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Fix cellrangermulti handling of crispr data #402

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Fix cellrangermulti handling of crispr data #402

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svigneau
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@svigneau svigneau commented Dec 6, 2024 •
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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! --> A test will be submitted through a different PR pending the approval of PR 1415
  • If necessary, also make a PR on the nf-core/scrnaseq branch on the nf-core/test-datasets repository. --> PR 1415
  • Make sure your code lints (nf-core lint). --> Code fixes lint properly. However, the linter reports one preexisting error and multiple preexisting warnings that may need to be addressed separately.
  • 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>).
  • CHANGELOG.md is updated.

The proposed changes are described in issue 401 and intended to fix a bug that prevents handling of CRISPR data when using cellranger multi with gene expression and CRISPR libraries.

The addition of a test dataset with CRISPR data has been requested in PR 1415. A dedicated test for CRISPR data handling by cellranger multi will be submitted in a separate PR once the test dataset is approved.

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github-actions bot commented Dec 6, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 54f52e0

+| ✅ 218 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • 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 3.0.2
  • Run at 2024-12-06 06:26:16

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svigneau commented Dec 6, 2024

The PR has been moved to the nf-core/modules repository (PR 7175) and will be closed in this directory.

@svigneau svigneau closed this Dec 6, 2024
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