Merge pull request #15 from sanger-tol/dev

Version 0.6.2
sanger-tol · Jan 14, 2025 · d4b0715 · d4b0715
2 parents 20cb5a4 + c5bdd33
commit d4b0715
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -29,42 +29,14 @@ jobs:
           - "24.04.0"
           - "latest-everything"
     steps:
-      - name: Get branch names
-        # Pulls the names of current branches in repo
-        # steps.branch-names.outputs.current_branch is used later and returns the name of the branch the PR is made FROM not to
-        id: branch-names
-        uses: tj-actions/branch-names@v8
-
-      - name: Setup apptainer
-        uses: eWaterCycle/setup-apptainer@main
-
-      - name: Set up Singularity
-        run: |
-          mkdir -p $NXF_SINGULARITY_CACHEDIR
-          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
-
-      - name: Install Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.10"
-
-      - name: Install nf-core
-        run: |
-          pip install nf-core
-
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      # This will only download the main pipeline containers, subpipelines need their own nf-download
-      - name: NF-Core Download - download singularity containers
-        run: |
-          nf-core download sanger-tol/ear --revision ${{ steps.branch-names.outputs.current_branch }} --compress none -d --force --outdir sanger-ear --container-cache-utilisation amend --container-system singularity
-
       - name: Download Tiny test data
         # Download A fungal test data set that is full enough to show some real output.
         # Needs a kmer db for merqury
@@ -73,9 +45,6 @@ jobs:
           cp TreeValTinyData/assembly/draft/grTriPseu1.fa TreeValTinyData/assembly/draft/grTriPseu1-hap.fa
           cp TreeValTinyData/assembly/draft/grTriPseu1.fa TreeValTinyData/assembly/draft/grTriPseu1-all_hap.fa
 
-      # - name: Disk space cleanup
-      #   uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
-
       - 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

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -14,7 +14,7 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@v4
 
       - name: Set up Python 3.12
         uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
@@ -31,7 +31,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -44,7 +44,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install nf-core
+          pip install nf-core==2.8.0
 
       - name: Run nf-core lint
         env:

diff --git a/.nf-core.yml b/.nf-core.yml
@@ -5,6 +5,10 @@ lint:
     - docs/images/nf-core-ear_logo_light.png
     - docs/images/nf-core-ear_logo_dark.png
     - lib/nfcore_external_java_deps.jar
+    - lib/NfcoreSchema.groovy
+    - lib/NfcoreTemplate.groovy
+    - lib/Utils.groovy
+    - lib/WorkflowMain.groovy
     - .github/ISSUE_TEMPLATE/config.yml
     - .github/workflows/awstest.yml
     - .github/workflows/awsfulltest.yml
@@ -16,11 +20,20 @@ lint:
     - docs/images/nf-core-ear_logo_light.png
     - docs/images/nf-core-ear_logo_dark.png
     - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/CONTRIBUTING.md
+    - .github/PULL_REQUEST_TEMPLATE.md
+    - .github/workflows/branch.yml
+    - .github/workflows/linting_comment.yml
+    - .github/workflows/linting.yml
+    - assets/email_template.html
   multiqc_config:
     - report_comment
   nextflow_config:
     - manifest.name
     - manifest.homePage
+    - params.show_hidden_params
+    - params.schema_ignore_params
+    - params.validationSchemaIgnoreParams
 nf_core_version: 2.14.1
 repository_type: pipeline
 template:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,7 +2,23 @@
 
 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).
-Naming based on: [Mythical creatures](https://en.wikipedia.org/wiki/List_of_legendary_creatures_by_type).
+Naming based on: [Audiologists](https://en.wikipedia.org/wiki/Category:Audiologists).
+
+## v0.6.2 - Robert Beiny H2 [09/01/2025]
+
+- Modules have been updated to remove conda defaults.
+
+### Software dependencies
+
+| Dependency                   | Old version         | New version         |
+| ---------------------------- | ------------------- | ------------------- |
+| sanger-tol/blobtoolkit\*     |                     | 0.6.0 (Bellsprout)  |
+| sanger-tol/curationpretext\* | 1.0.0 (UNSC Cradle) | 1.1.0 (UNSC Delphi) |
+| GFASTATS                     |                     | 1.3.6--hdcf5f25_3   |
+| MERQUERY_FK                  |                     | 1.2                 |
+| MINIMAP2_ALIGN               |                     | 2.28                |
+| SAMTOOLS_MERGE               | 1.20--h50ea8bc_0    | 1.21--h50ea8bc_0    |
+| SAMTOOLS_SORT                | 1.21--h50ea8bc_0    | 1.21--h50ea8bc_0    |
 
 ## v0.6.1 - Robert Beiny H1 [08/10/2024]
 

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -36,9 +36,9 @@
 
 ## Software packaging/containerisation tools
 
-- [Anaconda](https://anaconda.com)
+- [Conda](https://conda.org/)
 
-  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
+  > conda contributors. conda: A system-level, binary package and environment manager running on all major operating systems and platforms. Computer software. https://github.com/conda/conda
 
 - [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
 

diff --git a/README.md b/README.md
@@ -2,7 +2,6 @@
 [![GitHub Actions Linting Status](https://github.com/sanger-tol/ear/actions/workflows/linting.yml/badge.svg)](https://github.com/sanger-tol/ear/actions/workflows/linting.yml)[![DOI](https://zenodo.org/badge/833605808.svg)](https://doi.org/10.5281/zenodo.13819520)
 [![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%A524.04.0-23aa62.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/)
 [![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/)
 [![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/sanger-tol/ear)

diff --git a/conf/base.config b/conf/base.config
@@ -25,8 +25,8 @@ process {
 
     withName: "MINIMAP2_ALIGN_SE" {
         cpus            = { check_max( 16                  , 'cpus'    ) }
-        memory          = { check_max( 1.GB     * ( reference.size() < 2e9 ? 40 : Math.ceil( ( reference.size() / 1e+9 ) * 20 ) * task.attempt ) , 'memory') }
-        time            = { check_max( 1.h      * ( reference.size() < 1e9 ? 10 : reference.size() < 10e9 ? 30 : 48), 'time'      ) }
+        memory          = { check_max( 1.GB     * ( reference.size() < 2e9 ? 60 : Math.ceil( ( reference.size() / 1e+9 ) * 20 ) * task.attempt ) , 'memory') }
+        time            = { check_max( 1.h      * ( reference.size() < 1e9 ? 15 : reference.size() < 10e9 ? 30 : 48), 'time'      ) }
     }
 
     // Process-specific resource requirements

diff --git a/conf/modules.config b/conf/modules.config
@@ -51,7 +51,7 @@ process {
         ext.executor        = "bsub -Is -tty -e test.e -o test.log -n 2 -q oversubscribed -M1400 -R'select[mem>1400] rusage[mem=1400] span[hosts=1]'"
         ext.profiles        = "singularity,sanger"
         ext.get_versions    = "lsid | head -n1 | cut -d ',' -f 1"
-        ext.version         = "1.0.0"
+        ext.version         = "1.1.0"
     }
 
 }
diff --git a/modules.json b/modules.json
@@ -7,34 +7,34 @@
                 "nf-core": {
                     "cat/cat": {
                         "branch": "master",
-                        "git_sha": "5bb8ca085e17549e185e1823495ab8d20727a805",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "gfastats": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/gfastats/gfastats.diff"
                     },
                     "merquryfk/merquryfk": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/merquryfk/merquryfk/merquryfk-merquryfk.diff"
                     },
                     "minimap2/align": {
                         "branch": "master",
-                        "git_sha": "a33ef9475558c6b8da08c5f522ddaca1ec810306",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "samtools/merge": {
                         "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/nf-core/cat/cat/environment.yml b/modules/nf-core/cat/cat/environment.yml
diff --git a/modules/nf-core/cat/cat/meta.yml b/modules/nf-core/cat/cat/meta.yml
diff --git a/modules/nf-core/gfastats/environment.yml b/modules/nf-core/gfastats/environment.yml
diff --git a/modules/nf-core/gfastats/meta.yml b/modules/nf-core/gfastats/meta.yml