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Add tests to local subworkflows, improve fai generation#142

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famosab merged 10 commits into
devfrom
tests
May 7, 2026
Merged

Add tests to local subworkflows, improve fai generation#142
famosab merged 10 commits into
devfrom
tests

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@famosab

@famosab famosab commented May 6, 2026 •
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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/bamtofastq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines 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 May 6, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4162f42

+| ✅ 246 tests passed       |+
#| ❔   1 tests had warnings |#
!| ❗   4 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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 fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-05-07 09:31:42

mashehu
mashehu reviewed May 7, 2026
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Comment thread workflows/bamtofastq.nf

@mashehu mashehu May 7, 2026 •
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the changes here seem unrelated to the swf test

@famosab famosab May 7, 2026

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yes I needed to adapt the index file handling to get the params out of a sbwf

@famosab famosab changed the title Add tests to local subworkflows Add tests to local subworkflows, improve fai generation May 7, 2026
famosab
famosab commented May 7, 2026
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Comment thread CHANGELOG.md Outdated
@famosab famosab merged commit 891ca2b into dev May 7, 2026
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@famosab famosab deleted the tests branch May 7, 2026 10:51
@pinin4fjords pinin4fjords mentioned this pull request May 7, 2026
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@mashehu mashehu mashehu approved these changes

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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@famosab @mashehu