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Add software versions in nf-test and check column presence in .Rmd #359

Merged
merged 6 commits into from
Nov 19, 2024
Merged

Add software versions in nf-test and check column presence in .Rmd #359

merged 6 commits into from
Nov 19, 2024

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atrigila
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@atrigila atrigila commented Nov 17, 2024 •
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This PR addresses the following:

  • Check for the gene biotype column before plotting in the .Rmd . If the column is missing, plotting is skipped.
  • Remove --changed-since HEAD^ from ci.yml to ensure .Rmd file changes are detected, triggering test re-runs. I noticed that since we moved to nf-tests in other PRs these tests are not running due to this line.
  • Update nf.tests to use removeNextflowVersion("$outputDir/pipeline_info/collated_versions.yml"), now verifying all software versions used in the pipeline.

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!
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • CHANGELOG.md is updated.

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github-actions bot commented Nov 17, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit be51725

+| ✅ 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 2024-11-19 16:31:14

@atrigila atrigila marked this pull request as ready for review November 17, 2024 22:18
pinin4fjords
pinin4fjords requested changes Nov 18, 2024
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Really nice work, thank you, one tiny thing

assets/differentialabundance_report.Rmd Outdated Show resolved Hide resolved
@atrigila atrigila merged commit 7b7536a into nf-core:dev Nov 19, 2024
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@pinin4fjords pinin4fjords pinin4fjords approved these changes

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@atrigila @pinin4fjords