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fix probe-set inclusion assertion - #12601

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12600-cellranger-multi-fails-in-scrnaseq-when-running-cmo
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fix probe-set inclusion assertion#12601
fmalmeida wants to merge 4 commits into
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12600-cellranger-multi-fails-in-scrnaseq-when-running-cmo

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@fmalmeida fmalmeida commented Aug 6, 2026

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Resolves #12600

Updating the frna probes-set reference assertion.
It was seen when running the nf-core/scrnaseq pipeline test dataset, that the probe-set was still being included even though data was cmo.

@fmalmeida fmalmeida self-assigned this Aug 6, 2026
@fmalmeida fmalmeida linked an issue Aug 6, 2026 that may be closed by this pull request
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fmalmeida removed the request for review from mahesh-panchal August 6, 2026 08:31
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fmalmeida marked this pull request as draft August 6, 2026 08:32

@mahesh-panchal mahesh-panchal left a comment

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Can you add nf-tests for this change please?

@github-actions github-actions Bot added size/m and removed size/xs labels Aug 6, 2026
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Hi @mahesh-panchal ;
The change should be still checked by the already present Flex test ... where frna should still be using.

But also, added a new test for mimicking the pipeline scenario where we might have multiple references loaded for samples with different library types, and thus, avoid loading the reference for the mutually exclusive types.

Example added is CMO with probeset frna present ... but then, module should not load it in the execution.

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fmalmeida marked this pull request as ready for review August 6, 2026 10:27
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Cellranger Multi fails in scrnaseq when running CMO

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