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[FIX/FEATURE] Add exp. wide PSM-FDR. Rename FDR params. Slightly change usage. #187

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merged 4 commits into from
May 20, 2022
Merged

[FIX/FEATURE] Add exp. wide PSM-FDR. Rename FDR params. Slightly change usage. #187

merged 4 commits into from
May 20, 2022

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jpfeuffer
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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/quantms 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 May 20, 2022 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit bc65327

+| ✅ 146 tests passed       |+
#| ❔   3 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-05-20 20:37:30

ypriverol
ypriverol approved these changes May 20, 2022
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conf/test_lfq.config
@@ -32,5 +32,6 @@ params {
enable_qc = true
add_triqler_output = true
protein_level_fdr_cutoff = 1.0
psm_level_fdr_cutoff = 1.0
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@jpfeuffer why this is 1.0 and not 0.01

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To bem backwards compatible in the tests. This has so few peptides that it might fail.

@jpfeuffer jpfeuffer merged commit 15a5379 into bigbio:dev May 20, 2022
@ypriverol ypriverol deleted the fix/FDRusageAndNaming branch March 24, 2023 09:13
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@ypriverol ypriverol ypriverol approved these changes

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@jpfeuffer @ypriverol