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311 add module gsea #327

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311 add module gsea #327

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thomas-tams
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@thomas-tams thomas-tams commented Oct 28, 2024 •
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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!
  • Make sure your code lints (nf-core lint).
  • 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>).
  • 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).

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.

@thomas-tams thomas-tams linked an issue Oct 28, 2024 that may be closed by this pull request
add module GSEA #311
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@github-actions GitHub Actions
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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @thomas-tams,

It looks like this pull-request is has been made against the nf-core/differentialabundance master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/differentialabundance dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

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github-actions bot commented Oct 28, 2024 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit b093261

+| ✅ 317 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   5 tests had warnings |!
-| ❌   2 tests failed       |-

❌ Test failures:

❗ 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
  • included_configs - Pipeline config does not include custom configs. Please add the includeConfig line.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-28 15:12:38

@thomas-tams thomas-tams changed the base branch from master to dev-ratio October 28, 2024 17:59
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add module GSEA
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