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Error fix in msgf+ module. #316

Merged
merged 5 commits into from
Oct 27, 2023
Merged

Error fix in msgf+ module. #316

merged 5 commits into from
Oct 27, 2023

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ypriverol
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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).

@ypriverol ypriverol requested a review from daichengxin October 27, 2023 13:40
@ypriverol ypriverol linked an issue Oct 27, 2023 that may be closed by this pull request
While testing the last release of OpenMS found again problem with MSGF+ #315
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github-actions bot commented Oct 27, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 07f115e

+| ✅ 156 tests passed       |+
#| ❔   4 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-27 14:15:41

@jpfeuffer
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But what if you have a non-biocontainer singularity container?

@ypriverol @jpfeuffer
Update modules/local/openms/thirdparty/searchenginemsgf/main.nf
bf520e1 
Co-authored-by: Julianus Pfeuffer <julianus.pfeuffer@pfizer.com>
@ypriverol
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BTW, this needs to be done also for Luciphor2.

@ypriverol ypriverol merged commit 0568535 into bigbio:dev Oct 27, 2023
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@jpfeuffer jpfeuffer jpfeuffer left review comments

@daichengxin daichengxin daichengxin approved these changes

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While testing the last release of OpenMS found again problem with MSGF+
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@ypriverol @jpfeuffer @daichengxin