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Matrixfilter NA options #244

Merged
merged 3 commits into from
Feb 28, 2024
Merged

Matrixfilter NA options #244

merged 3 commits into from
Feb 28, 2024

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WackerO
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@WackerO WackerO commented Feb 27, 2024 •
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When updating the matrixfilter module with the NA options, I totally forgot to also add them to the pipeline to make them actually callable; sneaking in this small PR to do that now.

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 (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 Feb 27, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9af81ed

+| ✅ 274 tests passed       |+
!| ❗   3 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!

✅ Tests passed:

Run details

  • nf-core/tools version 2.13
  • Run at 2024-02-27 15:07:51

pinin4fjords
pinin4fjords reviewed Feb 27, 2024
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Minor q on the option handling

conf/modules.config Outdated
@@ -463,8 +463,10 @@ process {
"--sample_id_col \"${params.observations_id_col}\"",
"--minimum_samples ${params.filtering_min_samples}",
"--minimum_abundance ${params.filtering_min_abundance}",
"--minimum_proportion_not_na ${params.filtering_min_proportion_not_na}",
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This needs conditional treatment as well, right?

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No, there is a default value for that param in the nextflow.config. If it is provided together with the min sample number, the latter will be used in the module

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What if someone sets the value to null?

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Ah, fair enough!

@WackerO WackerO merged commit 1e52820 into nf-core:dev Feb 28, 2024
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@WackerO WackerO deleted the matrixfilter_na branch February 28, 2024 13:18
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@pinin4fjords pinin4fjords pinin4fjords approved these changes

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@WackerO @pinin4fjords