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409 cellranger multi fails without fb reference even if not needed #410

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409 cellranger multi fails without fb reference even if not needed #410

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@fmalmeida fmalmeida commented Dec 16, 2024 •
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Should fix #409 allowing cellranger multi to run without ab data and without --fb_reference.

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 pipelines 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>).
  • CHANGELOG.md is updated.

@fmalmeida fmalmeida requested a review from grst December 16, 2024 14:19
@fmalmeida fmalmeida self-assigned this Dec 16, 2024
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@fmalmeida fmalmeida linked an issue Dec 16, 2024 that may be closed by this pull request
Cellranger multi fails without --fb_reference even if not needed #409
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit ef2cda4

+| ✅ 214 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   3 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

  • multiqc_config - assets/multiqc_config.yml does not contain a matching 'report_comment'.
    The expected comment is:
    This report has been generated by the <a href="https://github.com/nf-core/scrnaseq/tree/dev" target="_blank">nf-core/scrnaseq</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/scrnaseq/dev/docs/output" target="_blank">documentation</a>.
    The current comment is:
    This report has been generated by the <a href="https://github.com/nf-core/scrnaseq/releases/tag/3.0.0" target="_blank">nf-core/scrnaseq</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/scrnaseq/3.0.0/docs/output" target="_blank">documentation</a>.

❗ 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 ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-12-16 14:21:00

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@grst grst grst approved these changes

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Cellranger multi fails without --fb_reference even if not needed
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@fmalmeida @nf-core-bot @grst