Issues

• First class support for zarr input and output

  enhancement
  nf-core/scdownstream#285 · Filter by author Zethson opened on May 13, 2026
  2

• Accelerate scverse/scanpy steps with rapids-singlecell

  enhancement
  nf-core/scdownstream#283 · Filter by author Zethson opened on May 7, 2026
  4

  

• Switch to topics for fragments

  enhancement
  nf-core/scdownstream#275 · Filter by author nictru opened on Apr 2, 2026

• Reduce containers overhead

  enhancement
  nf-core/scdownstream#267 · Filter by author kim-fehl opened on Mar 14, 2026
  2

  

• Add support for local/custom celltypist models

  enhancement
  nf-core/scdownstream#213 · Filter by author nictru opened on Aug 9, 2025

• Implement gene annotation

  enhancementNBIS
  nf-core/scdownstream#173 · Filter by author nictru opened on May 18, 2025

• Implement batch effect quantification

  enhancementNBIS
  nf-core/scdownstream#172 · Filter by author nictru opened on May 18, 2025

• Implement sample sex prediction

  enhancementNBIS
  nf-core/scdownstream#171 · Filter by author nictru opened on May 18, 2025
  11

  

• Add flag to prevent writing of intermediate anndata objects to the working directory

  enhancement
  nf-core/scdownstream#151 · Filter by author nictru opened on Apr 7, 2025

• Remove duplicate execution of Cellbender

  enhancement
  nf-core/scdownstream#147 · Filter by author milos7250 opened on Apr 1, 2025

• Implement gene regulatory network analyses

  enhancement
  nf-core/scdownstream#119 · Filter by author nictru opened on Oct 27, 2024
  1