nf-core / nf-core/sopa

Accelerate scverse/scanpy steps with rapids-singlecell

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#24 2 comments 0 reactions 1 assignee View on GitHub

@Zethson is already working on this.

Since May 7, 2026.

enhancement
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Description

Description of feature
Description of feature

Heyy,

the pipeline currently uses scanpy for several steps - mostly for UMAP calculation and Leiden clustering.
I suggest that we integrate github.com/scverse/rapids-singlecell to optionally GPU accelerate these steps as soon as I've added a nf-core module for it.

Any thoughts, concerns, or helpful pointers?

CC @gburnett-nvidia @DCGenomics

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