template update#164
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Pull request overview
This PR updates the pipeline template and supporting infrastructure to align with newer nf-core / Nextflow tooling, refreshes MultiQC assets, and removes webhook notification support.
Changes:
- Updates nf-core template metadata, CI workflows, docs, pre-commit tooling, and Nextflow/nf-test configuration.
- Updates MultiQC to 1.34 with refreshed containers, conda locks, tests, and snapshots.
- Removes IM notification support and related assets, and adds / updates template-generated documentation and config files.
Reviewed changes
Copilot reviewed 55 out of 56 changed files in this pull request and generated 5 comments.
Show a summary per file
| File | Description |
|---|---|
.devcontainer/devcontainer.json |
Adds devcontainer schema metadata. |
.github/CONTRIBUTING.md |
Removes old contributing guide. |
.github/ISSUE_TEMPLATE/config.yml |
Adds nf-core contact links. |
.github/PULL_REQUEST_TEMPLATE.md |
Updates contributing documentation links. |
.github/actions/get-shards/action.yml |
Updates nf-test setup action. |
.github/actions/nf-test/action.yml |
Updates action versions used by nf-test CI. |
.github/workflows/branch.yml |
Updates PR comment action. |
.github/workflows/clean-up.yml |
Updates stale action pin. |
.github/workflows/download_pipeline.yml |
Updates download test dependencies and action pins. |
.github/workflows/fix_linting.yml |
Switches lint autofix workflow to prek and updated actions. |
.github/workflows/linting.yml |
Updates lint workflow tooling and action versions. |
.github/workflows/linting_comment.yml |
Updates artifact download and sticky comment actions. |
.github/workflows/nf-test.yml |
Updates nf-test / Nextflow versions and checkout action. |
.github/workflows/template-version-comment.yml |
Updates template-version comment workflow actions and docs link. |
.gitignore |
Updates ignored generated files. |
.nf-core.yml |
Updates nf-core template version metadata. |
.pre-commit-config.yaml |
Updates prettier and hook configuration. |
.prettierignore |
Removes deleted notification templates from ignore list. |
README.md |
Updates badges, docs links, and contributing link. |
assets/adaptivecard.json |
Removes Teams notification template. |
assets/slackreport.json |
Removes Slack notification template. |
conf/base.config |
Updates retry exit statuses and adds GPU label config. |
conf/containers_conda_lock_files_amd64.config |
Adds MultiQC amd64 conda-lock container config. |
conf/containers_conda_lock_files_arm64.config |
Adds MultiQC arm64 conda-lock container config. |
conf/containers_docker_amd64.config |
Adds MultiQC amd64 Docker container config. |
conf/containers_docker_arm64.config |
Adds MultiQC arm64 Docker container config. |
conf/containers_singularity_https_amd64.config |
Adds MultiQC amd64 Singularity HTTPS container config. |
conf/containers_singularity_https_arm64.config |
Adds MultiQC arm64 Singularity HTTPS container config. |
conf/containers_singularity_oras_amd64.config |
Adds MultiQC amd64 ORAS container config. |
conf/containers_singularity_oras_arm64.config |
Adds MultiQC arm64 ORAS container config. |
docs/CONTRIBUTING.md |
Adds new nf-core-style contributing documentation. |
docs/usage.md |
Updates nf-core documentation links. |
main.nf |
Removes webhook URL from completion workflow call. |
modules.json |
Updates tracked module / subworkflow SHAs. |
modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt |
Adds MultiQC 1.34 amd64 lock file. |
modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt |
Adds arm64 lock file. |
modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt |
Adds MultiQC 1.34 arm64 lock file. |
modules/nf-core/multiqc/environment.yml |
Updates MultiQC conda version to 1.34. |
modules/nf-core/multiqc/main.nf |
Updates MultiQC containers and apptainer handling. |
modules/nf-core/multiqc/meta.yml |
Updates MultiQC container metadata and lock file references. |
modules/nf-core/multiqc/tests/main.nf.test |
Expands MultiQC snapshot assertions and updates test config URL. |
modules/nf-core/multiqc/tests/main.nf.test.snap |
Refreshes MultiQC test snapshots. |
modules/nf-core/multiqc/tests/nextflow.config |
Enables MultiQC plot generation in tests. |
nextflow.config |
Removes duplicate params / hook URL and adds output mode compatibility settings. |
nextflow_schema.json |
Adds / updates schema parameters and removes hook URL. |
nf-test.config |
Updates nf-test config syntax, ignores, and triggers. |
ro-crate-metadata.json |
Updates RO-Crate version, Nextflow requirement, and contributor metadata. |
subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf |
Removes webhook notification input and call. |
subworkflows/nf-core/deepvariant/tests/deepvariant-workflow-and-process-equality-tester.nf |
Removes DeepVariant equality test helper. |
subworkflows/nf-core/deepvariant/tests/equality.nf.test |
Removes DeepVariant equality test. |
subworkflows/nf-core/utils_nfcore_pipeline/main.nf |
Updates emitted config value and removes IM notification helper. |
subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test |
Adds utility subworkflow nf-test. |
subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap |
Adds snapshot for utility subworkflow test. |
subworkflows/nf-core/utils_nfschema_plugin/main.nf |
Adjusts help parameter handling. |
subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config |
Updates nf-schema plugin version. |
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| - name: Run nf-core pipelines lint | ||
| if: ${{ github.base_ref != 'master' }} | ||
| if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }} |
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| - name: Read .nf-core.yml | ||
| uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 | ||
| id: read_yml | ||
| with: | ||
| config: ${{ github.workspace }}/.nf-core.yml |
| - [ ] Add validation for relevant parameters to the pipeline utilisation section of `utils_nfcore_\_pipeline/main.nf` subworkflow. | ||
| - [ ] Perform local tests to validate that the new code works as expected. | ||
| - [ ] If applicable, add a new test in the `tests` directory. | ||
| - [ ] Update `usage.md`, `output.md`, and `citation.md` as appropriate. |
| - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/markupsafe-3.0.3-py314hb76de3f_1.conda | ||
| - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/mathjax-2.7.7-h8af1aa0_3.tar.bz2 | ||
| - conda: https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda | ||
| - conda: https://conda.anaconda.org/bioconda/noarch/multiqc-1.33-pyhdfd78af_0.conda |
| assert snapshot( | ||
| sanitizeOutput(process.out).collectEntries { key, val -> | ||
| if (key == "data") { | ||
| return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] |
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| - name: Run nf-core pipelines lint | ||
| if: ${{ github.base_ref != 'master' }} | ||
| if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }} |
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| - name: Read .nf-core.yml | ||
| uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 | ||
| id: read_yml | ||
| with: | ||
| config: ${{ github.workspace }}/.nf-core.yml |
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| "type": "string", | ||
| "description": "Comma-separated list of germline variant callers to use. Valid values: deepvariant, clair. Example: 'deepvariant,clair'", | ||
| "default": "deepvariant,clair" |
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| "type": "string", | ||
| "description": "Comma-separated list of somatic variant callers to use. Valid values: deepsomatic, clair. Example: 'deepsomatic,clair'", | ||
| "default": "deepsomatic,clair" |
| "@id": "https://www.nextflow.io/" | ||
| }, | ||
| "version": "!>=25.04.0" | ||
| "version": "!>=25.10.4" |
robert-a-forsyth
approved these changes
May 28, 2026
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).