Merge pull request #3369 from nf-core/dev

dev -> main for 3.1.1

Author: mirpedrol

CHANGELOG.md

@@ -1,5 +1,24 @@
 # nf-core/tools: Changelog
 
+## [v3.1.1 - Brass Boxfish Patch](https://github.com/nf-core/tools/releases/tag/3.1.1) - [2024-12-20]
+
+### Template
+
+- Use outputs instead of the environment to pass around values between steps in the Download Test Action ([#3351](https://github.com/nf-core/tools/pull/3351))
+- Fix pre commit template ([#3358](https://github.com/nf-core/tools/pull/3358))
+- Set LICENSE copyright to nf-core community ([#3366](https://github.com/nf-core/tools/pull/3366))
+- fix including modules.config ([#3356](https://github.com/nf-core/tools/pull/3356))
+
+### Linting
+
+- Linting of pipeline LICENSE file is a warning to allow for author/maintainer names ([#3366](https://github.com/nf-core/tools/pull/3366))
+
+### General
+
+- Add missing p ([#3357](https://github.com/nf-core/tools/pull/3357))
+- Use `manifest.contributors` names if available, otherwise default to `manifest.author` ([#3362](https://github.com/nf-core/tools/pull/3362))
+- Properly parse the names form `manifest.contributors` ([#3364](https://github.com/nf-core/tools/pull/3364))
+
 ## [v3.1.0 - Brass Boxfish](https://github.com/nf-core/tools/releases/tag/3.1.0) - [2024-12-09]
 
 **Highlights**

nf_core/pipeline-template/.editorconfig

@@ -35,3 +35,7 @@ indent_size = unset
 # ignore python and markdown
 [*.{py,md}]
 indent_style = unset
+
+# ignore ro-crate metadata files
+[**/ro-crate-metadata.json]
+insert_final_newline = unset

nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml

@@ -11,7 +11,6 @@ body:
         - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
         - [{{ name }} pipeline documentation](https://nf-co.re/{{ short_name }}/usage)
 {%- endif %}
-
   - type: textarea
     id: description
     attributes:

nf_core/pipeline-template/.github/workflows/download_pipeline.yml

@@ -28,10 +28,14 @@ env:
   NXF_ANSI_LOG: false
 
 jobs:
-  download:
-    runs-on: ubuntu-latest
+  configure:
+    runs-on: ubuntu-latest{% raw %}
+    outputs:
+      REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }}
+      REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }}
+      REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }}
     steps:
-      - name: Install Nextflow
+      - name: Install Nextflow{% endraw %}
         uses: nf-core/setup-nextflow@v2
 
       - name: Disk space cleanup
@@ -53,65 +57,70 @@ jobs:
           pip install git+https://github.com/nf-core/tools.git@dev
 
       - name: Get the repository name and current branch set as environment variable
+        id: get_repo_properties
         run: |
-          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
-          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
-          echo "{% raw %}REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
+          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
+          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
+          echo "{% raw %}REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
 
       - name: Make a cache directory for the container images
         run: |
           mkdir -p ./singularity_container_images
 
+  download:
+    runs-on: ubuntu-latest
+    needs: configure
+    steps:
       - name: Download the pipeline
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
         run: |
-          nf-core pipelines download ${{ env.REPO_LOWERCASE }} \
-          --revision ${{ env.REPO_BRANCH }} \
-          --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
+          nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \
+          --revision ${{ needs.configure.outputs.REPO_BRANCH }} \
+          --outdir ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} \
           --compress "none" \
           --container-system 'singularity' \
           --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \
           --container-cache-utilisation 'amend' \
           --download-configuration 'yes'
 
       - name: Inspect download
-        run: tree ./${{ env.REPOTITLE_LOWERCASE }}{% endraw %}{% if test_config %}{% raw %}
+        run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}{% endraw %}{% if test_config %}{% raw %}
 
       - name: Count the downloaded number of container images
         id: count_initial
         run: |
           image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
           echo "Initial container image count: $image_count"
-          echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV}
+          echo "IMAGE_COUNT_INITIAL=$image_count" >> "$GITHUB_OUTPUT"
 
       - name: Run the downloaded pipeline (stub)
         id: stub_run_pipeline
         continue-on-error: true
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+        run: nextflow run ./${{needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.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() }}
+        if: ${{ steps.stub_run_pipeline.outcome == 'failure' }}
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
+        run: nextflow run ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -profile test,singularity --outdir ./results
 
       - name: Count the downloaded number of container images
         id: count_afterwards
         run: |
           image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
           echo "Post-pipeline run container image count: $image_count"
-          echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV}
+          echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT"
 
       - name: Compare container image counts
         run: |
-          if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then
-            initial_count=${{ env.IMAGE_COUNT_INITIAL }}
-            final_count=${{ env.IMAGE_COUNT_AFTER }}
+          if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then
+            initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}
+            final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}
             difference=$((final_count - initial_count))
             echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
             tree ./singularity_container_images

nf_core/pipeline-template/.gitpod.yml

@@ -3,7 +3,7 @@ tasks:
   - name: Update Nextflow and setup pre-commit
     command: |
       pre-commit install --install-hooks
-      nextflow self-update {% if code_linters %}
+      nextflow self-update {%- if code_linters %}
 
 vscode:
   extensions:

nf_core/pipeline-template/.prettierignore

@@ -16,3 +16,6 @@ testing/
 testing*
 *.pyc
 bin/
+{%- if rocrate %}
+ro-crate-metadata.json
+{%- endif %}

nf_core/pipeline-template/CITATIONS.md

@@ -18,7 +18,7 @@
 
 {%- endif %}
 
-{% if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+{%- if multiqc %}- [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.
 

nf_core/pipeline-template/LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) {{ author }}
+Copyright (c) The {{ name }} team
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

nf_core/pipeline-template/README.md

@@ -7,7 +7,7 @@
   </picture>
 </h1>
 
-{% else %}
+{%- else -%}
 
 # {{ name }}
 
@@ -48,13 +48,13 @@
      workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
 <!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
 
-{% if fastqc %}1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)){% endif %}
-{% if multiqc %}2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)){% endif %}
+{%- if fastqc %}1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)){% endif %}
+{%- if multiqc %}2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)){% endif %}
 
 ## Usage
 
 > [!NOTE]
-> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. {% if test_config %}Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.{% endif %}
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. {%- if test_config %}Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.{% endif %}
 
 <!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
      Explain what rows and columns represent. For instance (please edit as appropriate):
@@ -120,10 +120,11 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 <!-- 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 {{ name }} for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
-{% if citations %}<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
+{%- if citations %}<!-- 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.
-{% endif %}
+{%- endif %}
+
 {% if is_nfcore -%}
 You can cite the `nf-core` publication as follows:
 

nf_core/pipeline-template/docs/output.md

@@ -2,7 +2,7 @@
 
 ## Introduction
 
-This document describes the output produced by the pipeline. {% if multiqc %}Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.{% endif %}
+This document describes the output produced by the pipeline.{% if multiqc %} Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.{% endif %}
 
 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.
 
@@ -14,9 +14,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 {% if fastqc -%}
 
-- [FastQC](#fastqc) - Raw read QC
-  {%- endif %}
-  {%- if multiqc %}
+- [FastQC](#fastqc) - Raw read QC{% endif %}
+  {%- if multiqc -%}
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
   {%- endif %}
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
@@ -35,7 +34,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 </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/).
-{%- endif %}
+{%- endif -%}
 
 {% if multiqc -%}
 
@@ -54,7 +53,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 [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>.
-{%- endif %}
+{%- endif -%}
 
 ### Pipeline information