Fix cellranger multi's singplex flex failure and add tests #9652

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tgelafr-pfzr wants to merge 1 commit into nf-core:master from tgelafr-pfzr:bug/9639-cellrangermulti-fails-singpleplex-flex

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tgelafr-pfzr commented Jan 14, 2026 •

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Closes #9639 (nf-core/scrnaseq#515), and adds a new test that would have captured the bug. Corresponding test dataset here: nf-core/test-datasets#1832

In draft until the test-datasets PR is merged so the CI can pass.

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 necessary, include test data in your PR.
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


          Fix cellranger multi's singplex flex failure and add tests

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tgelafr-pfzr mentioned this pull request

Add new test dataset for singleplex flex nf-core/test-datasets#1832

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tgelafr-pfzr requested a review from nictru

January 14, 2026 18:19

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