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Ensure Percolator target decoy competition #279

Merged
merged 2 commits into from
Aug 30, 2023
Merged

Ensure Percolator target decoy competition #279

merged 2 commits into from
Aug 30, 2023

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jonasscheid
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@jonasscheid jonasscheid commented Aug 28, 2023 •
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This percolator flag should ensure target decoy competition instead of mix-max method.

Percolator description of post_processing_tdc flag:

Replace the mix-max method by target-decoy competition for assigning q-values and PEPs. If the input PSMs are from separate target and decoy searches, Percolator's SVM scores will be used to eliminate the lower scoring target or decoy PSM(s) of each scan+expMass combination. If the input PSMs are detected to be coming from a concatenated search, this option will be turned on automatically, as this is incompatible with the mix-max method. In case this detection fails, turn this option on explicitly.

Some tests proof that percolator detects the concatenated search, but lets ensure it.

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>).
  • 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 Aug 28, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b79c8a7

+| ✅ 156 tests passed       |+
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 51]
  • system_exit - System.exit in WorkflowMhcquant.groovy: System.exit(1) [line 18]
  • system_exit - System.exit in WorkflowMhcquant.groovy: System.exit(1) [line 45]
  • system_exit - System.exit in WorkflowMhcquant.groovy: System.exit(1) [line 51]

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-28 13:46:30

@jonasscheid jonasscheid merged commit bc326d4 into nf-core:dev Aug 30, 2023
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@steffenlem steffenlem steffenlem approved these changes

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@jonasscheid @steffenlem