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first PR about identification subworkflow #351

Merged
merged 22 commits into from
Mar 24, 2024
Merged

first PR about identification subworkflow #351

merged 22 commits into from
Mar 24, 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 (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • 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).

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github-actions bot commented Feb 1, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0b9c5ab

+| ✅ 277 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-02 09:36:49

@ypriverol ypriverol linked an issue Feb 1, 2024 that may be closed by this pull request
Identification workflow needed. #346
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@daichengxin daichengxin changed the title first PR about identification subworkflow (Don't merge) first PR about identification subworkflow Mar 2, 2024
@ypriverol ypriverol requested a review from jpfeuffer March 2, 2024 13:03
jpfeuffer
jpfeuffer reviewed Mar 2, 2024
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Looks good. Maybe one could have reused/refactored a bit more from the DDA workflow?

I.e. DDA(quant) consists of the main part of DDA_ID plus some quant steps.

ypriverol
ypriverol reviewed Mar 4, 2024
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modules/local/extract_psm/main.nf
tuple val(meta), path(idxml_file), path(spectrum_df)

output:
path "*_psm.csv", emit: psm_info
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@daichengxin would be good I think to continue following the previous stategy of quantms and export to a proper standard file format. Could we export here also to mzIdentML? @jpfeuffer Is that possible, or have another step that export the results to mzIdentml.

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I would do it in the same step. Especially if this step is specific to identification-only anyway.
I am not a big fan of mzIdentML. Why not the PSM section only as parquet of quantms.io?

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I was going to export PSM to parquet format in this step, but didn't have the right package/container for it.

@daichengxin daichengxin merged commit 0c87e02 into bigbio:dev Mar 24, 2024
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@daichengxin daichengxin mentioned this pull request Mar 24, 2024
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Identification workflow needed.
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@daichengxin @ypriverol @jpfeuffer @nf-core-bot