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ms2rescore for quant workflow and fixed some bugs #378

Merged
merged 8 commits into from
Jun 17, 2024
Merged

ms2rescore for quant workflow and fixed some bugs #378

merged 8 commits into from
Jun 17, 2024

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daichengxin
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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 (nf-test test main.nf.test -profile test,docker).
  • 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).

@daichengxin daichengxin changed the title Dev ms2rescore for quant workflow and fixed some bugs Jun 15, 2024
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github-actions bot commented Jun 15, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4111c36

+| ✅ 292 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-15 16:48:32

@ypriverol ypriverol self-requested a review June 17, 2024 08:09
timosachsenberg
timosachsenberg approved these changes Jun 17, 2024
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subworkflows/local/dda_id.nf
}
}
} else {
position = file(file_name).name.lastIndexOf('_sage_ms2rescore.idXML')
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why does sage not have the _feat extension like comet and msgf?

@ypriverol ypriverol merged commit 274d082 into bigbio:dev Jun 17, 2024
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@jpfeuffer jpfeuffer jpfeuffer left review comments

@ypriverol ypriverol ypriverol approved these changes

@timosachsenberg timosachsenberg timosachsenberg approved these changes

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@daichengxin @ypriverol @timosachsenberg @jpfeuffer