Revert dev to release 1.10

This reverts commit 624d420, reversing
changes made to 1b9d187.

.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

.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 }}

.gitignore

@@ -6,5 +6,3 @@ results/
 testing/
 testing*
 *.pyc
-.nf-test/
-nf-test

.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

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

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:

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'

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`.

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",