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Fix issues with R modules changing sample names #1380

Merged
merged 2 commits into from
Sep 13, 2024
Merged

Fix issues with R modules changing sample names #1380

merged 2 commits into from
Sep 13, 2024

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pinin4fjords
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Addresses #1377. Basically R will mangle names with symbols when constructing data frames and the like, unless you explicitly tell it not too, which I am doing here. This was neglected when we factored out and tidied up these modules in the last release.

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/rnaseq 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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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @pinin4fjords,

It looks like this pull-request is has been made against the nf-core/rnaseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/rnaseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@pinin4fjords pinin4fjords changed the base branch from master to dev September 13, 2024 10:32
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github-actions bot commented Sep 13, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 765e67d

+| ✅ 173 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • 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 ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-13 10:38:09

@pinin4fjords pinin4fjords linked an issue Sep 13, 2024 that may be closed by this pull request
Pipeline fails if sample names have hyphens #1377
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@pinin4fjords pinin4fjords merged commit ffb223e into dev Sep 13, 2024
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@pinin4fjords pinin4fjords deleted the fix_tximport_summarizedexperiment branch September 13, 2024 11:30
@pinin4fjords pinin4fjords mentioned this pull request Sep 16, 2024
Merged
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@pinin4fjords pinin4fjords mentioned this pull request Oct 16, 2024
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@maxulysse maxulysse maxulysse approved these changes

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Pipeline fails if sample names have hyphens
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@pinin4fjords @maxulysse