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Enable all genes for exploratory #188

Merged
merged 10 commits into from
Nov 13, 2023
Merged

Enable all genes for exploratory #188

merged 10 commits into from
Nov 13, 2023

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WackerO
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@WackerO WackerO commented Nov 8, 2023 •
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This PR allows users to choose all genes for the explanatory analysis (by setting the param to -1), as done in the attached example. As this caused problems with a previous version (the --exploratory_n_features param is defined as int, but old nextflow validations interpret -1 as string), I also had to bump the nextflow min version.

SRP254919_allgenes.html.zip

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 Nov 8, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 9a11027

+| ✅ 160 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-13 12:49:19

pinin4fjords
pinin4fjords requested changes Nov 9, 2023
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Looking good, but update the CHANGELOG, and add documentation to the schema to explain the '-1'.

assets/differentialabundance_report.Rmd Outdated Show resolved Hide resolved
pinin4fjords
pinin4fjords approved these changes Nov 9, 2023
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Looks good!

@WackerO WackerO merged commit 8f9a70c into nf-core:dev Nov 13, 2023
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@WackerO WackerO deleted the allgenes branch November 13, 2023 13:54
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@pinin4fjords pinin4fjords pinin4fjords approved these changes

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@WackerO @pinin4fjords