nf-core / nf-core/scdownstream

Accelerate scverse/scanpy steps with rapids-singlecell

Open
#283 4 comments 0 reactions 1 assignee View on GitHub

@Zethson is already working on this.

Since May 7, 2026.

enhancement
Dominant language
Nextflow
Stars
115
Forks
66
Avg merge
11d 6h
Merged PRs (30d)
4

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

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.