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311 add module gsea #329

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@thomas-tams thomas-tams commented Oct 29, 2024 •
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PR checklist

  • This comment contains a description of changes (with reason).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test_experimental,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

Contribution

Adding the GSEA code from workflows/differentialabundance.nf into subworkflow/enrichment/main.nf.

Adding channel parsing from differentialabundance.nf through EXPERIMENTAL down to ENRICHMENT in order to run the code. Maybe some of this parsing can be done better with fewer args? However this is outside my current knowledge.

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github-actions bot commented Oct 29, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4ade9e2

+| ✅ 317 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • 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!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-29 14:50:22

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@suzannejin suzannejin Awaiting requested review from suzannejin

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@thomas-tams @suzannejin