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Fix logic to accept singplex flex libraries in cellranger_multi#10922

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delfiterradas wants to merge 5 commits intonf-core:masterfrom
delfiterradas:cellranger_multi
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Fix logic to accept singplex flex libraries in cellranger_multi#10922
delfiterradas wants to merge 5 commits intonf-core:masterfrom
delfiterradas:cellranger_multi

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@delfiterradas
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PR checklist

Closes nf-core/scrnaseq#529
In reference to #9652

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Broadcast software version numbers to topic: versions - See version_topics
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@delfiterradas delfiterradas self-assigned this Mar 16, 2026
@delfiterradas delfiterradas marked this pull request as ready for review March 16, 2026 18:10
@delfiterradas delfiterradas requested a review from fmalmeida March 16, 2026 18:11
@fmalmeida
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Hi @delfiterradas , many thanks for opening this PR.

@grst , I discussed yesterday with Delfina regarding this change, and I personally think it is the best.

As we keep the normal behaviour but, still give the ability to force the singleplex.

When the first edition was made regarding singleplex, I had commented something in these lines.

What do you think of it?

@delfiterradas delfiterradas requested a review from fmalmeida March 17, 2026 13:41
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CELLRANGER_MKVDJREF and CELLRANGER_MULTI failing in the tests

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