Merge pull request #1297 from nf-core/nf-core-template-merge-2.14.1

drpatelh · web-flow · commit 431edb0c5698 · 2024-05-13T17:04:59.000+01:00
Important! Template update for nf-core/tools v2.14.1
diff --git a/.editorconfig b/.editorconfig
@@ -28,10 +28,6 @@ indent_style = unset
 [/assets/email*]
 indent_size = unset
 
-# ignore Readme
-[README.md]
-indent_style = unset
-
-# ignore python
+# ignore python and markdown
 [*.{py,md}]
 indent_style = unset
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rnas
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnaseq/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/rnaseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nf-test test tests/ --verbose --profile +docker`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -69,7 +69,7 @@ jobs:
 
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
@@ -14,6 +14,8 @@ on:
   pull_request:
     types:
       - opened
+      - edited
+      - synchronize
     branches:
       - master
   pull_request_target:
@@ -28,11 +30,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
       - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
         with:
@@ -65,8 +70,17 @@ jobs:
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}
 
-      - name: Run the downloaded pipeline
+      - name: Run the downloaded pipeline (stub)
+        id: stub_run_pipeline
+        continue-on-error: true
         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
+      - name: Run the downloaded pipeline (stub run not supported)
+        id: run_pipeline
+        if: ${{ job.steps.stub_run_pipeline.status == failure() }}
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_HOME_MOUNT: true
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -14,13 +14,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
-          cache: "pip"
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -32,14 +31,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: Install dependencies
@@ -60,7 +59,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
+        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
@@ -12,7 +12,7 @@ jobs:
       - name: get topics and convert to hashtags
         id: get_topics
         run: |
-          curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT
+          echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')"  >> $GITHUB_OUTPUT
 
       - uses: rzr/fediverse-action@master
         with:
@@ -25,13 +25,13 @@ jobs:
 
             Please see the changelog: ${{ github.event.release.html_url }}
 
-            ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics
+            ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
 
   send-tweet:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.10"
       - name: Install dependencies
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,13 +1,15 @@
 repository_type: pipeline
+nf_core_version: "2.14.1"
 lint:
-  actions_ci: false
   files_unchanged:
     - assets/email_template.html
     - assets/email_template.txt
     - .gitignore
-    - .github/PULL_REQUEST_TEMPLATE.md
   files_exist:
     - conf/modules.config
+  actions_ci: false
+  multiqc_config: false
+  modules_config: false
   nextflow_config:
     - config_defaults:
         - params.ribo_database_manifest
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,6 +3,9 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+        additional_dependencies:
+          - prettier@3.2.5
+
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"
     hooks:
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -60,14 +60,15 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1249](https://github.com/nf-core/rnaseq/pull/1249) - Include nf-tests for rsem_merge_counts module
 - [PR #1250](https://github.com/nf-core/rnaseq/pull/1250) - Remove all tags.yml files because the testing system has changed
 - [PR #1251](https://github.com/nf-core/rnaseq/pull/1251) - Replace deseq2qc paths
+- [PR #1253](https://github.com/nf-core/rnaseq/pull/1253) - Use nf-test files as matrix to test over in CI/CD for efficiency
 - [PR #1261](https://github.com/nf-core/rnaseq/pull/1261) - Add more tests for PREPARE_GENOME
 - [PR #1265](https://github.com/nf-core/rnaseq/pull/1265) - Small updates noticed during code review
 - [PR #1266](https://github.com/nf-core/rnaseq/pull/1266) - Delete unecessary tags from nf.test files for modules and subworkflows
-- [PR #1253](https://github.com/nf-core/rnaseq/pull/1253) - Use nf-test files as matrix to test over in CI/CD for efficiency
 - [PR #1278](https://github.com/nf-core/rnaseq/pull/1278) - Delocalise pseudo quant workflow
 - [PR #1280](https://github.com/nf-core/rnaseq/pull/1280) - Reorganise pipeline level tests into flat directory structure
 - [PR #1283](https://github.com/nf-core/rnaseq/pull/1283) - Add output files to nf-test snapshot
 - [PR #1293](https://github.com/nf-core/rnaseq/pull/1293) - Update subworkflow utils_nfcore_pipeline
+- [PR #1297](https://github.com/nf-core/rnaseq/pull/1297) - Important! Template update for nf-core/tools v2.14.1
 
 ### Parameters
 
diff --git a/README.md b/README.md
@@ -12,7 +12,7 @@
 [![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://tower.nf/launch?pipeline=https://github.com/nf-core/rnaseq)
+[![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/nf-core/rnaseq)
 
 [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnaseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnaseq)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
diff --git a/conf/test.config b/conf/test.config
@@ -19,21 +19,20 @@ params {
     max_memory = '6.GB'
     max_time   = '6.h'
 
-
     // Input data
-    input = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv"
+    input              = params.pipelines_testdata_base_path + 'samplesheet/v3.10/samplesheet_test.csv'
 
     // Genome references
-    fasta              = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genome.fasta"
-    gtf                = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genes_with_empty_tid.gtf.gz"
-    gff                = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genes.gff.gz"
-    transcript_fasta   = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/transcriptome.fasta"
-    additional_fasta   = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/gfp.fa.gz"
-
-    bbsplit_fasta_list = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/bbsplit_fasta_list.txt"
-    hisat2_index       = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/hisat2.tar.gz"
-    salmon_index       = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/salmon.tar.gz"
-    rsem_index         = "https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/rsem.tar.gz"
+    fasta              = params.pipelines_testdata_base_path + 'reference/genome.fasta'
+    gtf                = params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf.gz'
+    gff                = params.pipelines_testdata_base_path + 'reference/genes.gff.gz'
+    transcript_fasta   = params.pipelines_testdata_base_path + 'reference/transcriptome.fasta'
+    additional_fasta   = params.pipelines_testdata_base_path + 'reference/gfp.fa.gz'
+
+    bbsplit_fasta_list = params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt'
+    hisat2_index       = params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz'
+    salmon_index       = params.pipelines_testdata_base_path + 'reference/salmon.tar.gz'
+    rsem_index         = params.pipelines_testdata_base_path + 'reference/rsem.tar.gz'
 
     // Other parameters
     skip_bbsplit        = false
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -15,7 +15,7 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Parameters for full-size test
-    input          = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/v3.10/samplesheet_full.csv'
+    input          = params.pipelines_testdata_base_path + 'samplesheet/v3.10/samplesheet_full.csv'
     genome         = 'GRCh37'
     pseudo_aligner = 'salmon'
 }
diff --git a/docs/usage.md b/docs/usage.md
@@ -314,6 +314,8 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
   - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
 - `apptainer`
   - A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
+- `wave`
+  - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
 - `conda`
   - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
 
diff --git a/modules.json b/modules.json
@@ -47,7 +47,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
+                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
                         "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
                     },
                     "fq/subsample": {
@@ -314,7 +314,7 @@
                     },
                     "fastq_fastqc_umitools_fastp": {
                         "branch": "master",
-                        "git_sha": "cabcc0dadf8366aa7a9930066a7b3dd90d9825d5",
+                        "git_sha": "e98edb838fb0072c0783139ed16723bbc5d48d23",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_fastqc_umitools_trimgalore": {
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
diff --git a/nextflow.config b/nextflow.config
diff --git a/nextflow_schema.json b/nextflow_schema.json
diff --git a/pyproject.toml b/pyproject.toml
diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/nextflow.config b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/nextflow.config
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/nextflow.save_trimmed.config b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/nextflow.save_trimmed.config
