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Add optional global FDR functionality #339

Merged
merged 8 commits into from
Nov 26, 2024
Merged

Add optional global FDR functionality #339

merged 8 commits into from
Nov 26, 2024

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jonasscheid
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@jonasscheid jonasscheid commented Nov 25, 2024 •
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Closing #331

This PR implements the option to compute the global FDR of all runs specified in the input samplesheet and backfilters the sample_condition specific output files based on the global q-value. This feature is specifically relevant for controlling the FDR of large-scale datasets.

Global FDR:
Screenshot 2024-11-25 at 11 07 51

Local FDR:
Screenshot 2024-11-25 at 11 08 11

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/mhcquant 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 Nov 25, 2024 •
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nf-core pipelines lint overall result: Passed ✅

Posted for pipeline commit 2c36477

+| ✅ 256 tests passed       |+
#| ❔   1 tests were ignored |#

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-25 14:44:04

mapo9
mapo9 approved these changes Nov 26, 2024
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lgtm!

@jonasscheid jonasscheid merged commit 07cdcbb into nf-core:dev Nov 26, 2024
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@mapo9 mapo9 mapo9 approved these changes

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@jonasscheid @mapo9