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Merged in 2.13. #306

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Merged in 2.13. #306

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apeltzer
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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!
  • 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/scrnaseq 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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github-actions bot commented Feb 20, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 572b556

+| ✅ 172 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   5 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

  • schema_params - Default value for param gtf invalid: Not in pipeline parameters. Check nextflow.config.

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • 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!
  • schema_params - Schema param gtf not found from nextflow config

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13
  • Run at 2024-02-20 16:28:42

@apeltzer
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apeltzer commented Mar 1, 2024

Wiping this - its not up2date anymore and superseded by 2.13.1

@apeltzer apeltzer closed this Mar 1, 2024
@apeltzer apeltzer deleted the import-2.13-changes branch March 1, 2024 11:08
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