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Change simpleaf protocol name from 10xv4 to 10xv4-3p #452

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@milos7250 milos7250 commented Mar 21, 2025

At this moment, running the pipeline on samples with 10XV4 protocol and simpleaf aligner fails. As can be seen in the list of supported chemistries in simpleaf, the chemistry 10xv4 does not exist, they only have 10xv4-3p available. This issue was not flagged in tests, as the test dataset is only using 10xv2 protocol.

This PR only changes the protocol name for this particular chemistry, but perhaps the whole list should be changed to more closely follow the list of available chemistries of simpleaf?

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 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>).
  • 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).

@milos7250 milos7250 self-assigned this Mar 21, 2025
@milos7250 milos7250 added the bug Something isn't working label Mar 21, 2025
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