-    test("Parameters: --force_sratools_download") {
+    test("Parameters: --download_method sratools") {
 
         when {
             workflow {
@@ -22,7 +22,7 @@ nextflow_workflow {
             }
             params {
                 outdir = "$outputDir"
-                force_sratools_download = true
+                download_method = 'sratools'
             }
         }
 

From 177be25a1c4c1a362cc7d9f080e6b8de983d9128 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 19 Feb 2024 12:10:37 +0000
Subject: [PATCH 781/852] Update .nf-core.yml relative to latest tools release

---
 .nf-core.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index 707d5cd8..8694fced 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -7,5 +7,4 @@ lint:
     - lib/Utils.groovy
     - lib/WorkflowMain.groovy
   files_unchanged:
-    - .gitignore
     - assets/sendmail_template.txt

From 4573cdd502438f63210b710f7ec0ef0d3e0c5d5f Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 19 Feb 2024 12:11:08 +0000
Subject: [PATCH 782/852] Use strict validation of parameters since deprecating
 --force_sratools_download

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 40333478..5b82d5b2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -45,7 +45,7 @@ params {
     max_time                    = '240.h'
 
     // Schema validation default options
-    validationFailUnrecognisedParams = false
+    validationFailUnrecognisedParams = true
     validationLenientMode            = false
     validationShowHiddenParams       = false
     validationSchemaIgnoreParams     = ''

From 502d58f1d138d8beb318dfddc2bdbf3808d99460 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Mon, 19 Feb 2024 12:58:36 +0000
Subject: [PATCH 783/852] Add deprecated parameter section for
 --force_sratools_download

---
 nextflow.config      |  6 +++++-
 nextflow_schema.json | 19 +++++++++++++++++++
 2 files changed, 24 insertions(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 5b82d5b2..0b2abf8c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -45,12 +45,16 @@ params {
     max_time                    = '240.h'
 
     // Schema validation default options
-    validationFailUnrecognisedParams = true
+    validationFailUnrecognisedParams = false
     validationLenientMode            = false
     validationShowHiddenParams       = false
     validationSchemaIgnoreParams     = ''
     validate_params                  = true
 
+    // Deprecated options
+    // See: https://github.com/nf-core/fetchngs/pull/279/files#r1494459480
+    force_sratools_download          = false
+
 }
 
 // Load base.config by default for all pipelines
diff --git a/nextflow_schema.json b/nextflow_schema.json
index e870974a..5d5e48d3 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -249,6 +249,22 @@
                     "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
                 }
             }
+        },
+        "deprecated_options": {
+            "title": "Deprecated options",
+            "type": "object",
+            "description": "List of parameters that have been deprecated.",
+            "default": "",
+            "fa_icon": "fas fa-calendar-times",
+            "properties": {
+                "force_sratools_download": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-times-circle",
+                    "description": "This parameter has been deprecated. Please use '--download_method sratools' instead.",
+                    "enum": [false],
+                    "hidden": true
+                }
+            }
         }
     },
     "allOf": [
@@ -263,6 +279,9 @@
         },
         {
             "$ref": "#/definitions/generic_options"
+        },
+        {
+            "$ref": "#/definitions/deprecated_options"
         }
     ]
 }

From c8ec03b57a9ad2e7a486dc9eee1c312135b60975 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Tue, 20 Feb 2024 13:47:44 +0100
Subject: [PATCH 784/852] Update README.md

---
 README.md | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 05a8f2b5..9f59aec2 100644
--- a/README.md
+++ b/README.md
@@ -41,16 +41,15 @@ flowchart LR
       Links")
     end
     subgraph SG_FETCH_FASTQ[Download FastQ]
-      LINKS --> |"(default)"| FTP("FTP")
-      LINKS --> |--force_aspera_download| ASPERA("Aspera")
-      LINKS --> |--force_sra_tools_download| SRATOOLS("sra-tools")
+      LINKS --> |--download_method 'ftp' | FTP("FTP")
+      LINKS --> |--download_method 'aspera' | ASPERA("Aspera")
+      LINKS --> |--download_method 'sratools' | SRATOOLS("sra-tools")
     end
     subgraph SG_FASTQ[Pipeline Outputs]
       ASPERA & FTP & SRATOOLS --> FASTQ("FastQ")
       FASTQ --> SAMPLESHEET("Samplesheet")
     end
     LINKS --> |--skip_fastq_download| SAMPLESHEET
-
 ```
 
 ## Usage

From 9e5e301d968ab2495d48bf64a2866f81e3523046 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 20 Feb 2024 18:24:19 +0000
Subject: [PATCH 785/852] Update CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5e6c085b..62b239b8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -47,6 +47,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #266](https://github.com/nf-core/fetchngs/pull/266) - Make .gitignore match template
 - [PR #268](https://github.com/nf-core/fetchngs/pull/268) - Add mermaid diagram
 - [PR #273](https://github.com/nf-core/fetchngs/pull/273) - Update utility subworkflows
+- [PR #283](https://github.com/nf-core/fetchngs/pull/283) - Template update for nf-core/tools v2.13
 
 ### Software dependencies
 

From 5e3bb4ae28958367105a10e2733c82283a1751a4 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 20 Feb 2024 20:11:47 +0000
Subject: [PATCH 786/852] Remove tags.yml files

---
 subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml   | 2 --
 subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml     | 2 --
 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml | 2 --
 3 files changed, 6 deletions(-)
 delete mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
 delete mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
 delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml

diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
deleted file mode 100644
index f8476112..00000000
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nextflow_pipeline:
-  - subworkflows/nf-core/utils_nextflow_pipeline/**
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
deleted file mode 100644
index ac8523c9..00000000
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nfcore_pipeline:
-  - subworkflows/nf-core/utils_nfcore_pipeline/**
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
deleted file mode 100644
index 60b1cfff..00000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nfvalidation_plugin:
-  - subworkflows/nf-core/utils_nfvalidation_plugin/**

From eae9cb43f211a77b2cad648f12be7a309c2ca425 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 20 Feb 2024 20:12:04 +0000
Subject: [PATCH 787/852] Remove duplicate schema entry in nextflow_schema.json

---
 nextflow_schema.json | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 9fdea4e8..29f7b710 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -19,7 +19,6 @@
                     "schema": "assets/schema_input.json",
                     "mimetype": "text/csv",
                     "pattern": "^\\S+\\.(csv|tsv|txt)$",
-                    "schema": "assets/schema_input.json",
                     "fa_icon": "fas fa-file-excel",
                     "description": "File containing SRA/ENA/GEO/DDBJ identifiers one per line to download their associated metadata and FastQ files."
                 },

From 3a92ac0ece3266b0634e6869dab81ec95acfdb6f Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 20 Feb 2024 20:13:58 +0000
Subject: [PATCH 788/852] Fix ECLint

---
 subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
index 68b91255..22079228 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
@@ -68,8 +68,8 @@ workflow PIPELINE_INITIALISATION {
     //
     // Check config provided to the pipeline
     //
-    UTILS_NFCORE_PIPELINE ( 
-        nextflow_cli_args 
+    UTILS_NFCORE_PIPELINE (
+        nextflow_cli_args
     )
 
     //

From 61a5b18a4bea376c44b4fa242f21f5ea6a2feae5 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 20 Feb 2024 20:19:15 +0000
Subject: [PATCH 789/852] Fix PIPELINE_INITIALISATION tests

---
 main.nf                                                   | 2 +-
 .../tests/main.workflow_pipeline_initialisation.nf.test   | 8 +++++---
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/main.nf b/main.nf
index 46b4b0e3..52539e40 100644
--- a/main.nf
+++ b/main.nf
@@ -90,4 +90,4 @@ workflow {
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     THE END
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
\ No newline at end of file
+*/
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
index 356961e6..5d3a2fcf 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
@@ -17,6 +17,7 @@ nextflow_workflow {
                 help                = false
                 validate_params     = false
                 monochrome_logs     = false
+                nextflow_cli_args   = ''
                 outdir              = "$params.outdir"
                 ena_metadata_fields = null
 
@@ -24,9 +25,10 @@ nextflow_workflow {
                 input[1] = help
                 input[2] = validate_params
                 input[3] = monochrome_logs
-                input[4] = outdir
-                input[5] = 'https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/testdata/v1.12.0/sra_ids_test.csv'
-                input[6] = ena_metadata_fields
+                input[4] = nextflow_cli_args
+                input[5] = outdir
+                input[6] = 'https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/testdata/v1.12.0/sra_ids_test.csv'
+                input[7] = ena_metadata_fields
                 """
             }
         }

From 5ab509a07deb6662273bd8b54ead630f4263aaab Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Tue, 20 Feb 2024 20:34:04 +0000
Subject: [PATCH 790/852] nextflow_cli_args is a list not a string

---
 .../tests/main.workflow_pipeline_initialisation.nf.test         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
index 5d3a2fcf..377d91f2 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
                 help                = false
                 validate_params     = false
                 monochrome_logs     = false
-                nextflow_cli_args   = ''
+                nextflow_cli_args   = []
                 outdir              = "$params.outdir"
                 ena_metadata_fields = null
 

From fe16845833516530364d9d27eb560b40a7d969fd Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 21 Feb 2024 09:38:47 +0000
Subject: [PATCH 791/852] Update nf-test badge

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index e6035281..bc17b5de 100644
--- a/README.md
+++ b/README.md
@@ -6,7 +6,7 @@
 </h1>
 
 [![GitHub Actions CI Status](https://github.com/nf-core/fetchngs/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/fetchngs/actions/workflows/ci.yml)
-[![GitHub Actions Linting Status](https://github.com/nf-core/fetchngs/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/fetchngs/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/fetchngs/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.5070524-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.5070524)[![nf-test](https://img.shields.io/badge/unit_testing-nf--test-337ab7.svg)](https://github.com/askimed/nf-test)
+[![GitHub Actions Linting Status](https://github.com/nf-core/fetchngs/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/fetchngs/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/fetchngs/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.5070524-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.5070524)[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)

From 1a8e68293c75f79c7b322b4a78b541d191df53b3 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 22 Feb 2024 11:40:56 +0000
Subject: [PATCH 792/852] Update Github Action to run full-sized test for all 3
 download methods

---
 .github/workflows/cloud_tests_full.yml | 23 +++++++++++++++++------
 1 file changed, 17 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/cloud_tests_full.yml b/.github/workflows/cloud_tests_full.yml
index 2748b542..7b049497 100644
--- a/.github/workflows/cloud_tests_full.yml
+++ b/.github/workflows/cloud_tests_full.yml
@@ -19,6 +19,9 @@ jobs:
   run-full-tests-on-aws:
     if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' || !github.event.inputs }}
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        download_method: ["aspera", "ftp", "sratools"]
     steps:
       - uses: seqeralabs/action-tower-launch@v2
         with:
@@ -26,13 +29,14 @@ jobs:
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
           workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/fetchngs/work-${{ github.sha }}"
-          run_name: "aws_fetchngs_full"
+          run_name: "aws_fetchngs_full_${{ matrix.download_method }}"
           revision: ${{ github.sha }}
           profiles: test_full
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-                "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/fetchngs/results-${{ github.sha }}/"
+                "download_method": "${{ matrix.download_method }}",
+                "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/fetchngs/results-${{ github.sha }}/download_method_${{ matrix.download_method }}/"
             }
       - uses: actions/upload-artifact@v3
         with:
@@ -42,6 +46,9 @@ jobs:
   run-full-tests-on-azure:
     if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' || !github.event.inputs }}
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        download_method: ["aspera", "ftp", "sratools"]
     steps:
       - uses: seqeralabs/action-tower-launch@v2
         with:
@@ -49,13 +56,14 @@ jobs:
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }}
           workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/fetchngs/work-${{ github.sha }}"
-          run_name: "azure_fetchngs_full"
+          run_name: "azure_fetchngs_full_${{ matrix.download_method }}"
           revision: ${{ github.sha }}
           profiles: test_full
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-                "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/fetchngs/results-${{ github.sha }}/"
+                "download_method": "${{ matrix.download_method }}",
+                "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/fetchngs/results-${{ github.sha }}/download_method_${{ matrix.download_method }}/"
             }
       - uses: actions/upload-artifact@v3
         with:
@@ -65,6 +73,8 @@ jobs:
   run-full-tests-on-gcp:
     if: ${{ github.event.inputs.platform == 'gcp' || !github.event.inputs }}
     runs-on: ubuntu-latest
+    matrix:
+      download_method: ["aspera", "ftp", "sratools"]
     steps:
       - uses: seqeralabs/action-tower-launch@v2
         with:
@@ -72,13 +82,14 @@ jobs:
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_CE_GCP_CPU }}
           workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/fetchngs/work-${{ github.sha }}"
-          run_name: "gcp_fetchngs_full"
+          run_name: "gcp_fetchngs_full_${{ matrix.download_method }}"
           revision: ${{ github.sha }}
           profiles: test_full
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-                "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/fetchngs/results-${{ github.sha }}/"
+                "download_method": "${{ matrix.download_method }}",
+                "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/fetchngs/results-${{ github.sha }}/download_method_${{ matrix.download_method }}/"
             }
       - uses: actions/upload-artifact@v3
         with:

From 430c520267cc80ea0b24c9e84f626d4de55ec662 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 22 Feb 2024 11:42:54 +0000
Subject: [PATCH 793/852] Update CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 62b239b8..20aa37c5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -48,6 +48,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #268](https://github.com/nf-core/fetchngs/pull/268) - Add mermaid diagram
 - [PR #273](https://github.com/nf-core/fetchngs/pull/273) - Update utility subworkflows
 - [PR #283](https://github.com/nf-core/fetchngs/pull/283) - Template update for nf-core/tools v2.13
+- [PR #288](https://github.com/nf-core/fetchngs/pull/288) - Update Github Action to run full-sized test for all 3 download methods
 
 ### Software dependencies
 

From 68d96f1f28f559ae81858b09834db717d059f676 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 22 Feb 2024 11:45:07 +0000
Subject: [PATCH 794/852] Add in missing strategy section

---
 .github/workflows/cloud_tests_full.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cloud_tests_full.yml b/.github/workflows/cloud_tests_full.yml
index 7b049497..81cabbfd 100644
--- a/.github/workflows/cloud_tests_full.yml
+++ b/.github/workflows/cloud_tests_full.yml
@@ -73,8 +73,9 @@ jobs:
   run-full-tests-on-gcp:
     if: ${{ github.event.inputs.platform == 'gcp' || !github.event.inputs }}
     runs-on: ubuntu-latest
-    matrix:
-      download_method: ["aspera", "ftp", "sratools"]
+    strategy:
+      matrix:
+        download_method: ["aspera", "ftp", "sratools"]
     steps:
       - uses: seqeralabs/action-tower-launch@v2
         with:

From 58cc000570c229ee896a81337ea950ed3b662f4d Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 22 Feb 2024 12:25:21 +0000
Subject: [PATCH 795/852] Remove mentions of deprecated Synapse functionality
 in pipeline

---
 CITATIONS.md                                                | 3 ---
 README.md                                                   | 4 ++--
 docs/usage.md                                               | 2 +-
 subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf   | 2 +-
 .../tests/main.function.nf.test.snap                        | 6 ------
 5 files changed, 4 insertions(+), 13 deletions(-)

diff --git a/CITATIONS.md b/CITATIONS.md
index a982bfd2..62235e72 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -36,9 +36,6 @@
 
   > Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A. NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5. doi: 10.1093/nar/gks1193. Epub 2012 Nov 27. PubMed PMID: 23193258; PubMed Central PMCID: PMC3531084.
 
-- [Synapse](https://pubmed.ncbi.nlm.nih.gov/24071850/)
-  > Omberg L, Ellrott K, Yuan Y, Kandoth C, Wong C, Kellen MR, Friend SH, Stuart J, Liang H, Margolin AA. Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas. Nat Genet. 2013 Oct;45(10):1121-6. doi: 10.1038/ng.2761. PMID: 24071850; PMCID: PMC3950337.
-
 ## Software packaging/containerisation/testing tools
 
 - [Anaconda](https://anaconda.com)
diff --git a/README.md b/README.md
index bc17b5de..7d869500 100644
--- a/README.md
+++ b/README.md
@@ -18,7 +18,7 @@
 
 ## Introduction
 
-**nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from both public and private databases. At present, the pipeline supports SRA / ENA / DDBJ / GEO / Synapse ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)).
+**nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from both public databases. At present, the pipeline supports SRA / ENA / DDBJ / GEO ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)).
 
 ```mermaid
 flowchart LR
@@ -114,7 +114,7 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/fetchngs was originally written by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [Seqera Labs, Spain](https://seqera.io/) and Jose Espinosa-Carrasco ([@JoseEspinosa](https://github.com/JoseEspinosa)) from [The Comparative Bioinformatics Group](https://www.crg.eu/en/cedric_notredame) at [The Centre for Genomic Regulation, Spain](https://www.crg.eu/). Support for download of sequencing reads without FTP links via sra-tools was added by Moritz E. Beber ([@Midnighter](https://github.com/Midnighter)) from [Unseen Bio ApS, Denmark](https://unseenbio.com). The Synapse workflow was added by Daisy Han [@daisyhan97](https://github.com/daisyhan97) and Bruno Grande [@BrunoGrandePhD](https://github.com/BrunoGrandePhD) from [Sage Bionetworks, Seattle](https://sagebionetworks.org/).
+nf-core/fetchngs was originally written by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [Seqera Labs, Spain](https://seqera.io/) and Jose Espinosa-Carrasco ([@JoseEspinosa](https://github.com/JoseEspinosa)) from [The Comparative Bioinformatics Group](https://www.crg.eu/en/cedric_notredame) at [The Centre for Genomic Regulation, Spain](https://www.crg.eu/). Support for download of sequencing reads without FTP links via sra-tools was added by Moritz E. Beber ([@Midnighter](https://github.com/Midnighter)) from [Unseen Bio ApS, Denmark](https://unseenbio.com).
 
 ## Contributions and Support
 
diff --git a/docs/usage.md b/docs/usage.md
index 2bc9a125..8f27c3d5 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -6,7 +6,7 @@
 
 ## Introduction
 
-The pipeline has been set-up to automatically download and process the raw FastQ files from both public and private repositories. Identifiers can be provided in a file, one-per-line via the `--input` parameter. Currently, the following types of example identifiers are supported:
+The pipeline has been set-up to automatically download and process the raw FastQ files from public repositories. Identifiers can be provided in a file, one-per-line via the `--input` parameter. Currently, the following types of example identifiers are supported:
 
 | `SRA`        | `ENA`        | `DDBJ`       | `GEO`      |
 | ------------ | ------------ | ------------ | ---------- |
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
index 22079228..0c4307b5 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
@@ -158,7 +158,7 @@ def isSraId(input) {
         if (num_match == total_ids) {
             is_sra = true
         } else {
-            error("Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / GEO / DDBJ or Synapse ids!")
+            error("Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / GEO / DDBJ ids!")
         }
     }
     return is_sra
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test.snap b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test.snap
index 335967e6..05840fc8 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test.snap
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test.snap
@@ -12,11 +12,5 @@
             true
         ],
         "timestamp": "2024-01-19T16:36:43.68958"
-    },
-    "Function isSynapseId": {
-        "content": [
-            true
-        ],
-        "timestamp": "2024-01-19T16:37:12.992364"
     }
 }
\ No newline at end of file

From 0836b3b7c3dd15662ed3ffd09d73e4b96a28310a Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 22 Feb 2024 12:26:53 +0000
Subject: [PATCH 796/852] Update CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 62b239b8..1ab82afa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -48,6 +48,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #268](https://github.com/nf-core/fetchngs/pull/268) - Add mermaid diagram
 - [PR #273](https://github.com/nf-core/fetchngs/pull/273) - Update utility subworkflows
 - [PR #283](https://github.com/nf-core/fetchngs/pull/283) - Template update for nf-core/tools v2.13
+- [PR #290](https://github.com/nf-core/fetchngs/pull/290) - Remove mentions of deprecated Synapse functionality in pipeline
 
 ### Software dependencies
 

From b234c7123c9816e248a639a2922556c86f82fd99 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Thu, 22 Feb 2024 18:27:10 +0100
Subject: [PATCH 797/852] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c5530353..063b345e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[1.12.0](https://github.com/nf-core/fetchngs/releases/tag/1.12.0)] - 2024-02-02
+## [[1.12.0](https://github.com/nf-core/fetchngs/releases/tag/1.12.0)] - 2024-02-23
 
 ### :warning: Major enhancements
 

From 546120a0b0cb6eb5c6ecc64cdd45f04d373634a4 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 28 Feb 2024 12:15:36 +0100
Subject: [PATCH 798/852] replace mermaid diagram with subway map

---
 CHANGELOG.md                                  |     3 +-
 README.md                                     |    29 +-
 .../nf-core-fetchngs_metro_map_grey.png       |   Bin 0 -> 182235 bytes
 .../nf-core-fetchngs_metro_map_grey.svg       | 12733 ++++++++++++++++
 4 files changed, 12736 insertions(+), 29 deletions(-)
 create mode 100644 docs/images/nf-core-fetchngs_metro_map_grey.png
 create mode 100644 docs/images/nf-core-fetchngs_metro_map_grey.svg

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 063b345e..02ec0ebb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[1.12.0](https://github.com/nf-core/fetchngs/releases/tag/1.12.0)] - 2024-02-23
+## [[1.12.0](https://github.com/nf-core/fetchngs/releases/tag/1.12.0)] - 2024-02-29
 
 ### :warning: Major enhancements
 
@@ -50,6 +50,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #283](https://github.com/nf-core/fetchngs/pull/283) - Template update for nf-core/tools v2.13
 - [PR #288](https://github.com/nf-core/fetchngs/pull/288) - Update Github Action to run full-sized test for all 3 download methods
 - [PR #290](https://github.com/nf-core/fetchngs/pull/290) - Remove mentions of deprecated Synapse functionality in pipeline
+- [PR #291](https://github.com/nf-core/fetchngs/pull/291) - Replace mermaid diagram with subway map
 
 ### Software dependencies
 
diff --git a/README.md b/README.md
index 7d869500..d6c5c597 100644
--- a/README.md
+++ b/README.md
@@ -20,34 +20,7 @@
 
 **nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from both public databases. At present, the pipeline supports SRA / ENA / DDBJ / GEO ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)).
 
-```mermaid
-flowchart LR
-    IDS("Input
-    File") --> SRA & GEO & ENA & DDBJ
-    subgraph SG_DBIDS[Database IDs]
-      SRA("SRA")
-      GEO("GEO")
-      ENA("ENA")
-      DDBJ("DDBJ")
-    end
-    subgraph SG_METADATA[Download Metadata]
-      SRA & GEO & ENA & DDBJ --> META("Get
-      Metadata")
-      META --> LINKS("Get
-      Download
-      Links")
-    end
-    subgraph SG_FETCH_FASTQ[Download FastQ]
-      LINKS --> |--download_method 'ftp' | FTP("FTP")
-      LINKS --> |--download_method 'aspera' | ASPERA("Aspera")
-      LINKS --> |--download_method 'sratools' | SRATOOLS("sra-tools")
-    end
-    subgraph SG_FASTQ[Pipeline Outputs]
-      ASPERA & FTP & SRATOOLS --> FASTQ("FastQ")
-      FASTQ --> SAMPLESHEET("Samplesheet")
-    end
-    LINKS --> |--skip_fastq_download| SAMPLESHEET
-```
+![nf-core/fetchngs metro map](docs/images/nf-core-fetchngs_metro_map_grey.png)
 
 ## Usage
 
diff --git a/docs/images/nf-core-fetchngs_metro_map_grey.png b/docs/images/nf-core-fetchngs_metro_map_grey.png
new file mode 100644
index 0000000000000000000000000000000000000000..eb4b49bc94260eec9a9984c772f25642741cbbe3
GIT binary patch
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From 549ff23caa0838c37ee812b3c92c0770c8c88c48 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 28 Feb 2024 12:24:36 +0100
Subject: [PATCH 799/852] fix PR number

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 02ec0ebb..ca348513 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -50,7 +50,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #283](https://github.com/nf-core/fetchngs/pull/283) - Template update for nf-core/tools v2.13
 - [PR #288](https://github.com/nf-core/fetchngs/pull/288) - Update Github Action to run full-sized test for all 3 download methods
 - [PR #290](https://github.com/nf-core/fetchngs/pull/290) - Remove mentions of deprecated Synapse functionality in pipeline
-- [PR #291](https://github.com/nf-core/fetchngs/pull/291) - Replace mermaid diagram with subway map
+- [PR #294](https://github.com/nf-core/fetchngs/pull/294) - Replace mermaid diagram with subway map
 
 ### Software dependencies
 

From 5da86768b2acc166ec152995dcd02a9ea66fe2f3 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 28 Feb 2024 12:29:27 +0100
Subject: [PATCH 800/852] be less stringent with tests expectation

---
 .github/workflows/ci.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c474190e..fa75579f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -161,7 +161,9 @@ jobs:
 
   confirm-pass:
     runs-on: ubuntu-latest
-    needs: [test]
+    needs:
+      - changes
+      - test
     if: always()
     steps:
       - name: All tests ok

From a4463111cbd0beec6219b70ac3d00d56d73c7ab4 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 28 Feb 2024 12:30:44 +0100
Subject: [PATCH 801/852] revert changes

---
 .github/workflows/ci.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index fa75579f..c474190e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -161,9 +161,7 @@ jobs:
 
   confirm-pass:
     runs-on: ubuntu-latest
-    needs:
-      - changes
-      - test
+    needs: [test]
     if: always()
     steps:
       - name: All tests ok

From 9e5221e2c359ae5ed95eb4d3845e66e799e1d8a7 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 28 Feb 2024 12:32:15 +0100
Subject: [PATCH 802/852] be less stringent with tests expectation

---
 .github/workflows/ci.yml | 4 +++-
 CHANGELOG.md             | 1 +
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c474190e..fa75579f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -161,7 +161,9 @@ jobs:
 
   confirm-pass:
     runs-on: ubuntu-latest
-    needs: [test]
+    needs:
+      - changes
+      - test
     if: always()
     steps:
       - name: All tests ok
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 063b345e..625e4de9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -50,6 +50,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #283](https://github.com/nf-core/fetchngs/pull/283) - Template update for nf-core/tools v2.13
 - [PR #288](https://github.com/nf-core/fetchngs/pull/288) - Update Github Action to run full-sized test for all 3 download methods
 - [PR #290](https://github.com/nf-core/fetchngs/pull/290) - Remove mentions of deprecated Synapse functionality in pipeline
+- [PR #295](https://github.com/nf-core/fetchngs/pull/295) - Be less stringent with test expectations for CI
 
 ### Software dependencies
 

From d538a927c8959e861007d3c4c741092e3bd1c8ef Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 28 Feb 2024 11:41:56 +0000
Subject: [PATCH 803/852] Remove --outdir definition in nf-tests for local
 modules

---
 modules/local/aspera_cli/tests/main.nf.test              | 4 ----
 modules/local/multiqc_mappings_config/tests/main.nf.test | 4 ----
 modules/local/sra_fastq_ftp/tests/main.nf.test           | 4 ----
 modules/local/sra_ids_to_runinfo/tests/main.nf.test      | 4 ----
 modules/local/sra_runinfo_to_ftp/tests/main.nf.test      | 4 ----
 modules/local/sra_to_samplesheet/tests/main.nf.test      | 4 ----
 6 files changed, 24 deletions(-)

diff --git a/modules/local/aspera_cli/tests/main.nf.test b/modules/local/aspera_cli/tests/main.nf.test
index b2f5f1bd..63347000 100644
--- a/modules/local/aspera_cli/tests/main.nf.test
+++ b/modules/local/aspera_cli/tests/main.nf.test
@@ -7,10 +7,6 @@ nextflow_process {
     test("Should run without failures") {
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
-
             process {
                 """
                 input[0] = [
diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test
index 106f3248..dbb4d74f 100644
--- a/modules/local/multiqc_mappings_config/tests/main.nf.test
+++ b/modules/local/multiqc_mappings_config/tests/main.nf.test
@@ -7,10 +7,6 @@ nextflow_process {
     test("Should run without failures") {
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
-
             process {
                 """
                 input[0] = file(params.pipelines_testdata_base_path + 'csv/SRX9626017_SRR13191702.mappings.csv', checkIfExists: true)
diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test
index f58aaae2..bf005290 100644
--- a/modules/local/sra_fastq_ftp/tests/main.nf.test
+++ b/modules/local/sra_fastq_ftp/tests/main.nf.test
@@ -7,10 +7,6 @@ nextflow_process {
     test("Should run without failures") {
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
-
             process {
                 """
                 input[0] = [
diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test
index 2e510ea1..48797a1a 100644
--- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test
+++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test
@@ -7,10 +7,6 @@ nextflow_process {
     test("Should run without failures") {
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
-
             process {
                 """
                 input[0] = 'SRR13191702'
diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
index 4b03249c..39db814a 100644
--- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
+++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
@@ -7,10 +7,6 @@ nextflow_process {
     test("Should run without failures") {
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
-
             process {
                 """
                 input[0] = file(params.pipelines_testdata_base_path + 'tsv/SRR13191702.runinfo.tsv', checkIfExists: true)
diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test
index 4458858e..ed765158 100644
--- a/modules/local/sra_to_samplesheet/tests/main.nf.test
+++ b/modules/local/sra_to_samplesheet/tests/main.nf.test
@@ -7,10 +7,6 @@ nextflow_process {
     test("Should run without failures") {
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
-
             process {
                 """
                 input[0] = [id:'ERX1188904_ERR1109373', run_accession:'ERR1109373', experiment_accession:'ERX1188904', sample_accession:'SAMEA3643867',  experiment_alias:'ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7', run_alias:'ena-RUN-CAM-03-11-2015-17:01:52:847-7',  sample_alias:'sample_56', study_alias:'ena-STUDY-CAM-02-11-2015-17:42:24:189-13', library_layout:'PAIRED', experiment_title:'Illumina HiSeq 2500 paired end sequencing', sample_title:'RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome', sample_description:'RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome', fastq_md5:'8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9', fastq_ftp:'ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz', fastq_1:'./results/fastq/ERX1188904_ERR1109373_1.fastq.gz', fastq_2:'./results/fastq/ERX1188904_ERR1109373_2.fastq.gz', md5_1:'9fd57225d6c07a31843276d6df9b15c0', md5_2:'5a62e8f785687dce890cfb4fe3e607f9', single_end:false]

From 41f0a96d670ca8ad87e326a08e684542bb69725a Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 28 Feb 2024 11:50:42 +0000
Subject: [PATCH 804/852] Remove --outdir definition in nf-tests for
 nf-core/modules and update snapshots

---
 .../sratoolsncbisettings/tests/main.nf.test.snap     |  8 ++++++--
 .../nf-core/sratools/fasterqdump/tests/main.nf.test  |  8 --------
 .../sratools/fasterqdump/tests/main.nf.test.snap     | 12 ++++++++++--
 modules/nf-core/sratools/prefetch/tests/main.nf.test |  6 ------
 .../sratools/prefetch/tests/main.nf.test.snap        | 12 ++++++++++--
 modules/nf-core/untar/tests/main.nf.test             |  6 ------
 modules/nf-core/untar/tests/main.nf.test.snap        | 12 ++++++++++--
 7 files changed, 36 insertions(+), 28 deletions(-)

diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap
index 65a706d4..5e314f0b 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap
+++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap
@@ -5,6 +5,10 @@
                 "versions.yml:md5,3d6ee88cce1ee517e198633f062589a8"
             ]
         ],
-        "timestamp": "2024-01-09T22:43:44.996003"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:47:15.824443"
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
index c64f6fc1..695394d4 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
@@ -20,10 +20,6 @@ nextflow_process {
         }
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
-
             process {
                 """
                 input[0] = UNTAR.out.untar.map{ meta, files -> [ [ id:'test_single_end', single_end:true ], files]}
@@ -55,10 +51,6 @@ nextflow_process {
         }
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
-
             process {
                 """
                 input[0] = UNTAR.out.untar.map{ meta, files -> [ [ id:'test_paired_end', single_end:false ], files]}
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
index 0e590311..3439b400 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
@@ -28,7 +28,11 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-30T18:02:53.958171"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:47:42.981471"
     },
     "Paired-end": {
         "content": [
@@ -65,6 +69,10 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-30T18:03:20.841426"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:48:09.914497"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test
index b0f5ffa2..c3ebd91e 100644
--- a/modules/nf-core/sratools/prefetch/tests/main.nf.test
+++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test
@@ -6,9 +6,6 @@ nextflow_process {
     test("sratools/prefetch") {
 
         when {
-            params {
-                outdir = "output"
-            }
             process {
                 """
                 input[0] = Channel.of([ [ id:'test', single_end:false ], 'DRR000774' ])
@@ -29,9 +26,6 @@ nextflow_process {
     test("sratools/prefetch with sralite") {
 
         when {
-            params {
-                outdir = "output"
-            }
             process {
                 """
                 input[0] = Channel.of([ [ id:'test', single_end:false ], 'SRR1170046' ])
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap
index ab1d2088..946fc869 100644
--- a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap
+++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap
@@ -32,7 +32,11 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-13T12:11:24.563510389"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:49:02.309737"
     },
     "sratools/prefetch": {
         "content": [
@@ -67,6 +71,10 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-13T12:11:02.75256571"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:48:37.428307"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test
index 05134043..98b769ad 100644
--- a/modules/nf-core/untar/tests/main.nf.test
+++ b/modules/nf-core/untar/tests/main.nf.test
@@ -7,9 +7,6 @@ nextflow_process {
     test("test_untar") {
 
         when {
-            params {
-                outdir   = "$outputDir"
-            }
             process {
                 """
                 input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ]
@@ -29,9 +26,6 @@ nextflow_process {
     test("test_untar_onlyfiles") {
 
         when {
-            params {
-                outdir   = "$outputDir"
-            }
             process {
                 """
                 input[0] = [ [], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) ]
diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap
index ace42576..64550292 100644
--- a/modules/nf-core/untar/tests/main.nf.test.snap
+++ b/modules/nf-core/untar/tests/main.nf.test.snap
@@ -12,7 +12,11 @@
                 ]
             ]
         ],
-        "timestamp": "2023-10-18T11:56:46.878844"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:49:41.320643"
     },
     "test_untar": {
         "content": [
@@ -29,6 +33,10 @@
                 ]
             ]
         ],
-        "timestamp": "2023-10-18T11:56:08.16574"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:49:33.795172"
     }
 }
\ No newline at end of file

From f8da74e62842c960969e4cd1cd6d4f328c9d3ae6 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 28 Feb 2024 11:52:55 +0000
Subject: [PATCH 805/852] Update snapshots for local modules

---
 modules/local/aspera_cli/tests/main.nf.test.snap            | 6 +++++-
 .../local/multiqc_mappings_config/tests/main.nf.test.snap   | 6 +++++-
 modules/local/sra_fastq_ftp/tests/main.nf.test.snap         | 6 +++++-
 modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap    | 6 +++++-
 modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap    | 6 +++++-
 modules/local/sra_to_samplesheet/tests/main.nf.test.snap    | 6 +++++-
 6 files changed, 30 insertions(+), 6 deletions(-)

diff --git a/modules/local/aspera_cli/tests/main.nf.test.snap b/modules/local/aspera_cli/tests/main.nf.test.snap
index 15497822..0ba6a643 100644
--- a/modules/local/aspera_cli/tests/main.nf.test.snap
+++ b/modules/local/aspera_cli/tests/main.nf.test.snap
@@ -66,6 +66,10 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-29T13:00:29.847293"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:52:00.601018"
     }
 }
\ No newline at end of file
diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap
index 1a4d16c4..43e46f61 100644
--- a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap
+++ b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap
@@ -22,6 +22,10 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-22T10:58:18.132284"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:52:12.65888"
     }
 }
\ No newline at end of file
diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap
index 531a5ec3..5b300f8c 100644
--- a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap
+++ b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap
@@ -66,6 +66,10 @@
                 ]
             }
         ],
-        "timestamp": "2023-12-20T23:33:35.159073"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:51:51.301654"
     }
 }
\ No newline at end of file
diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap
index 241efe2a..f7b6cee5 100644
--- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap
+++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap
@@ -16,6 +16,10 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-22T10:58:56.721948"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:52:05.345153"
     }
 }
\ No newline at end of file
diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap
index cd246303..be190f5a 100644
--- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap
+++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap
@@ -16,6 +16,10 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-22T10:58:36.16611"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:51:45.748227"
     }
 }
\ No newline at end of file
diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap
index 8cc8686a..568f3ea7 100644
--- a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap
+++ b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap
@@ -108,6 +108,10 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-22T10:58:27.169349"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:51:38.244046"
     }
 }
\ No newline at end of file

From 03374f8a2b115602db138e8433a03cd1d7486984 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 28 Feb 2024 11:57:17 +0000
Subject: [PATCH 806/852] Remove --outdir definition in nf-tests for local
 subworkflows and update snapshots

---
 .../tests/main.function.nf.test                |  6 ++++--
 .../tests/main.function.nf.test.snap           | 18 +++++++++++++++---
 .../main.workflow_pipeline_completion.nf.test  |  3 ---
 ...in.workflow_pipeline_initialisation.nf.test |  3 ---
 4 files changed, 19 insertions(+), 11 deletions(-)

diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test
index 85c16bf9..f2e3f12a 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test
@@ -69,8 +69,10 @@ nextflow_function {
         function "sraCurateSamplesheetWarn"
 
         then {
-            assert function.success
-            assert snapshot(function.result).match()
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
         }
     }
 
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test.snap b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test.snap
index 05840fc8..99fb20e7 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test.snap
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test.snap
@@ -1,16 +1,28 @@
 {
     "Function sraCurateSamplesheetWarn": {
         "content": null,
-        "timestamp": "2024-01-19T16:37:05.668505"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:55:41.001798"
     },
     "Function sraCheckENAMetadataFields [success]": {
         "content": null,
-        "timestamp": "2024-01-19T16:36:51.121603"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:55:33.679255"
     },
     "Function isSraId": {
         "content": [
             true
         ],
-        "timestamp": "2024-01-19T16:36:43.68958"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:55:29.999289"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.nf.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.nf.test
index b2114675..da87b66b 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.nf.test
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.nf.test
@@ -8,9 +8,6 @@ nextflow_workflow {
     test("Should run") {
 
         when {
-            params {
-                outdir = "tests/results"
-            }
             workflow {
                 """
                 email           = null
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
index 377d91f2..2b6878a3 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
@@ -8,9 +8,6 @@ nextflow_workflow {
     test("Should run") {
 
         when {
-            params {
-                outdir = "tests/results"
-            }
             workflow {
                 """
                 version             = false

From cd8f66db4962555263e7d2b67a12ef7f09e457e7 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 28 Feb 2024 12:05:48 +0000
Subject: [PATCH 807/852] Remove --outdir definition in nf-tests for nf-core
 subworkflows and update snapshots

---
 .../tests/main.nf.test                        |  3 --
 .../tests/main.nf.test.snap                   | 14 +++----
 .../tests/main.function.nf.test.snap          | 12 +++++-
 .../tests/main.workflow.nf.test               | 18 ++------
 .../tests/main.function.nf.test.snap          | 42 +++++++++++++++----
 .../tests/main.workflow.nf.test.snap          |  6 ++-
 6 files changed, 60 insertions(+), 35 deletions(-)

diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
index 7293a792..7b41ed7e 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
@@ -20,9 +20,6 @@ nextflow_workflow {
                 input[1] = []
                 """
             }
-            params {
-                outdir = "output"
-            }
         }
 
         then {
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
index d64857ef..bec84076 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
@@ -7,7 +7,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-01T08:34:54.56022"
+        "timestamp": "2024-02-28T12:02:56.176292"
     },
     "test_pe_reads_2_lines": {
         "content": [
@@ -24,7 +24,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-01T08:34:54.532626"
+        "timestamp": "2024-02-28T12:02:56.166207"
     },
     "test_pe_reads_2_size": {
         "content": [
@@ -34,7 +34,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-01T08:34:54.542804"
+        "timestamp": "2024-02-28T12:02:56.168869"
     },
     "versions": {
         "content": [
@@ -48,7 +48,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-01T08:34:54.570734"
+        "timestamp": "2024-02-28T12:02:56.17931"
     },
     "test_pe_reads_1_size": {
         "content": [
@@ -58,7 +58,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-01T08:34:54.525795"
+        "timestamp": "2024-02-28T12:02:56.163669"
     },
     "test_se_reads_lines": {
         "content": [
@@ -75,7 +75,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-01T08:34:54.550392"
+        "timestamp": "2024-02-28T12:02:56.171227"
     },
     "test_pe_reads_1_lines": {
         "content": [
@@ -92,6 +92,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-01T08:34:54.509486"
+        "timestamp": "2024-02-28T12:02:56.161354"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap
index db2030f8..e3f0baf4 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap
@@ -3,10 +3,18 @@
         "content": [
             "v9.9.9"
         ],
-        "timestamp": "2024-01-19T11:32:36.031083"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:02:05.308243"
     },
     "Test Function checkCondaChannels": {
         "content": null,
-        "timestamp": "2024-01-19T11:32:50.456"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:02:12.425833"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
index 94e7198c..530cca54 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -8,9 +8,6 @@ nextflow_workflow {
     test("Should run no inputs") {
 
         when {
-            params {
-                outdir = "tests/results"
-            }
             workflow {
                 """
                 print_version        = false
@@ -36,9 +33,6 @@ nextflow_workflow {
     test("Should print version") {
 
         when {
-            params {
-                outdir = "tests/results"
-            }
             workflow {
                 """
                 print_version        = true
@@ -65,19 +59,16 @@ nextflow_workflow {
     test("Should dump params") {
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
             workflow {
                 """
                 print_version        = false
                 dump_parameters      = true
-                outdir               = params.outdir
+                outdir               = 'results'
                 check_conda_channels = false
 
                 input[0] = false
                 input[1] = true
-                input[2] = params.outdir
+                input[2] = outdir
                 input[3] = false
                 """
             }
@@ -93,14 +84,11 @@ nextflow_workflow {
     test("Should not create params JSON if no output directory") {
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
             workflow {
                 """
                 print_version        = false
                 dump_parameters      = true
-                outdir               = params.outdir
+                outdir               = 'results'
                 check_conda_channels = false
 
                 input[0] = false
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
index 10f948e6..1037232c 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
@@ -1,25 +1,41 @@
 {
     "Test Function checkProfileProvided": {
         "content": null,
-        "timestamp": "2024-02-09T15:43:55.145717"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:03.360873"
     },
     "Test Function checkConfigProvided": {
         "content": [
             true
         ],
-        "timestamp": "2024-01-19T11:34:13.548431224"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:02:59.729647"
     },
     "Test Function nfCoreLogo": {
         "content": [
             "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n                                        \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m        ___     __   __   __   ___     \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \u001b[0;33m}  {\u001b[0m\n\u001b[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \u001b[0;32m\\`-._,-`-,\u001b[0m\n                                        \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m  nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n"
         ],
-        "timestamp": "2024-01-19T11:34:38.840454873"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:10.562934"
     },
     "Test Function workflowCitation": {
         "content": [
             "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n  https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n  https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n  https://github.com/nextflow_workflow/blob/master/CITATIONS.md"
         ],
-        "timestamp": "2024-01-19T11:34:22.24352016"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:07.019761"
     },
     "Test Function without logColours": {
         "content": [
@@ -73,13 +89,21 @@
                 "biwhite": ""
             }
         ],
-        "timestamp": "2024-01-19T11:35:04.418416984"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:17.969323"
     },
     "Test Function dashedLine": {
         "content": [
             "-\u001b[2m----------------------------------------------------\u001b[0m-"
         ],
-        "timestamp": "2024-01-19T11:34:55.420000755"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:14.366181"
     },
     "Test Function with logColours": {
         "content": [
@@ -133,6 +157,10 @@
                 "biwhite": "\u001b[1;97m"
             }
         ],
-        "timestamp": "2024-01-19T11:35:13.436366565"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:21.714424"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
index d07ce54c..859d1030 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
@@ -10,6 +10,10 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-19T11:35:22.538940073"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:25.726491"
     }
 }
\ No newline at end of file

From 669b8686f6ac326e554b6bd4c73feb3c4882c4e2 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 28 Feb 2024 12:08:46 +0000
Subject: [PATCH 808/852] Update CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ca348513..dbd7ac4d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -51,6 +51,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #288](https://github.com/nf-core/fetchngs/pull/288) - Update Github Action to run full-sized test for all 3 download methods
 - [PR #290](https://github.com/nf-core/fetchngs/pull/290) - Remove mentions of deprecated Synapse functionality in pipeline
 - [PR #294](https://github.com/nf-core/fetchngs/pull/294) - Replace mermaid diagram with subway map
+- [PR #296](https://github.com/nf-core/fetchngs/pull/296) - Remove params.outdir from tests where required and update snapshots
 
 ### Software dependencies
 

From cbe835e4906e8dde78461d9ff48f0884701c6762 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 28 Feb 2024 12:15:59 +0000
Subject: [PATCH 809/852] Remove --outdir definition in nf-tests for workflows

---
 workflows/sra/tests/main.nf.test                             | 3 ---
 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test   | 1 -
 workflows/sra/tests/sra_download_method_aspera.nf.test       | 1 -
 workflows/sra/tests/sra_download_method_sratools.nf.test     | 1 -
 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test     | 1 -
 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test      | 1 -
 workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test | 1 -
 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test  | 1 -
 workflows/sra/tests/sra_skip_fastq_download.nf.test          | 1 -
 9 files changed, 11 deletions(-)

diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index dddc5275..1e2856c1 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -20,9 +20,6 @@ nextflow_workflow {
                 input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035")
                 """
             }
-            params {
-                outdir = "$outputDir"
-            }
         }
 
         then {
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index 98d1432d..c8d17876 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -21,7 +21,6 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
                 nf_core_pipeline = "rnaseq"
                 ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5"
                 sample_mapping_fields = "run_accession,library_layout"
diff --git a/workflows/sra/tests/sra_download_method_aspera.nf.test b/workflows/sra/tests/sra_download_method_aspera.nf.test
index d36f9095..d431a571 100644
--- a/workflows/sra/tests/sra_download_method_aspera.nf.test
+++ b/workflows/sra/tests/sra_download_method_aspera.nf.test
@@ -21,7 +21,6 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
                 download_method = 'aspera'
             }
         }
diff --git a/workflows/sra/tests/sra_download_method_sratools.nf.test b/workflows/sra/tests/sra_download_method_sratools.nf.test
index 05613f1e..e4f8c2d2 100644
--- a/workflows/sra/tests/sra_download_method_sratools.nf.test
+++ b/workflows/sra/tests/sra_download_method_sratools.nf.test
@@ -21,7 +21,6 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
                 download_method = 'sratools'
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index 522ab75b..72f8d595 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -21,7 +21,6 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
                 nf_core_pipeline = "atacseq"
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index f6f1b560..2e20902a 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -21,7 +21,6 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
                 nf_core_pipeline = "rnaseq"
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index b9373b57..50650b79 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -21,7 +21,6 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
                 nf_core_pipeline = "taxprofiler"
             }
         }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index 4985b9d0..1fe9cc41 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -21,7 +21,6 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
                 nf_core_pipeline = "viralrecon"
             }
         }
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index 245dbb80..8663cf3f 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -20,7 +20,6 @@ nextflow_workflow {
                 """
             }
             params {
-                outdir = "$outputDir"
                 skip_fastq_download = true
             }
         }

From 502bc7024925e3af1e707b45ab67dd27f5db63a8 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 28 Feb 2024 12:21:54 +0000
Subject: [PATCH 810/852] Fix missed tests for nf-core modules

---
 .../nf-core/custom/sratoolsncbisettings/tests/main.nf.test    | 1 -
 .../nf-core/custom/sratoolsncbisettings/tests/nextflow.config | 2 --
 .../utils_nextflow_pipeline/tests/main.workflow.nf.test       | 4 ++--
 3 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
index 8cd0de8a..e9ea68dc 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
+++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
@@ -11,7 +11,6 @@ nextflow_process {
             params {
                 settings_path = '/tmp/.ncbi'
                 settings_file  = "${params.settings_path}/user-settings.mkfg"
-                outdir         = "$outputDir"
             }
 
             process {
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config b/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config
index c4a96e94..df5def04 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config
+++ b/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config
@@ -4,8 +4,6 @@ params.settings_file = "${params.settings_path}/user-settings.mkfg"
 env.NCBI_SETTINGS = params.settings_file
 
 process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
     withName: CUSTOM_SRATOOLSNCBISETTINGS {
         containerOptions = {
             (workflow.containerEngine == 'singularity') ?
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
index 530cca54..13782037 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -88,12 +88,12 @@ nextflow_workflow {
                 """
                 print_version        = false
                 dump_parameters      = true
-                outdir               = 'results'
+                outdir               = null
                 check_conda_channels = false
 
                 input[0] = false
                 input[1] = true
-                input[2] = null
+                input[2] = outdir
                 input[3] = false
                 """
             }

From 5b20998323feafb763f458d58e8eadb6d25995bd Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 28 Feb 2024 12:28:57 +0000
Subject: [PATCH 811/852] Change outdir path in local subworkflow

---
 .../tests/main.workflow_pipeline_completion.nf.test             | 2 +-
 .../tests/main.workflow_pipeline_initialisation.nf.test         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.nf.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.nf.test
index da87b66b..b94f72cf 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.nf.test
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.nf.test
@@ -13,7 +13,7 @@ nextflow_workflow {
                 email           = null
                 email_on_fail   = null
                 plaintext_email = false
-                outdir          = "tests/results"
+                outdir          = 'results'
                 monochrome_logs = false
                 hook_url        = null
 
diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
index 2b6878a3..e04aa726 100644
--- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
+++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test
@@ -15,7 +15,7 @@ nextflow_workflow {
                 validate_params     = false
                 monochrome_logs     = false
                 nextflow_cli_args   = []
-                outdir              = "$params.outdir"
+                outdir              = 'results'
                 ena_metadata_fields = null
 
                 input[0] = version

From 92cbb7db1454f026e16e45db5fc13121453446e9 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 29 Feb 2024 09:36:59 +0000
Subject: [PATCH 812/852] Re-install modules and subworkflows from nf-core

---
 modules.json                                     | 16 ++++++++--------
 .../fasterqdump/sratools-fasterqdump.diff        |  3 +--
 .../sratools/fasterqdump/tests/main.nf.test.snap | 16 ++++++++--------
 .../tests/main.nf.test.snap                      | 14 +++++++-------
 4 files changed, 24 insertions(+), 25 deletions(-)

diff --git a/modules.json b/modules.json
index 71a3e25c..93f4553b 100644
--- a/modules.json
+++ b/modules.json
@@ -7,23 +7,23 @@
                 "nf-core": {
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
-                        "git_sha": "3aa09ac8899d7735cb5bc004da0ef5f35f9a7901",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"],
                         "patch": "modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff"
                     },
                     "sratools/prefetch": {
                         "branch": "master",
-                        "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["modules"]
                     }
                 }
@@ -32,22 +32,22 @@
                 "nf-core": {
                     "fastq_download_prefetch_fasterqdump_sratools": {
                         "branch": "master",
-                        "git_sha": "3aa09ac8899d7735cb5bc004da0ef5f35f9a7901",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {
                         "branch": "master",
-                        "git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff b/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff
index 1fb8cbf4..089862bf 100644
--- a/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff
+++ b/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff
@@ -38,7 +38,7 @@ Changes in module 'nf-core/sratools/fasterqdump'
 
 --- modules/nf-core/sratools/fasterqdump/tests/main.nf.test
 +++ modules/nf-core/sratools/fasterqdump/tests/main.nf.test
-@@ -3,11 +3,9 @@
+@@ -3,11 +3,8 @@
      script "../main.nf"
      config "./nextflow.config"
      process "SRATOOLS_FASTERQDUMP"
@@ -47,7 +47,6 @@ Changes in module 'nf-core/sratools/fasterqdump'
 -    tag "untar"
 -    tag "sratools"
 -    tag "sratools/fasterqdump"
-+    tag "SRATOOLS_FASTERQDUMP"
 +
 +    tag "UNTAR"
  
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
index 3439b400..14a6429d 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295"
+                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
                 ],
                 "reads": [
                     [
@@ -24,15 +24,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295"
+                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.01.0"
         },
-        "timestamp": "2024-02-28T11:47:42.981471"
+        "timestamp": "2024-02-28T15:25:52.837288"
     },
     "Paired-end": {
         "content": [
@@ -50,7 +50,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295"
+                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
                 ],
                 "reads": [
                     [
@@ -65,14 +65,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295"
+                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.01.0"
         },
-        "timestamp": "2024-02-28T11:48:09.914497"
+        "timestamp": "2024-02-28T15:26:42.466223"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
index bec84076..9972556a 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
@@ -40,25 +40,25 @@
         "content": [
             [
                 "versions.yml:md5,1a2218ff913fc33408bffccb081b5048",
-                "versions.yml:md5,2f3b3a13b36dabf13f09327613d5558d",
-                "versions.yml:md5,98d78bba9f3da39a0b7db6e9c7dcc224"
+                "versions.yml:md5,98d78bba9f3da39a0b7db6e9c7dcc224",
+                "versions.yml:md5,9c558ff624585a6eee82a19c8c0136db"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.01.0"
         },
-        "timestamp": "2024-02-28T12:02:56.17931"
+        "timestamp": "2024-02-28T15:19:18.755939"
     },
     "test_pe_reads_1_size": {
         "content": [
-            2013376
+            2011460
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.01.0"
         },
-        "timestamp": "2024-02-28T12:02:56.163669"
+        "timestamp": "2024-02-28T15:19:18.677234"
     },
     "test_se_reads_lines": {
         "content": [

From 7a9d81184b8f8cce3843bc0e8605ee62364f6294 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 29 Feb 2024 09:38:09 +0000
Subject: [PATCH 813/852] Add Sateesh to contributors for reviews

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6b7d76f2..588bc318 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,6 +21,7 @@ Special thanks to the following for their contributions to the release:
 - [Alexander Blaessle](https://github.com/alexblaessle)
 - [Lukas Forer](https://github.com/lukfor)
 - [Maxime Garcia](https://github.com/maxulysse)
+- [Sateesh Peri](https://github.com/sateeshperi)
 - [Sebastian Uhrig](https://github.com/suhrig)
 
 Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.

From f6cf223f533e940e55036b70508d82a777c325aa Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 29 Feb 2024 10:31:27 +0000
Subject: [PATCH 814/852] Fix nf-tests

---
 .../nf-core/sratools/fasterqdump/tests/main.nf.test.snap  | 8 ++++----
 .../tests/main.nf.test.snap                               | 6 +++---
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
index 14a6429d..ce0f9800 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
+                    "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295"
                 ],
                 "reads": [
                     [
@@ -24,7 +24,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
+                    "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295"
                 ]
             }
         ],
@@ -50,7 +50,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
+                    "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295"
                 ],
                 "reads": [
                     [
@@ -65,7 +65,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
+                    "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295"
                 ]
             }
         ],
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
index 9972556a..485411da 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
@@ -40,8 +40,8 @@
         "content": [
             [
                 "versions.yml:md5,1a2218ff913fc33408bffccb081b5048",
-                "versions.yml:md5,98d78bba9f3da39a0b7db6e9c7dcc224",
-                "versions.yml:md5,9c558ff624585a6eee82a19c8c0136db"
+                "versions.yml:md5,2f3b3a13b36dabf13f09327613d5558d",
+                "versions.yml:md5,98d78bba9f3da39a0b7db6e9c7dcc224"
             ]
         ],
         "meta": {
@@ -52,7 +52,7 @@
     },
     "test_pe_reads_1_size": {
         "content": [
-            2011460
+            2013376
         ],
         "meta": {
             "nf-test": "0.8.4",

From 06494258f6b5d307c5a9c2b43e6f6dc0cec2edb2 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 29 Feb 2024 11:49:47 +0000
Subject: [PATCH 815/852] export CONDA_PREFIX into container when using
 Singularity and Apptainer

---
 modules/local/aspera_cli/main.nf | 5 +++++
 nextflow.config                  | 8 --------
 2 files changed, 5 insertions(+), 8 deletions(-)

diff --git a/modules/local/aspera_cli/main.nf b/modules/local/aspera_cli/main.nf
index de78a7b2..b38d17c0 100644
--- a/modules/local/aspera_cli/main.nf
+++ b/modules/local/aspera_cli/main.nf
@@ -18,8 +18,11 @@ process ASPERA_CLI {
 
     script:
     def args = task.ext.args ?: ''
+    def conda_prefix = ['singularity', 'apptainer'].contains(workflow.containerEngine) ? "export CONDA_PREFIX=/usr/local" : ""
     if (meta.single_end) {
         """
+        $conda_prefix
+
         ascp \\
             $args \\
             -i \$CONDA_PREFIX/etc/aspera/aspera_bypass_dsa.pem \\
@@ -36,6 +39,8 @@ process ASPERA_CLI {
         """
     } else {
         """
+        $conda_prefix
+
         ascp \\
             $args \\
             -i \$CONDA_PREFIX/etc/aspera/aspera_bypass_dsa.pem \\
diff --git a/nextflow.config b/nextflow.config
index 0b2abf8c..bb6b6b79 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -70,14 +70,6 @@ try {
 // Workflow specific configs
 includeConfig './workflows/sra/nextflow.config'
 
-// Load nf-core/fetchngs custom profiles from different institutions.
-// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs!
-// try {
-//   includeConfig "${params.custom_config_base}/pipeline/fetchngs.config"
-// } catch (Exception e) {
-//   System.err.println("WARNING: Could not load nf-core/config/fetchngs profiles: ${params.custom_config_base}/pipeline/fetchngs.config")
-// }
-
 profiles {
     debug {
         dumpHashes             = true

From cdc31b97ffaa28948a010fe6857242729a3134f9 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 29 Feb 2024 12:03:08 +0000
Subject: [PATCH 816/852] Update CHANGELOG

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 588bc318..e0261675 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,6 +20,7 @@ Special thanks to the following for their contributions to the release:
 - [Alexandru Mizeranschi](https://github.com/nicolae06)
 - [Alexander Blaessle](https://github.com/alexblaessle)
 - [Lukas Forer](https://github.com/lukfor)
+- [Matt Niederhuber](https://github.com/mniederhuber)
 - [Maxime Garcia](https://github.com/maxulysse)
 - [Sateesh Peri](https://github.com/sateeshperi)
 - [Sebastian Uhrig](https://github.com/suhrig)
@@ -54,6 +55,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #294](https://github.com/nf-core/fetchngs/pull/294) - Replace mermaid diagram with subway map
 - [PR #295](https://github.com/nf-core/fetchngs/pull/295) - Be less stringent with test expectations for CI
 - [PR #296](https://github.com/nf-core/fetchngs/pull/296) - Remove params.outdir from tests where required and update snapshots
+- [PR #298](https://github.com/nf-core/fetchngs/pull/298) - `export CONDA_PREFIX` into container when using Singularity and Apptainer
 
 ### Software dependencies
 

From bc6ac0bbe0fcf2267a9ded5a3ade50dc9aec06cf Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 29 Feb 2024 17:55:02 +0000
Subject: [PATCH 817/852] Bump pipeline version to 1.13.0dev

---
 CHANGELOG.md    | 4 ++++
 nextflow.config | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e0261675..42dbdf32 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unpublished Version / DEV]
+
+### Enhancements & fixes
+
 ## [[1.12.0](https://github.com/nf-core/fetchngs/releases/tag/1.12.0)] - 2024-02-29
 
 ### :warning: Major enhancements
diff --git a/nextflow.config b/nextflow.config
index bb6b6b79..7f4f8ebf 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -221,7 +221,7 @@ manifest {
     description     = """Pipeline to fetch metadata and raw FastQ files from public databases"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.12.0'
+    version         = '1.13.0dev'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
 

From d15ce76ce2294a703e93afbf4183756085df4cd3 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 29 Feb 2024 17:56:05 +0000
Subject: [PATCH 818/852] Update CHANGELOG

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 42dbdf32..8bba6e9d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+- [PR #299](https://github.com/nf-core/fetchngs/pull/299) - Template update for nf-core/tools v2.13.1
+
 ## [[1.12.0](https://github.com/nf-core/fetchngs/releases/tag/1.12.0)] - 2024-02-29
 
 ### :warning: Major enhancements

From 0fc43a903d2ce44bd680a9cc87e842e31c91dd7f Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 4 Mar 2024 10:20:03 +0000
Subject: [PATCH 819/852] Use paths instead of tags as matrix variable

Additions:
 - find_changed_files returns a list of paths instead of tags
 - Uses this as input to matrix

Benefits:
 - More efficient testing (1 test per file).

Additional additions:
 - include.yaml file to specify files to include or exclude from test sets
 - Will include additional tests if major files have been modified, e.g. the .github/workflows/* files
 - Uses globbing for exclude statement to match multiple files.

Changes:
 - bump setup-nextflow
 - Adds pyyaml as dependency
 - Uses pathlib.Path object where possible to prevent coercion back and forth between strings
 - Splits find_files into two functions, find_changed_files and detect_nf_test_files
---
 .github/python/find_changed_files.py | 170 ++++++++++++++++++++++++---
 .github/python/include.yaml          |  10 ++
 .github/workflows/ci.yml             |  64 +++-------
 3 files changed, 179 insertions(+), 65 deletions(-)
 create mode 100644 .github/python/include.yaml

diff --git a/.github/python/find_changed_files.py b/.github/python/find_changed_files.py
index 6dc73449..ed1a8467 100644
--- a/.github/python/find_changed_files.py
+++ b/.github/python/find_changed_files.py
@@ -1,15 +1,17 @@
 #!/usr/bin/env python
 
-## This script is used to generate scan *.nf.test files for function/process/workflow name and return as a JSON list
-# It is functionally similar to nf-test list but fills a gap until feature https://github.com/askimed/nf-test/issues/196 is added
+# This script is used to identify *.nf.test files for changed functions/processs/workflows/pipelines and *.nf-test files
+# with changed dependencies, then return as a JSON list
 
 import argparse
 import json
 import logging
 import re
+import yaml
 
 from itertools import chain
 from pathlib import Path
+from git import Repo
 
 
 def parse_args() -> argparse.Namespace:
@@ -23,11 +25,40 @@ def parse_args() -> argparse.Namespace:
         description="Scan *.nf.test files for function/process/workflow name and return as a JSON list"
     )
     parser.add_argument(
-        "-p",
-        "--paths",
+        "-r",
+        "--head_ref",
+        required=True,
+        help="Head reference branch (Source branch for a PR).",
+    )
+    parser.add_argument(
+        "-b",
+        "--base_ref",
+        required=True,
+        help="Base reference branch (Target branch for a PR).",
+    )
+    parser.add_argument(
+        "-x",
+        "--ignored_files",
         nargs="+",
-        default=["."],
-        help="List of directories or files to scan",
+        default=[
+            ".git/*",
+            ".gitpod.yml",
+            ".prettierignore",
+            ".prettierrc.yml",
+            "*.md",
+            "*.png",
+            "modules.json",
+            "pyproject.toml",
+            "tower.yml",
+        ],
+        help="List of files or file substrings to ignore.",
+    )
+    parser.add_argument(
+        "-i",
+        "--include",
+        type=Path,
+        default=".github/python/include.yaml",
+        help="Path to an include file containing a YAML of key value pairs to include in changed files. I.e., return the current directory if an important file is changed.",
     )
     parser.add_argument(
         "-l",
@@ -47,19 +78,75 @@ def parse_args() -> argparse.Namespace:
     return parser.parse_args()
 
 
-def find_files(paths: list[str]) -> list[Path]:
+def read_yaml_inverted(file_path: str) -> dict:
     """
-    Find all files matching pattern *.nf.test recursively from a list of paths.
+    Read a YAML file and return its contents as a dictionary but reversed, i.e. the values become the keys and the keys become the values.
 
     Args:
-        paths (list): List of directories or files to scan.
+        file_path (str): The path to the YAML file.
 
     Returns:
-        list: List of files matching the pattern *.nf.test.
+        dict: The contents of the YAML file as a dictionary inverted.
     """
-    # this is a bit clunky
-    result = []
-    for path in paths:
+    with open(file_path, "r") as f:
+        data = yaml.safe_load(f)
+
+    # Invert dictionary of lists into contents of lists are keys, values are the original keys
+    # { "key": ["item1", "item2] } --> { "item1": "key", "item2": "key" }
+    return {value: key for key, values in data.items() for value in values}
+
+
+def find_changed_files(
+    branch1: str, branch2: str, ignore: list[str], include_files: dict[str, str]
+) -> list[Path]:
+    """
+    Find all *.nf.tests that are associated with files that have been changed between two specified branches.
+
+    Args:
+        branch1 (str)      : The first branch being compared
+        branch2 (str)      : The second branch being compared
+        ignore  (list)     : List of files or file substrings to ignore.
+        include_files (dict): Key value pairs to return if a certain file has changed, i.e. if a file in a directory has changed point to a different directory.
+
+    Returns:
+        list: List of files matching the pattern *.nf.test that have changed between branch2 and branch1.
+    """
+    # create repo
+    repo = Repo(".")
+    # identify commit on branch1
+    branch1_commit = repo.commit(branch1)
+    # identify commit on branch2
+    branch2_commit = repo.commit(branch2)
+    # compare two branches
+    diff_index = branch1_commit.diff(branch2_commit)
+    # collect changed files
+    changed_files = []
+    for file in diff_index:
+        changed_files.append(Path(file.a_path))
+    # remove ignored files
+    for file in changed_files:
+        for ignored_substring in ignore:
+            if file.match(ignored_substring):
+                changed_files.remove(file)
+        for include_path, include_key in include_files.items():
+            if file.match(include_path):
+                changed_files.append(Path(include_key))
+
+    return changed_files
+
+
+def detect_nf_test_files(changed_files: list[Path]) -> list[Path]:
+    """
+    Detects and returns a list of nf-test files from the given list of changed files.
+
+    Args:
+        changed_files (list[Path]): A list of file paths.
+
+    Returns:
+        list[Path]: A list of nf-test file paths.
+    """
+    result: list[Path] = []
+    for path in changed_files:
         path_obj = Path(path)
         # If Path is the exact nf-test file add to list:
         if path_obj.match("*.nf.test"):
@@ -131,15 +218,56 @@ def generate(
     return result
 
 
+def find_changed_dependencies(paths: list[Path], tags: list[str]) -> list[Path]:
+    """
+    Find all *.nf.test files with changed dependencies from a list of paths.
+
+    Args:
+        paths (list): List of directories or files to scan.
+        tags (list): List of tags identified as having changes.
+
+    Returns:
+        list: List of *.nf.test files with changed dependencies.
+    """
+    # this is a bit clunky
+    result = []
+    for path in paths:
+        # find all *.nf-test files
+        nf_test_files = []
+        for file in path.rglob("*.nf.test"):
+            nf_test_files.append(file)
+        # find nf-test files with changed dependencies
+        for nf_test_file in nf_test_files:
+            with open(nf_test_file, "r") as f:
+                lines = f.readlines()
+                for line in lines:
+                    line = line.strip()
+                    if line.startswith("tag"):
+                        words = line.split()
+                        if len(words) == 2 and re.match(r'^".*"$', words[1]):
+                            name = words[1].strip(
+                                "'\""
+                            )  # Strip both single and double quotes
+                            if name in tags:
+                                result.append(nf_test_file)
+
+    return list(set(result))
+
+
 if __name__ == "__main__":
 
     # Utility stuff
     args = parse_args()
     logging.basicConfig(level=args.log_level)
 
-    # Parse nf-test files for targets of tests
-    files = find_files(args.paths)
-    lines = process_files(files)
+    # Parse nf-test files for target test tags
+    if args.include:
+        include_files = read_yaml_inverted(args.include)
+    changed_files = find_changed_files(
+        args.head_ref, args.base_ref, args.ignored_files, include_files
+    )
+    nf_test_files = detect_nf_test_files(changed_files)
+    lines = process_files(nf_test_files)
     result = generate(lines)
 
     # Get only relevant results (specified by -t)
@@ -148,5 +276,13 @@ def generate(
         {item for sublist in map(result.get, args.types) for item in sublist}
     )
 
+    # Parse files to identify nf-tests with changed dependencies
+    changed_dep_files = find_changed_dependencies([Path(".")], target_results)
+
+    # Combine target nf-test files and nf-test files with changed dependencies
+    all_nf_tests = [
+        str(test_path) for test_path in set(changed_dep_files + nf_test_files)
+    ]
+
     # Print to stdout
-    print(json.dumps(target_results))
+    print(json.dumps(all_nf_tests))
diff --git a/.github/python/include.yaml b/.github/python/include.yaml
new file mode 100644
index 00000000..682073c5
--- /dev/null
+++ b/.github/python/include.yaml
@@ -0,0 +1,10 @@
+".":
+  - .github/workflows/**
+  - nf-test.config
+  - nextflow.config
+tests:
+  - assets/*
+  - bin/*
+  - conf/*
+  - main.nf
+  - nextflow_schema.json
\ No newline at end of file
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8a8d0935..7d226968 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -27,8 +27,7 @@ jobs:
     name: Check for changes
     runs-on: ubuntu-latest
     outputs:
-      changes: ${{ steps.changed_files.outputs.any_modified }}
-      tags: ${{ steps.list.outputs.tags }}
+      nf_test_files: ${{ steps.list.outputs.nf_test_files }}
     steps:
       - uses: actions/setup-python@v4
         with:
@@ -39,60 +38,29 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: tj-actions/changed-files@v42
-        id: changed_files
-        with:
-          dir_names: "true"
-          output_renamed_files_as_deleted_and_added: "true"
-          # Define list of additional rules for testing paths
-          # Mostly, we define additional 'pipeline' or 'all' tests here
-          files_yaml: |
-            ".":
-              - .github/workflows/**
-              - nf-test.config
-              - nextflow.config
-            tests:
-              - assets/*
-              - bin/*
-              - conf/*
-              - main.nf
-              - nextflow_schema.json
-
-          files_ignore: |
-            .git*
-            .gitpod.yml
-            .prettierignore
-            .prettierrc.yml
-            **.md
-            **.png
-            modules.json
-            pyproject.toml
-            tower.yml
-
-      - name: debug
+      - name: Install gitpython find changed files
         run: |
-          echo ${{ steps.changed_files.outputs.any_modified }}
-          echo ${{ steps.changed_files.outputs.all_changed_files }}
-          echo ${{ steps.changed_files.outputs.changed_keys }}
+          python -m pip install --upgrade pip
+          pip install gitpython pyyaml
 
-      - name: nf-test list tags
+      - name: nf-test list nf_test_files
         id: list
-        if: ${{ steps.changed_files.outputs.any_modified }}
         run: |
-          echo tags=$(python \
+          echo nf_test_files=$(python \
             .github/python/find_changed_files.py \
             -t pipeline workflow process \
-            -p ${{ steps.changed_files.outputs.all_changed_files }} ${{ steps.changed_files.outputs.changed_keys }} \
+            --head_ref ${{ github.sha }} \
+            --base_ref origin/${{ github.base_ref }} \
           ) >> $GITHUB_OUTPUT
 
-      - name: debug2
+      - name: debug
         run: |
-          echo ${{ steps.list.outputs.tags }}
+          echo ${{ steps.list.outputs.nf_test_files }}
 
   test:
-    name: ${{ matrix.tags }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
+    name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
     needs: [changes]
-    if: needs.changes.outputs.changes
+    if: needs.changes.outputs.nf_test_files != '[]'
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -100,16 +68,16 @@ jobs:
         NXF_VER:
           - "latest-everything"
           - "23.04"
-        tags: ["${{ fromJson(needs.changes.outputs.tags) }}"]
+        nf_test_files: ["${{ fromJson(needs.changes.outputs.nf_test_files) }}"]
         profile:
           - "docker"
 
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@2
         with:
           version: "${{ matrix.NXF_VER }}"
 
@@ -140,7 +108,7 @@ jobs:
 
       - name: Run nf-test
         run: |
-          nf-test test --verbose --tag ${{ matrix.tags }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
+          nf-test test --verbose --tag ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
 
       - uses: pcolby/tap-summary@v1
         with:

From c92b31be4cbfdec46504c0f8cacdfcdc117c281e Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 4 Mar 2024 11:15:30 +0000
Subject: [PATCH 820/852] prettier

---
 .github/python/include.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/python/include.yaml b/.github/python/include.yaml
index 682073c5..c3b69246 100644
--- a/.github/python/include.yaml
+++ b/.github/python/include.yaml
@@ -7,4 +7,4 @@ tests:
   - bin/*
   - conf/*
   - main.nf
-  - nextflow_schema.json
\ No newline at end of file
+  - nextflow_schema.json

From ce56e5ef0a536593364e2b28ac2b12446afd790c Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 4 Mar 2024 11:24:46 +0000
Subject: [PATCH 821/852] Fix action versions

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 7d226968..b2af8b16 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -74,10 +74,10 @@ jobs:
 
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@4
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@2
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 

From b2516474199cf5d02acee1054a804c9dd2ed6157 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 4 Mar 2024 13:21:43 +0000
Subject: [PATCH 822/852] remove tag

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b2af8b16..bed5a12e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -108,7 +108,7 @@ jobs:
 
       - name: Run nf-test
         run: |
-          nf-test test --verbose --tag ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
+          nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
 
       - uses: pcolby/tap-summary@v1
         with:

From 7dfbf1cc934e537d803faa467369f6253108c372 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Wed, 6 Mar 2024 16:34:27 +0000
Subject: [PATCH 823/852] Check if nf-test file exists before adding

---
 .github/python/find_changed_files.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/python/find_changed_files.py b/.github/python/find_changed_files.py
index ed1a8467..a50b3525 100644
--- a/.github/python/find_changed_files.py
+++ b/.github/python/find_changed_files.py
@@ -149,7 +149,7 @@ def detect_nf_test_files(changed_files: list[Path]) -> list[Path]:
     for path in changed_files:
         path_obj = Path(path)
         # If Path is the exact nf-test file add to list:
-        if path_obj.match("*.nf.test"):
+        if path_obj.match("*.nf.test") and path_obj.exists():
             result.append(path_obj)
         # Else recursively search for nf-test files:
         else:

From fab42ea611d51f778b216a39796d91c73b62eeb5 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 7 Mar 2024 10:16:09 +0000
Subject: [PATCH 824/852] Changes:  - Better logic for detecting changed files
 and excluding the ignore list  - Break out include statement into separate
 function  - Correctly identify changed files in the same dir as changed files
  - Better name for function than 'generate'

---
 .github/python/find_changed_files.py | 74 +++++++++++++++++++---------
 1 file changed, 52 insertions(+), 22 deletions(-)

diff --git a/.github/python/find_changed_files.py b/.github/python/find_changed_files.py
index a50b3525..ac506a25 100644
--- a/.github/python/find_changed_files.py
+++ b/.github/python/find_changed_files.py
@@ -97,7 +97,9 @@ def read_yaml_inverted(file_path: str) -> dict:
 
 
 def find_changed_files(
-    branch1: str, branch2: str, ignore: list[str], include_files: dict[str, str]
+    branch1: str,
+    branch2: str,
+    ignore: list[str],
 ) -> list[Path]:
     """
     Find all *.nf.tests that are associated with files that have been changed between two specified branches.
@@ -106,7 +108,6 @@ def find_changed_files(
         branch1 (str)      : The first branch being compared
         branch2 (str)      : The second branch being compared
         ignore  (list)     : List of files or file substrings to ignore.
-        include_files (dict): Key value pairs to return if a certain file has changed, i.e. if a file in a directory has changed point to a different directory.
 
     Returns:
         list: List of files matching the pattern *.nf.test that have changed between branch2 and branch1.
@@ -119,20 +120,42 @@ def find_changed_files(
     branch2_commit = repo.commit(branch2)
     # compare two branches
     diff_index = branch1_commit.diff(branch2_commit)
-    # collect changed files
+
+    # Start empty list of changed files
     changed_files = []
+
+    # For every file that has changed between commits
     for file in diff_index:
-        changed_files.append(Path(file.a_path))
-    # remove ignored files
-    for file in changed_files:
-        for ignored_substring in ignore:
-            if file.match(ignored_substring):
-                changed_files.remove(file)
-        for include_path, include_key in include_files.items():
-            if file.match(include_path):
-                changed_files.append(Path(include_key))
+        # Get pathlib.Path object
+        filepath = Path(file.a_path)
+        # If file does not match any in the ignore list, add containing directory to changed_files
+        if not any(filepath.match(ignored_path) for ignored_path in ignore):
+            changed_files.append(filepath)
+
+    # Uniqueify the results before returning for efficiency
+    return list(set(changed_files))
 
-    return changed_files
+
+def detect_include_files(
+    changed_files: list[Path], include_files: dict[str, str]
+) -> list[Path]:
+    """
+    Detects the include files based on the changed files.
+
+    Args:
+        changed_files (list[Path]): List of paths to the changed files.
+        include_files (dict[str, str]): Key-value pairs to return if a certain file has changed. If a file in a directory has changed, it points to a different directory.
+
+    Returns:
+        list[Path]: List of paths to representing the keys of the include_files dictionary, where a value matched a path in changed_files.
+    """
+    new_changed_files = []
+    for filepath in changed_files:
+        # If file is in the include_files, we return the key instead of the value
+        for include_path, include_key in include_files.items():
+            if filepath.match(include_path):
+                new_changed_files.append(Path(include_key))
+    return new_changed_files
 
 
 def detect_nf_test_files(changed_files: list[Path]) -> list[Path]:
@@ -147,13 +170,17 @@ def detect_nf_test_files(changed_files: list[Path]) -> list[Path]:
     """
     result: list[Path] = []
     for path in changed_files:
-        path_obj = Path(path)
         # If Path is the exact nf-test file add to list:
-        if path_obj.match("*.nf.test") and path_obj.exists():
-            result.append(path_obj)
+        if path.match("*.nf.test") and path.exists():
+            result.append(path)
         # Else recursively search for nf-test files:
         else:
-            for file in path_obj.rglob("*.nf.test"):
+            # Get the enclosing dir so files in the same dir can be found.
+            # e.g.
+            # dir/
+            # ├─ main.nf
+            # ├─ main.nf.test
+            for file in path.parent.rglob("*.nf.test"):
                 result.append(file)
     return result
 
@@ -189,7 +216,7 @@ def process_files(files: list[Path]) -> list[str]:
     return result
 
 
-def generate(
+def convert_nf_test_files_to_test_types(
     lines: list[str], types: list[str] = ["function", "process", "workflow", "pipeline"]
 ) -> dict[str, list[str]]:
     """
@@ -261,14 +288,17 @@ def find_changed_dependencies(paths: list[Path], tags: list[str]) -> list[Path]:
     logging.basicConfig(level=args.log_level)
 
     # Parse nf-test files for target test tags
+    changed_files = find_changed_files(args.head_ref, args.base_ref, args.ignored_files)
+
+    # If an additional include YAML is added, we detect additional changed dirs to include
     if args.include:
         include_files = read_yaml_inverted(args.include)
-    changed_files = find_changed_files(
-        args.head_ref, args.base_ref, args.ignored_files, include_files
-    )
+        changed_files = changed_files + detect_include_files(
+            changed_files, include_files
+        )
     nf_test_files = detect_nf_test_files(changed_files)
     lines = process_files(nf_test_files)
-    result = generate(lines)
+    result = convert_nf_test_files_to_test_types(lines)
 
     # Get only relevant results (specified by -t)
     # Unique using a set

From 3e2665f8103ffb306c57b5cb2de05b530c12da1a Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 7 Mar 2024 10:29:42 +0000
Subject: [PATCH 825/852] Code re-use so we don't duplicate functions
 everywhere

---
 .github/python/find_changed_files.py | 51 ++++++++++++----------------
 1 file changed, 21 insertions(+), 30 deletions(-)

diff --git a/.github/python/find_changed_files.py b/.github/python/find_changed_files.py
index ac506a25..117000ae 100644
--- a/.github/python/find_changed_files.py
+++ b/.github/python/find_changed_files.py
@@ -229,15 +229,12 @@ def convert_nf_test_files_to_test_types(
     Returns:
         dict: Dictionary with function, process and workflow lists.
     """
-    result: dict[str, list[str]] = {
-        "function": [],
-        "process": [],
-        "workflow": [],
-        "pipeline": [],
-    }
+    # Populate empty dict from types
+    result: dict[str, list[str]] = {key: [] for key in types}
+
     for line in lines:
         words = line.split()
-        if len(words) == 2:
+        if len(words) == 2 and re.match(r'^".*"$', words[1]):
             keyword = words[0]
             name = words[1].strip("'\"")  # Strip both single and double quotes
             if keyword in types:
@@ -256,29 +253,23 @@ def find_changed_dependencies(paths: list[Path], tags: list[str]) -> list[Path]:
     Returns:
         list: List of *.nf.test files with changed dependencies.
     """
-    # this is a bit clunky
-    result = []
-    for path in paths:
-        # find all *.nf-test files
-        nf_test_files = []
-        for file in path.rglob("*.nf.test"):
-            nf_test_files.append(file)
-        # find nf-test files with changed dependencies
-        for nf_test_file in nf_test_files:
-            with open(nf_test_file, "r") as f:
-                lines = f.readlines()
-                for line in lines:
-                    line = line.strip()
-                    if line.startswith("tag"):
-                        words = line.split()
-                        if len(words) == 2 and re.match(r'^".*"$', words[1]):
-                            name = words[1].strip(
-                                "'\""
-                            )  # Strip both single and double quotes
-                            if name in tags:
-                                result.append(nf_test_file)
-
-    return list(set(result))
+
+    result: list[Path] = []
+
+    nf_test_files = detect_nf_test_files(paths)
+
+    # find nf-test files with changed dependencies
+    for nf_test_file in nf_test_files:
+        with open(nf_test_file, "r") as f:
+            lines = f.readlines()
+            tags_in_nf_test_file = convert_nf_test_files_to_test_types(
+                lines, types=["tag"]
+            )
+            # Check if tag in nf-test file appears in a tag
+            if any(tag in tags_in_nf_test_file["tag"] for tag in tags):
+                result.append(nf_test_file)
+
+    return result
 
 
 if __name__ == "__main__":

From 30702552903c81b2c8b1f9ef0c5195deac878100 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 8 Mar 2024 15:56:35 +0000
Subject: [PATCH 826/852] Make tags check case insensitive

---
 .github/python/find_changed_files.py | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/.github/python/find_changed_files.py b/.github/python/find_changed_files.py
index 117000ae..2e24ab74 100644
--- a/.github/python/find_changed_files.py
+++ b/.github/python/find_changed_files.py
@@ -262,11 +262,17 @@ def find_changed_dependencies(paths: list[Path], tags: list[str]) -> list[Path]:
     for nf_test_file in nf_test_files:
         with open(nf_test_file, "r") as f:
             lines = f.readlines()
-            tags_in_nf_test_file = convert_nf_test_files_to_test_types(
-                lines, types=["tag"]
-            )
-            # Check if tag in nf-test file appears in a tag
-            if any(tag in tags_in_nf_test_file["tag"] for tag in tags):
+            # Get all tags from nf-test file
+            # Make case insensitive with .casefold()
+            tags_in_nf_test_file = [
+                tag.casefold()
+                for tag in convert_nf_test_files_to_test_types(lines, types=["tag"])[
+                    "tag"
+                ]
+            ]
+            # Check if tag in nf-test file appears in a tag.
+            # Use .casefold() to be case insensitive
+            if any(tag.casefold() in tags_in_nf_test_file for tag in tags):
                 result.append(nf_test_file)
 
     return result

From f23ae011f919fb4edd461d338e99c76552a0bc88 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 12 Mar 2024 11:14:19 +0000
Subject: [PATCH 827/852] Replace slashes with underscores

---
 .github/python/find_changed_files.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/python/find_changed_files.py b/.github/python/find_changed_files.py
index 2e24ab74..c0c61752 100644
--- a/.github/python/find_changed_files.py
+++ b/.github/python/find_changed_files.py
@@ -265,14 +265,16 @@ def find_changed_dependencies(paths: list[Path], tags: list[str]) -> list[Path]:
             # Get all tags from nf-test file
             # Make case insensitive with .casefold()
             tags_in_nf_test_file = [
-                tag.casefold()
+                tag.casefold().replace("/", "_")
                 for tag in convert_nf_test_files_to_test_types(lines, types=["tag"])[
                     "tag"
                 ]
             ]
             # Check if tag in nf-test file appears in a tag.
             # Use .casefold() to be case insensitive
-            if any(tag.casefold() in tags_in_nf_test_file for tag in tags):
+            if any(
+                tag.casefold().replace("/", "_") in tags_in_nf_test_file for tag in tags
+            ):
                 result.append(nf_test_file)
 
     return result

From a2b0ccfe55f5538736ca7b475260e38b4b356849 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 12 Mar 2024 11:24:25 +0000
Subject: [PATCH 828/852] Be more explicit about file patterns

---
 .github/python/include.yaml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/python/include.yaml b/.github/python/include.yaml
index c3b69246..a3629f4c 100644
--- a/.github/python/include.yaml
+++ b/.github/python/include.yaml
@@ -1,10 +1,10 @@
 ".":
-  - .github/workflows/**
-  - nf-test.config
-  - nextflow.config
+  - ./.github/workflows/**
+  - ./nf-test.config
+  - ./nextflow.config
 tests:
-  - assets/*
-  - bin/*
-  - conf/*
-  - main.nf
-  - nextflow_schema.json
+  - ./assets/*
+  - ./bin/*
+  - ./conf/*
+  - ./main.nf
+  - ./nextflow_schema.json

From a9b246c69a2c463395aa57f14695ece4fe603fb0 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Wed, 13 Mar 2024 11:28:02 +0000
Subject: [PATCH 829/852] Fixup some names

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index bed5a12e..527048fe 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -43,7 +43,7 @@ jobs:
           python -m pip install --upgrade pip
           pip install gitpython pyyaml
 
-      - name: nf-test list nf_test_files
+      - name: List nf-test files
         id: list
         run: |
           echo nf_test_files=$(python \
@@ -53,7 +53,7 @@ jobs:
             --base_ref origin/${{ github.base_ref }} \
           ) >> $GITHUB_OUTPUT
 
-      - name: debug
+      - name: print list of nf-test files
         run: |
           echo ${{ steps.list.outputs.nf_test_files }}
 

From 18b56273175aef22d70771edae9b48e192da9f1b Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Wed, 13 Mar 2024 11:30:32 +0000
Subject: [PATCH 830/852] CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8bba6e9d..b9232710 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Enhancements & fixes
 
 - [PR #299](https://github.com/nf-core/fetchngs/pull/299) - Template update for nf-core/tools v2.13.1
+- [PR #300](https://github.com/nf-core/fetchngs/pull/300) - Use file paths instead of tags for testing matrix, should make matrices more efficient
 
 ## [[1.12.0](https://github.com/nf-core/fetchngs/releases/tag/1.12.0)] - 2024-02-29
 

From fe2756912803b988a3407586c7264578b0c147f2 Mon Sep 17 00:00:00 2001
From: Adrian Janucik <adrian.janucik@ardigen.com>
Date: Thu, 21 Mar 2024 16:20:07 +0100
Subject: [PATCH 831/852] update wget container for SRA_FASTQ_FTP from 1.20.1
 to 1.21.4

---
 modules/local/sra_fastq_ftp/main.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/local/sra_fastq_ftp/main.nf b/modules/local/sra_fastq_ftp/main.nf
index e2274d46..017a08c9 100644
--- a/modules/local/sra_fastq_ftp/main.nf
+++ b/modules/local/sra_fastq_ftp/main.nf
@@ -4,10 +4,10 @@ process SRA_FASTQ_FTP {
     label 'process_low'
     label 'error_retry'
 
-    conda "conda-forge::wget=1.20.1"
+    conda "conda-forge::wget=1.21.4"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/wget:1.20.1' :
-        'biocontainers/wget:1.20.1' }"
+        'https://depot.galaxyproject.org/singularity/wget:1.21.4' :
+        'biocontainers/wget:1.21.4' }"
 
     input:
     tuple val(meta), val(fastq)

From 7208db1af766e847d840f9a84c0b26665e962917 Mon Sep 17 00:00:00 2001
From: Adrian Janucik <adrian.janucik@ardigen.com>
Date: Thu, 21 Mar 2024 16:39:27 +0100
Subject: [PATCH 832/852] update CHANGELOG.md to reflect newer version of wget

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b9232710..bdbdb580 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -68,7 +68,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
-| `wget`     |             | 1.20.1      |
+| `wget`     | 1.20.1      | 1.21.4      |
 
 > **NB:** Dependency has been **updated** if both old and new version information is present.
 >

From 0c23f923dd4293db3c39cdb54cb48d48f5968acc Mon Sep 17 00:00:00 2001
From: Adrian <adrian.janucik@gmail.com>
Date: Thu, 21 Mar 2024 17:05:04 +0100
Subject: [PATCH 833/852] update md5 for versions.yml in sra_fastq_ftp

---
 modules/local/sra_fastq_ftp/tests/main.nf.test.snap | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap
index 5b300f8c..229ad4fe 100644
--- a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap
+++ b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap
@@ -31,7 +31,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,6b60ed6d5805271a1b97798e29c0635c"
+                    "versions.yml:md5,7bfc86ca1f3e3236dbb91eb85c1d7af0"
                 ],
                 "fastq": [
                     [
@@ -62,7 +62,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6b60ed6d5805271a1b97798e29c0635c"
+                    "versions.yml:md5,7bfc86ca1f3e3236dbb91eb85c1d7af0"
                 ]
             }
         ],
@@ -72,4 +72,4 @@
         },
         "timestamp": "2024-02-28T11:51:51.301654"
     }
-}
\ No newline at end of file
+}

From ebb0e5271fca0c5465e67fc441c45ee5b515ca6a Mon Sep 17 00:00:00 2001
From: Adrian <adrian.janucik@gmail.com>
Date: Fri, 22 Mar 2024 12:24:20 +0100
Subject: [PATCH 834/852] Move wget update notice to Unpublished Version / DEV
 section

---
 CHANGELOG.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index bdbdb580..30128dcf 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [PR #299](https://github.com/nf-core/fetchngs/pull/299) - Template update for nf-core/tools v2.13.1
 - [PR #300](https://github.com/nf-core/fetchngs/pull/300) - Use file paths instead of tags for testing matrix, should make matrices more efficient
+- [PR #303](https://github.com/nf-core/fetchngs/pull/303) - Update wget container for SRA_FASTQ_FTP from 1.20.1 to 1.21.4
 
 ## [[1.12.0](https://github.com/nf-core/fetchngs/releases/tag/1.12.0)] - 2024-02-29
 
@@ -68,7 +69,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
-| `wget`     | 1.20.1      | 1.21.4      |
+| `wget`     |             | 1.20.1      |
 
 > **NB:** Dependency has been **updated** if both old and new version information is present.
 >

From d2641e48616dd20e51fd9f86723de3e5ffa6e089 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Fri, 22 Mar 2024 13:14:55 +0100
Subject: [PATCH 835/852] Update CHANGELOG.md

---
 CHANGELOG.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 30128dcf..ecb962d6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #300](https://github.com/nf-core/fetchngs/pull/300) - Use file paths instead of tags for testing matrix, should make matrices more efficient
 - [PR #303](https://github.com/nf-core/fetchngs/pull/303) - Update wget container for SRA_FASTQ_FTP from 1.20.1 to 1.21.4
 
+### Software dependencies
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `wget`     | 1.20.1      | 1.21.4      |
+
 ## [[1.12.0](https://github.com/nf-core/fetchngs/releases/tag/1.12.0)] - 2024-02-29
 
 ### :warning: Major enhancements

From 42ccce6d9ce6c70cd91d9808891f8368521ed4cd Mon Sep 17 00:00:00 2001
From: Sebastian Uhrig <suhrig@altoslabs.com>
Date: Sun, 7 Apr 2024 20:27:50 +0000
Subject: [PATCH 836/852] update module sratools/prefetch

---
 modules.json                                         |  4 ++--
 modules/nf-core/sratools/prefetch/environment.yml    |  3 ++-
 modules/nf-core/sratools/prefetch/main.nf            |  4 ++--
 .../prefetch/templates/retry_with_backoff.sh         | 12 +++++++++++-
 modules/nf-core/sratools/prefetch/tests/main.nf.test |  4 ++++
 .../sratools/prefetch/tests/main.nf.test.snap        | 10 +++++-----
 modules/nf-core/sratools/prefetch/tests/tags.yml     |  2 ++
 .../tests/main.nf.test                               | 10 ++++++----
 .../tests/main.nf.test.snap                          |  8 ++++----
 .../tests/tags.yml                                   |  2 ++
 10 files changed, 40 insertions(+), 19 deletions(-)
 create mode 100644 modules/nf-core/sratools/prefetch/tests/tags.yml
 create mode 100644 subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml

diff --git a/modules.json b/modules.json
index 93f4553b..c6b234bb 100644
--- a/modules.json
+++ b/modules.json
@@ -18,7 +18,7 @@
                     },
                     "sratools/prefetch": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "1fc29f92e439d5631fdf34b8ac4687297d70f5ec",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "untar": {
@@ -32,7 +32,7 @@
                 "nf-core": {
                     "fastq_download_prefetch_fasterqdump_sratools": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "1fc29f92e439d5631fdf34b8ac4687297d70f5ec",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {
diff --git a/modules/nf-core/sratools/prefetch/environment.yml b/modules/nf-core/sratools/prefetch/environment.yml
index cfc7d9a8..0abad336 100644
--- a/modules/nf-core/sratools/prefetch/environment.yml
+++ b/modules/nf-core/sratools/prefetch/environment.yml
@@ -4,4 +4,5 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::sra-tools=3.0.8
+  - bioconda::sra-tools=3.1.0
+  - conda-forge::curl=8.5.0
diff --git a/modules/nf-core/sratools/prefetch/main.nf b/modules/nf-core/sratools/prefetch/main.nf
index 3c30739a..170f1753 100644
--- a/modules/nf-core/sratools/prefetch/main.nf
+++ b/modules/nf-core/sratools/prefetch/main.nf
@@ -4,8 +4,8 @@ process SRATOOLS_PREFETCH {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sra-tools:3.0.8--h9f5acd7_0' :
-        'biocontainers/sra-tools:3.0.8--h9f5acd7_0' }"
+        'https://depot.galaxyproject.org/singularity/sra-tools:3.1.0--h9f5acd7_0' :
+        'biocontainers/sra-tools:3.1.0--h9f5acd7_0' }"
 
     input:
     tuple val(meta), val(id)
diff --git a/modules/nf-core/sratools/prefetch/templates/retry_with_backoff.sh b/modules/nf-core/sratools/prefetch/templates/retry_with_backoff.sh
index a72a4bfb..bfee6070 100755
--- a/modules/nf-core/sratools/prefetch/templates/retry_with_backoff.sh
+++ b/modules/nf-core/sratools/prefetch/templates/retry_with_backoff.sh
@@ -47,9 +47,19 @@ retry_with_backoff !{args2} \
     !{args} \
     !{id}
 
-[ -f !{id}.sralite ] && vdb-validate !{id}.sralite || vdb-validate !{id}
+# check file integrity using vdb-validate or (when archive contains no checksums) md5sum
+vdb-validate !{id} > vdb-validate_result.txt 2>&1 || exit 1
+if grep -q "checksums missing" vdb-validate_result.txt; then
+    VALID_MD5SUMS=$(curl --silent --fail --location --retry 3 --retry-delay 60 'https://locate.ncbi.nlm.nih.gov/sdl/2/retrieve?filetype=run&acc=!{id}')
+    LOCAL_MD5SUMS=$(md5sum !{id}/* | cut -f1 -d' ')
+    if ! grep -q -F -f <(echo "$LOCAL_MD5SUMS") <(echo "$VALID_MD5SUMS"); then
+        echo "MD5 sum check failed" 1>&2
+        exit 1
+    fi
+fi
 
 cat <<-END_VERSIONS > versions.yml
 "!{task.process}":
     sratools: $(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
+    curl: $(curl --version | head -n 1 | sed 's/^curl //; s/ .*$//')
 END_VERSIONS
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test
index c3ebd91e..f59de7cb 100644
--- a/modules/nf-core/sratools/prefetch/tests/main.nf.test
+++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test
@@ -2,6 +2,10 @@ nextflow_process {
     name "Test Process SRATOOLS_PREFETCH"
     script "../main.nf"
     process "SRATOOLS_PREFETCH"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "sratools"
+    tag "sratools/prefetch"
 
     test("sratools/prefetch") {
 
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap
index 946fc869..67795ebb 100644
--- a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap
+++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap
@@ -14,7 +14,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,c967dea4135cb75490e1e801c4639efc"
+                    "versions.yml:md5,83d1b23f5ff5b2ad1b96d17d7d7594ee"
                 ],
                 "sra": [
                     [
@@ -28,7 +28,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c967dea4135cb75490e1e801c4639efc"
+                    "versions.yml:md5,83d1b23f5ff5b2ad1b96d17d7d7594ee"
                 ]
             }
         ],
@@ -53,7 +53,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,c967dea4135cb75490e1e801c4639efc"
+                    "versions.yml:md5,83d1b23f5ff5b2ad1b96d17d7d7594ee"
                 ],
                 "sra": [
                     [
@@ -67,7 +67,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c967dea4135cb75490e1e801c4639efc"
+                    "versions.yml:md5,83d1b23f5ff5b2ad1b96d17d7d7594ee"
                 ]
             }
         ],
@@ -77,4 +77,4 @@
         },
         "timestamp": "2024-02-28T11:48:37.428307"
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/sratools/prefetch/tests/tags.yml b/modules/nf-core/sratools/prefetch/tests/tags.yml
new file mode 100644
index 00000000..52110bfd
--- /dev/null
+++ b/modules/nf-core/sratools/prefetch/tests/tags.yml
@@ -0,0 +1,2 @@
+sratools/prefetch:
+  - modules/nf-core/sratools/prefetch/**
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
index 7b41ed7e..5f74ed20 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
@@ -3,10 +3,12 @@ nextflow_workflow {
     name "Test workflow: fastq_download_prefetch_fasterqdump_sratools/main.nf"
     script "../main.nf"
     workflow "FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS"
-
-    tag "CUSTOM_SRATOOLSNCBISETTINGS"
-    tag "SRATOOLS_PREFETCH"
-    tag "SRATOOLS_FASTERQDUMP"
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "custom/sratoolsncbisettings"
+    tag "sratools/prefetch"
+    tag "sratools/fasterqdump"
+    tag "subworkflows/fastq_download_prefetch_fasterqdump_sratools"
 
     test("Parameters: default") {
 
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
index 485411da..1a34e0b8 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
@@ -40,8 +40,8 @@
         "content": [
             [
                 "versions.yml:md5,1a2218ff913fc33408bffccb081b5048",
-                "versions.yml:md5,2f3b3a13b36dabf13f09327613d5558d",
-                "versions.yml:md5,98d78bba9f3da39a0b7db6e9c7dcc224"
+                "versions.yml:md5,53d6e983afde3a28add2ffc6b7eba4f3",
+                "versions.yml:md5,9c558ff624585a6eee82a19c8c0136db"
             ]
         ],
         "meta": {
@@ -52,7 +52,7 @@
     },
     "test_pe_reads_1_size": {
         "content": [
-            2013376
+            2011460
         ],
         "meta": {
             "nf-test": "0.8.4",
@@ -94,4 +94,4 @@
         },
         "timestamp": "2024-02-28T12:02:56.161354"
     }
-}
\ No newline at end of file
+}
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml
new file mode 100644
index 00000000..03028c32
--- /dev/null
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/fastq_download_prefetch_fasterqdump_sratools:
+  - subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/**

From 3896fd35a4f750c75de9419559406c752bd5277b Mon Sep 17 00:00:00 2001
From: Sebastian Uhrig <suhrig@altoslabs.com>
Date: Sun, 7 Apr 2024 20:33:29 +0000
Subject: [PATCH 837/852] update CHANGELOG.md

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ecb962d6..dbfb81be 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,12 +10,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #299](https://github.com/nf-core/fetchngs/pull/299) - Template update for nf-core/tools v2.13.1
 - [PR #300](https://github.com/nf-core/fetchngs/pull/300) - Use file paths instead of tags for testing matrix, should make matrices more efficient
 - [PR #303](https://github.com/nf-core/fetchngs/pull/303) - Update wget container for SRA_FASTQ_FTP from 1.20.1 to 1.21.4
+- [PR #305](https://github.com/nf-core/fetchngs/pull/305) - Update module sratools/prefetch for reliable download integrity check
 
 ### Software dependencies
 
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
 | `wget`     | 1.20.1      | 1.21.4      |
+| `sratools` | 3.0.8       | 3.1.0       |
 
 ## [[1.12.0](https://github.com/nf-core/fetchngs/releases/tag/1.12.0)] - 2024-02-29
 

From 577af8a7973fe085146590a1be5d1bc1d92c0d78 Mon Sep 17 00:00:00 2001
From: Sebastian Uhrig <suhrig@altoslabs.com>
Date: Mon, 8 Apr 2024 09:32:23 +0000
Subject: [PATCH 838/852] update MD5 sum of versions.yml for nf-test

---
 .../tests/main.nf.test.snap                                     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
index 1a34e0b8..6872d8d2 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
@@ -41,7 +41,7 @@
             [
                 "versions.yml:md5,1a2218ff913fc33408bffccb081b5048",
                 "versions.yml:md5,53d6e983afde3a28add2ffc6b7eba4f3",
-                "versions.yml:md5,9c558ff624585a6eee82a19c8c0136db"
+                "versions.yml:md5,2f3b3a13b36dabf13f09327613d5558d"
             ]
         ],
         "meta": {

From 445577f72d4cff32aa2b19dbe90aa7101d8c688e Mon Sep 17 00:00:00 2001
From: Sebastian Uhrig <suhrig@altoslabs.com>
Date: Mon, 8 Apr 2024 09:51:42 +0000
Subject: [PATCH 839/852] update MD5 sum of versions.yml for nf-test

---
 .../tests/main.nf.test.snap                                   | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
index 6872d8d2..e10ffeb3 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
@@ -40,8 +40,8 @@
         "content": [
             [
                 "versions.yml:md5,1a2218ff913fc33408bffccb081b5048",
-                "versions.yml:md5,53d6e983afde3a28add2ffc6b7eba4f3",
-                "versions.yml:md5,2f3b3a13b36dabf13f09327613d5558d"
+                "versions.yml:md5,2f3b3a13b36dabf13f09327613d5558d",
+                "versions.yml:md5,53d6e983afde3a28add2ffc6b7eba4f3"
             ]
         ],
         "meta": {

From dd4d19cc2285825435e60c044ea9a8f57cc3734b Mon Sep 17 00:00:00 2001
From: Sebastian Uhrig <suhrig@altoslabs.com>
Date: Mon, 8 Apr 2024 10:39:42 +0000
Subject: [PATCH 840/852] update snapshots for nf-test

---
 .../tests/main.nf.test.snap                                   | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
index e10ffeb3..2530372b 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
@@ -28,7 +28,7 @@
     },
     "test_pe_reads_2_size": {
         "content": [
-            2011460
+            2013376
         ],
         "meta": {
             "nf-test": "0.8.4",
@@ -52,7 +52,7 @@
     },
     "test_pe_reads_1_size": {
         "content": [
-            2011460
+            2013376
         ],
         "meta": {
             "nf-test": "0.8.4",

From 3056a3ad09306ce58159093c8ee013d59dc5e682 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Mon, 8 Apr 2024 14:51:27 +0200
Subject: [PATCH 841/852] Update
 subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap

---
 .../tests/main.nf.test.snap                                     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
index 2530372b..0c0be2a4 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
@@ -28,7 +28,7 @@
     },
     "test_pe_reads_2_size": {
         "content": [
-            2013376
+            2011460
         ],
         "meta": {
             "nf-test": "0.8.4",

From 32abe41ce5af745147b0559e92a6124e39350b53 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 15 Apr 2024 09:54:36 +0100
Subject: [PATCH 842/852] feat: use github action instead of custom python

---
 .github/workflows/ci.yml | 25 ++++++-------------------
 1 file changed, 6 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 527048fe..53859060 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -27,35 +27,22 @@ jobs:
     name: Check for changes
     runs-on: ubuntu-latest
     outputs:
-      nf_test_files: ${{ steps.list.outputs.nf_test_files }}
+      nf_test_files: ${{ steps.list.outputs.components }}
     steps:
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-          architecture: "x64"
-
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
-      - name: Install gitpython find changed files
-        run: |
-          python -m pip install --upgrade pip
-          pip install gitpython pyyaml
-
       - name: List nf-test files
         id: list
-        run: |
-          echo nf_test_files=$(python \
-            .github/python/find_changed_files.py \
-            -t pipeline workflow process \
-            --head_ref ${{ github.sha }} \
-            --base_ref origin/${{ github.base_ref }} \
-          ) >> $GITHUB_OUTPUT
+        uses: adamrtalbot/detect-nf-test-changes@main
+        with:
+          head: ${{ github.sha }}
+          base: origin/${{ github.base_ref }}
 
       - name: print list of nf-test files
         run: |
-          echo ${{ steps.list.outputs.nf_test_files }}
+          echo ${{ steps.list.outputs.components }}
 
   test:
     name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}

From cfa6a262ee590a5fa2c718fdc54d203d7612e6ab Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 15 Apr 2024 09:55:34 +0100
Subject: [PATCH 843/852] Fixup: Add include file

---
 .github/workflows/ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 53859060..8c2107ea 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -39,6 +39,7 @@ jobs:
         with:
           head: ${{ github.sha }}
           base: origin/${{ github.base_ref }}
+          include: .github/python/include.yaml
 
       - name: print list of nf-test files
         run: |

From d4cd896df7a7ca6b9d9e4548d04c1ed5555c30dc Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 15 Apr 2024 10:19:20 +0100
Subject: [PATCH 844/852] move include.yaml

---
 .github/{python => }/include.yaml    |   0
 .github/python/find_changed_files.py | 317 ---------------------------
 .github/workflows/ci.yml             |   2 +-
 3 files changed, 1 insertion(+), 318 deletions(-)
 rename .github/{python => }/include.yaml (100%)
 delete mode 100644 .github/python/find_changed_files.py

diff --git a/.github/python/include.yaml b/.github/include.yaml
similarity index 100%
rename from .github/python/include.yaml
rename to .github/include.yaml
diff --git a/.github/python/find_changed_files.py b/.github/python/find_changed_files.py
deleted file mode 100644
index c0c61752..00000000
--- a/.github/python/find_changed_files.py
+++ /dev/null
@@ -1,317 +0,0 @@
-#!/usr/bin/env python
-
-# This script is used to identify *.nf.test files for changed functions/processs/workflows/pipelines and *.nf-test files
-# with changed dependencies, then return as a JSON list
-
-import argparse
-import json
-import logging
-import re
-import yaml
-
-from itertools import chain
-from pathlib import Path
-from git import Repo
-
-
-def parse_args() -> argparse.Namespace:
-    """
-    Parse command line arguments and return an ArgumentParser object.
-
-    Returns:
-        argparse.ArgumentParser: The ArgumentParser object with the parsed arguments.
-    """
-    parser = argparse.ArgumentParser(
-        description="Scan *.nf.test files for function/process/workflow name and return as a JSON list"
-    )
-    parser.add_argument(
-        "-r",
-        "--head_ref",
-        required=True,
-        help="Head reference branch (Source branch for a PR).",
-    )
-    parser.add_argument(
-        "-b",
-        "--base_ref",
-        required=True,
-        help="Base reference branch (Target branch for a PR).",
-    )
-    parser.add_argument(
-        "-x",
-        "--ignored_files",
-        nargs="+",
-        default=[
-            ".git/*",
-            ".gitpod.yml",
-            ".prettierignore",
-            ".prettierrc.yml",
-            "*.md",
-            "*.png",
-            "modules.json",
-            "pyproject.toml",
-            "tower.yml",
-        ],
-        help="List of files or file substrings to ignore.",
-    )
-    parser.add_argument(
-        "-i",
-        "--include",
-        type=Path,
-        default=".github/python/include.yaml",
-        help="Path to an include file containing a YAML of key value pairs to include in changed files. I.e., return the current directory if an important file is changed.",
-    )
-    parser.add_argument(
-        "-l",
-        "--log-level",
-        choices=["DEBUG", "INFO", "WARNING", "ERROR"],
-        default="INFO",
-        help="Logging level",
-    )
-    parser.add_argument(
-        "-t",
-        "--types",
-        nargs="+",
-        choices=["function", "process", "workflow", "pipeline"],
-        default=["function", "process", "workflow", "pipeline"],
-        help="Types of tests to include.",
-    )
-    return parser.parse_args()
-
-
-def read_yaml_inverted(file_path: str) -> dict:
-    """
-    Read a YAML file and return its contents as a dictionary but reversed, i.e. the values become the keys and the keys become the values.
-
-    Args:
-        file_path (str): The path to the YAML file.
-
-    Returns:
-        dict: The contents of the YAML file as a dictionary inverted.
-    """
-    with open(file_path, "r") as f:
-        data = yaml.safe_load(f)
-
-    # Invert dictionary of lists into contents of lists are keys, values are the original keys
-    # { "key": ["item1", "item2] } --> { "item1": "key", "item2": "key" }
-    return {value: key for key, values in data.items() for value in values}
-
-
-def find_changed_files(
-    branch1: str,
-    branch2: str,
-    ignore: list[str],
-) -> list[Path]:
-    """
-    Find all *.nf.tests that are associated with files that have been changed between two specified branches.
-
-    Args:
-        branch1 (str)      : The first branch being compared
-        branch2 (str)      : The second branch being compared
-        ignore  (list)     : List of files or file substrings to ignore.
-
-    Returns:
-        list: List of files matching the pattern *.nf.test that have changed between branch2 and branch1.
-    """
-    # create repo
-    repo = Repo(".")
-    # identify commit on branch1
-    branch1_commit = repo.commit(branch1)
-    # identify commit on branch2
-    branch2_commit = repo.commit(branch2)
-    # compare two branches
-    diff_index = branch1_commit.diff(branch2_commit)
-
-    # Start empty list of changed files
-    changed_files = []
-
-    # For every file that has changed between commits
-    for file in diff_index:
-        # Get pathlib.Path object
-        filepath = Path(file.a_path)
-        # If file does not match any in the ignore list, add containing directory to changed_files
-        if not any(filepath.match(ignored_path) for ignored_path in ignore):
-            changed_files.append(filepath)
-
-    # Uniqueify the results before returning for efficiency
-    return list(set(changed_files))
-
-
-def detect_include_files(
-    changed_files: list[Path], include_files: dict[str, str]
-) -> list[Path]:
-    """
-    Detects the include files based on the changed files.
-
-    Args:
-        changed_files (list[Path]): List of paths to the changed files.
-        include_files (dict[str, str]): Key-value pairs to return if a certain file has changed. If a file in a directory has changed, it points to a different directory.
-
-    Returns:
-        list[Path]: List of paths to representing the keys of the include_files dictionary, where a value matched a path in changed_files.
-    """
-    new_changed_files = []
-    for filepath in changed_files:
-        # If file is in the include_files, we return the key instead of the value
-        for include_path, include_key in include_files.items():
-            if filepath.match(include_path):
-                new_changed_files.append(Path(include_key))
-    return new_changed_files
-
-
-def detect_nf_test_files(changed_files: list[Path]) -> list[Path]:
-    """
-    Detects and returns a list of nf-test files from the given list of changed files.
-
-    Args:
-        changed_files (list[Path]): A list of file paths.
-
-    Returns:
-        list[Path]: A list of nf-test file paths.
-    """
-    result: list[Path] = []
-    for path in changed_files:
-        # If Path is the exact nf-test file add to list:
-        if path.match("*.nf.test") and path.exists():
-            result.append(path)
-        # Else recursively search for nf-test files:
-        else:
-            # Get the enclosing dir so files in the same dir can be found.
-            # e.g.
-            # dir/
-            # ├─ main.nf
-            # ├─ main.nf.test
-            for file in path.parent.rglob("*.nf.test"):
-                result.append(file)
-    return result
-
-
-def process_files(files: list[Path]) -> list[str]:
-    """
-    Process the files and return lines that begin with 'workflow', 'process', or 'function' and have a single string afterwards.
-
-    Args:
-        files (list): List of files to process.
-
-    Returns:
-        list: List of lines that match the criteria.
-    """
-    result = []
-    for file in files:
-        with open(file, "r") as f:
-            is_pipeline_test = True
-            lines = f.readlines()
-            for line in lines:
-                line = line.strip()
-                if line.startswith(("workflow", "process", "function")):
-                    words = line.split()
-                    if len(words) == 2 and re.match(r'^".*"$', words[1]):
-                        result.append(line)
-                        is_pipeline_test = False
-
-            # If no results included workflow, process or function
-            # Add a dummy result to fill the 'pipeline' category
-            if is_pipeline_test:
-                result.append("pipeline 'PIPELINE'")
-
-    return result
-
-
-def convert_nf_test_files_to_test_types(
-    lines: list[str], types: list[str] = ["function", "process", "workflow", "pipeline"]
-) -> dict[str, list[str]]:
-    """
-    Generate a dictionary of function, process and workflow lists from the lines.
-
-    Args:
-        lines (list): List of lines to process.
-        types (list): List of types to include.
-
-    Returns:
-        dict: Dictionary with function, process and workflow lists.
-    """
-    # Populate empty dict from types
-    result: dict[str, list[str]] = {key: [] for key in types}
-
-    for line in lines:
-        words = line.split()
-        if len(words) == 2 and re.match(r'^".*"$', words[1]):
-            keyword = words[0]
-            name = words[1].strip("'\"")  # Strip both single and double quotes
-            if keyword in types:
-                result[keyword].append(name)
-    return result
-
-
-def find_changed_dependencies(paths: list[Path], tags: list[str]) -> list[Path]:
-    """
-    Find all *.nf.test files with changed dependencies from a list of paths.
-
-    Args:
-        paths (list): List of directories or files to scan.
-        tags (list): List of tags identified as having changes.
-
-    Returns:
-        list: List of *.nf.test files with changed dependencies.
-    """
-
-    result: list[Path] = []
-
-    nf_test_files = detect_nf_test_files(paths)
-
-    # find nf-test files with changed dependencies
-    for nf_test_file in nf_test_files:
-        with open(nf_test_file, "r") as f:
-            lines = f.readlines()
-            # Get all tags from nf-test file
-            # Make case insensitive with .casefold()
-            tags_in_nf_test_file = [
-                tag.casefold().replace("/", "_")
-                for tag in convert_nf_test_files_to_test_types(lines, types=["tag"])[
-                    "tag"
-                ]
-            ]
-            # Check if tag in nf-test file appears in a tag.
-            # Use .casefold() to be case insensitive
-            if any(
-                tag.casefold().replace("/", "_") in tags_in_nf_test_file for tag in tags
-            ):
-                result.append(nf_test_file)
-
-    return result
-
-
-if __name__ == "__main__":
-
-    # Utility stuff
-    args = parse_args()
-    logging.basicConfig(level=args.log_level)
-
-    # Parse nf-test files for target test tags
-    changed_files = find_changed_files(args.head_ref, args.base_ref, args.ignored_files)
-
-    # If an additional include YAML is added, we detect additional changed dirs to include
-    if args.include:
-        include_files = read_yaml_inverted(args.include)
-        changed_files = changed_files + detect_include_files(
-            changed_files, include_files
-        )
-    nf_test_files = detect_nf_test_files(changed_files)
-    lines = process_files(nf_test_files)
-    result = convert_nf_test_files_to_test_types(lines)
-
-    # Get only relevant results (specified by -t)
-    # Unique using a set
-    target_results = list(
-        {item for sublist in map(result.get, args.types) for item in sublist}
-    )
-
-    # Parse files to identify nf-tests with changed dependencies
-    changed_dep_files = find_changed_dependencies([Path(".")], target_results)
-
-    # Combine target nf-test files and nf-test files with changed dependencies
-    all_nf_tests = [
-        str(test_path) for test_path in set(changed_dep_files + nf_test_files)
-    ]
-
-    # Print to stdout
-    print(json.dumps(all_nf_tests))
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8c2107ea..938c54ae 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -39,7 +39,7 @@ jobs:
         with:
           head: ${{ github.sha }}
           base: origin/${{ github.base_ref }}
-          include: .github/python/include.yaml
+          include: .github/include.yaml
 
       - name: print list of nf-test files
         run: |

From fd1d23f6310952b0861af1640718aaf4d010b3d8 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 23 Apr 2024 12:13:25 +0100
Subject: [PATCH 845/852] Update .github/workflows/ci.yml

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 938c54ae..7ddcf0bf 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -35,7 +35,7 @@ jobs:
 
       - name: List nf-test files
         id: list
-        uses: adamrtalbot/detect-nf-test-changes@main
+        uses: adamrtalbot/detect-nf-test-changes@rewrite-using-class-instead-of-loops
         with:
           head: ${{ github.sha }}
           base: origin/${{ github.base_ref }}

From e04589bb9298462716a5a4d7fafa64da7f196087 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 23 Apr 2024 16:12:38 +0100
Subject: [PATCH 846/852] Update .github/workflows/ci.yml

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 7ddcf0bf..4c535bd1 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -35,7 +35,7 @@ jobs:
 
       - name: List nf-test files
         id: list
-        uses: adamrtalbot/detect-nf-test-changes@rewrite-using-class-instead-of-loops
+        uses: adamrtalbot/detect-nf-test-changes@v0.0.1
         with:
           head: ${{ github.sha }}
           base: origin/${{ github.base_ref }}

From ce83591aa3002089614bd16c4e8fc2ddfebd5cb1 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 23 Apr 2024 18:01:57 +0100
Subject: [PATCH 847/852] Update detect-nf-test-changes to v0.0.2

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4c535bd1..b102cc21 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -35,7 +35,7 @@ jobs:
 
       - name: List nf-test files
         id: list
-        uses: adamrtalbot/detect-nf-test-changes@v0.0.1
+        uses: adamrtalbot/detect-nf-test-changes@v0.0.2
         with:
           head: ${{ github.sha }}
           base: origin/${{ github.base_ref }}

From 3e558c340968832179d04f878b78b18156ed22b1 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Wed, 24 Apr 2024 10:38:34 +0100
Subject: [PATCH 848/852] Update .github/workflows/ci.yml

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b102cc21..ad373fcf 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -35,7 +35,7 @@ jobs:
 
       - name: List nf-test files
         id: list
-        uses: adamrtalbot/detect-nf-test-changes@v0.0.2
+        uses: adamrtalbot/detect-nf-test-changes@9f8c94bee392098ca3e247e1004613a3728bbce5
         with:
           head: ${{ github.sha }}
           base: origin/${{ github.base_ref }}

From 31220181bf0af5adae56abfb77911d4e559a1f73 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Wed, 24 Apr 2024 16:02:18 +0100
Subject: [PATCH 849/852] Update .github/workflows/ci.yml

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index ad373fcf..83e11c56 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -35,7 +35,7 @@ jobs:
 
       - name: List nf-test files
         id: list
-        uses: adamrtalbot/detect-nf-test-changes@9f8c94bee392098ca3e247e1004613a3728bbce5
+        uses: adamrtalbot/detect-nf-test-changes@v0.0
         with:
           head: ${{ github.sha }}
           base: origin/${{ github.base_ref }}

From 2c49a44c87fef7cca1e11ed449483a9a3ed5edd4 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Wed, 24 Apr 2024 16:03:31 +0100
Subject: [PATCH 850/852] Update .github/workflows/ci.yml

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 83e11c56..3b1c9c6f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -35,7 +35,7 @@ jobs:
 
       - name: List nf-test files
         id: list
-        uses: adamrtalbot/detect-nf-test-changes@v0.0
+        uses: adamrtalbot/detect-nf-test-changes@v0.0.3
         with:
           head: ${{ github.sha }}
           base: origin/${{ github.base_ref }}

From d3b03cd222f77ffed59e8ddda86013ed6f2a5e21 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 5 Jul 2024 16:23:34 +0100
Subject: [PATCH 851/852] Use nf-core/setup-nf-test action for reusability

---
 .github/workflows/ci.yml | 17 ++---------------
 1 file changed, 2 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 3b1c9c6f..83ed7d5e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -69,6 +69,8 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      - uses: nf-core/setup-nf-test@v1
+
       - uses: actions/setup-python@v4
         with:
           python-version: "3.11"
@@ -79,21 +81,6 @@ jobs:
           python -m pip install --upgrade pip
           pip install pdiff
 
-      - name: Cache nf-test installation
-        id: cache-software
-        uses: actions/cache@v3
-        with:
-          path: |
-            /usr/local/bin/nf-test
-            /home/runner/.nf-test/nf-test.jar
-          key: ${{ runner.os }}-${{ env.NFT_VER }}-nftest
-
-      - name: Install nf-test
-        if: steps.cache-software.outputs.cache-hit != 'true'
-        run: |
-          wget -qO- https://code.askimed.com/install/nf-test | bash
-          sudo mv nf-test /usr/local/bin/
-
       - name: Run nf-test
         run: |
           nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap

From d96b1bc5933ea2bf8a63024a78cb51086a502f24 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 5 Jul 2024 16:27:20 +0100
Subject: [PATCH 852/852] changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index dbfb81be..89ad79bc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #300](https://github.com/nf-core/fetchngs/pull/300) - Use file paths instead of tags for testing matrix, should make matrices more efficient
 - [PR #303](https://github.com/nf-core/fetchngs/pull/303) - Update wget container for SRA_FASTQ_FTP from 1.20.1 to 1.21.4
 - [PR #305](https://github.com/nf-core/fetchngs/pull/305) - Update module sratools/prefetch for reliable download integrity check
+- [PR #316](https://github.com/nf-core/fetchngs/pull/316) - Use nf-core/setup-nf-test to install nf-test from cache during CI/CD
 
 ### Software dependencies