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Contrasts schema validation #410

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Contrasts schema validation #410

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nschcolnicov
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To close #405 once the issue in the schema plugin is sorted out

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/differentialabundance 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>).
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  • Output Documentation in docs/output.md is updated.
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Dec 20, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 65eb7e4

+| ✅ 300 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-12-20 13:10:07

grst
grst reviewed Jan 9, 2025
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workflows/differentialabundance.nf
Comment on lines +202 to +213
} else if (params.contrasts.endsWith(".csv")) {
//csv contrasts file processing
ch_contrast_variables = ch_contrasts_file
.splitCsv(header:true, sep:(params.contrasts.endsWith('csv') ? ',' : '\t'))
.map{ it.tail().first() }
.map{
tuple('id': it.variable)
}
.unique()
}

ch_contrast_variables.dump(tag:"ch_contrasts_variables")
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I think we should just get rid of the csv sheet right away. As we support more complex contrasts, csv won't be useful anymore and this is anyway why we decided to move towards yaml.

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@nschcolnicov @nf-core-bot @grst