nf-core / nf-core/scdownstream
Accelerate scverse/scanpy steps with rapids-singlecell
@Zethson is already working on this.
Since May 7, 2026.
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Description
Description of feature
Heyy,
the pipeline currently uses scanpy for several steps and might also use other scverse tools like decoupler or pertpy in the future for some steps like gene set enrichment or sample comparisons.
I suggest that we integrate github.com/scverse/rapids-singlecell to optionally GPU accelerate these steps. I saw that some GPU infrastructure already exists for scvi-tools related steps that I'm hoping to reuse. There's no RSC module yet so I'd start with that and then start integrating it into the pipeline.
Any thoughts, concerns, or helpful pointers?
CC @gburnett-nvidia @DCGenomics
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