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Add nf-test tests for local modules and subworkflows #123

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Add nf-test tests for local modules and subworkflows #123

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@fbdtemme fbdtemme commented Jan 14, 2025 •
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  • Add local and subworfklow tests.
  • Add stubs for all modules
  • Fix some missing version reporting
  • Add sharded CI/CD taken from nf-core/sarek

Depends on: nf-core/test-datasets#1458

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/pixelator branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • 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.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Jan 14, 2025 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 651a786

+| ✅ 224 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   7 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

  • actions_ci - '.github/workflows/ci.yml' is not triggered on expected events

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.4.0
  • files_unchanged - LICENSE does not match the template
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.1.1
  • Run at 2025-01-14 16:45:38

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