dev -> main for 3.1.1

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/.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
 

nf_core/pipeline-template/docs/usage.md

@@ -115,7 +115,7 @@ It is a good idea to specify the pipeline version when running the pipeline on y
 
 First, go to the [{{ name }} releases page](https://github.com/{{ name }}/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag.
 
-This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. {% if multiqc %}For example, at the bottom of the MultiQC reports.{% endif %}
+This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future.{% if multiqc %} For example, at the bottom of the MultiQC reports.{% endif %}
 
 To further assist in reproducibility, you can use share and reuse [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
 
@@ -138,7 +138,7 @@ Several generic profiles are bundled with the pipeline which instruct the pipeli
 
 {%- if nf_core_configs %}
 
-The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is suported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
+The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is supported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
 {% else %}
 {% endif %}
 Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important!

nf_core/pipeline-template/nextflow.config

@@ -77,11 +77,6 @@ params {
 includeConfig 'conf/base.config'
 {%- else %}
 
-{% if modules -%}
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
-{%- endif %}
-
 process {
     // TODO nf-core: Check the defaults for all processes
     cpus   = { 1    * task.attempt }
@@ -311,7 +306,7 @@ validation {
         command = "nextflow run {{ name }} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
         fullParameter = "help_full"
         showHiddenParameter = "show_hidden"
-        {% if is_nfcore -%}
+        {%- if is_nfcore %}
         beforeText = """
 -\033[2m----------------------------------------------------\033[0m-
                                         \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
@@ -336,3 +331,8 @@ validation {
     }{% endif %}
 }
 {%- endif %}
+
+{% if modules -%}
+// Load modules.config for DSL2 module specific options
+includeConfig 'conf/modules.config'
+{%- endif %}

nf_core/pipeline-template/nextflow_schema.json

@@ -243,10 +243,12 @@
         {
             "$ref": "#/$defs/input_output_options"
         },
-        {% if igenomes %}{
+        {%- if igenomes %}
+        {
             "$ref": "#/$defs/reference_genome_options"
         },{% endif %}
-        {% if nf_core_configs %}{
+        {%- if nf_core_configs %}
+        {
             "$ref": "#/$defs/institutional_config_options"
         },{% endif %}
         {

nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf

@@ -143,7 +143,7 @@ workflow PIPELINE_COMPLETION {
     {%- if multiqc %}
     def multiqc_reports = multiqc_report.toList()
     {%- endif %}
-    
+
     //
     // Completion email and summary
     //

nf_core/pipelines/bump_version.py

@@ -128,8 +128,9 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None:
         yaml_key=["template", "version"],
     )
 
-    # update rocrate
-    ROCrate(pipeline_obj.wf_path).update_rocrate()
+    # update rocrate if ro-crate is present
+    if Path(pipeline_obj.wf_path, "ro-crate-metadata.json").exists():
+        ROCrate(pipeline_obj.wf_path).update_rocrate()
 
 
 def bump_nextflow_version(pipeline_obj: Pipeline, new_version: str) -> None:

nf_core/pipelines/create/create.py

@@ -22,7 +22,7 @@
 from nf_core.pipelines.create_logo import create_logo
 from nf_core.pipelines.lint_utils import run_prettier_on_file
 from nf_core.pipelines.rocrate import ROCrate
-from nf_core.utils import NFCoreTemplateConfig, NFCoreYamlLintConfig
+from nf_core.utils import NFCoreTemplateConfig, NFCoreYamlLintConfig, custom_yaml_dumper
 
 log = logging.getLogger(__name__)
 
@@ -266,6 +266,14 @@ def init_pipeline(self):
         # Init the git repository and make the first commit
         if not self.no_git:
             self.git_init_pipeline()
+            # Run prettier on files
+            if self.config.skip_features is None or not (
+                "code_linters" in self.config.skip_features or "github" in self.config.skip_features
+            ):
+                current_dir = Path.cwd()
+                os.chdir(self.outdir)
+                run_prettier_on_file([str(f) for f in self.outdir.glob("**/*")])
+                os.chdir(current_dir)
 
         if self.config.is_nfcore and not self.is_interactive:
             log.info(
@@ -362,7 +370,7 @@ def render_template(self) -> None:
             # Make a logo and save it, if it is a nf-core pipeline
             self.make_pipeline_logo()
 
-        if self.config.skip_features is None or "ro-crate" not in self.config.skip_features:
+        if self.config.skip_features is None or "rocrate" not in self.config.skip_features:
             # Create the RO-Crate metadata file
             rocrate_obj = ROCrate(self.outdir)
             rocrate_obj.create_rocrate(json_path=self.outdir / "ro-crate-metadata.json")
@@ -375,12 +383,9 @@ def render_template(self) -> None:
             if config_fn is not None and config_yml is not None:
                 with open(str(config_fn), "w") as fh:
                     config_yml.template = NFCoreTemplateConfig(**self.config.model_dump(exclude_none=True))
-                    yaml.safe_dump(config_yml.model_dump(exclude_none=True), fh)
+                    yaml.dump(config_yml.model_dump(exclude_none=True), fh, Dumper=custom_yaml_dumper())
                     log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'")
 
-        # Run prettier on files
-        run_prettier_on_file([str(f) for f in self.outdir.glob("**/*")])
-
     def fix_linting(self):
         """
         Updates the .nf-core.yml with linting configurations
@@ -408,7 +413,13 @@ def fix_linting(self):
         if config_fn is not None and nf_core_yml is not None:
             nf_core_yml.lint = NFCoreYamlLintConfig(**lint_config)
             with open(self.outdir / config_fn, "w") as fh:
-                yaml.dump(nf_core_yml.model_dump(exclude_none=True), fh, default_flow_style=False, sort_keys=False)
+                yaml.dump(
+                    nf_core_yml.model_dump(exclude_none=True),
+                    fh,
+                    sort_keys=False,
+                    default_flow_style=False,
+                    Dumper=custom_yaml_dumper(),
+                )
 
     def make_pipeline_logo(self):
         """Fetch a logo for the new pipeline from the nf-core website"""