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major refactoring of PLFQ to a probabilistic approach #300

Merged
merged 8 commits into from
Oct 12, 2023
Merged

major refactoring of PLFQ to a probabilistic approach #300

merged 8 commits into from
Oct 12, 2023

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ypriverol
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@ypriverol ypriverol commented Oct 5, 2023 •
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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 Oct 5, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit c1b5874

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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-11 12:59:46

@timosachsenberg
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FYI I added the possibility to also filter by probabilistic score if targeted_only is true. Then only the feature_with_id* parameter is used.

ypriverol and others added 2 commits October 9, 2023 21:56
@ypriverol @jpfeuffer
Update modules/local/openms/proteomicslfq/main.nf
3cbfecb 
Co-authored-by: Julianus Pfeuffer <[email protected]>
@ypriverol
Update filters nextflow.config
c1b5874 
based on comment bigbio#301 (comment) and the corresponding benchamrks I have updated the filters and parameters for LFQ
@ypriverol ypriverol merged commit 982d2e3 into bigbio:dev Oct 12, 2023
13 of 17 checks passed
@ypriverol ypriverol mentioned this pull request Oct 13, 2023
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@ypriverol @timosachsenberg @jpfeuffer