Issues

• CELLBENDER_REMOVEBACKGROUND incompatibility on NVIDIA Hopper/Blackwell GPUs (+ working solution for v4.2.0)

  bugWIP
  Bug

  nf-core/scrnaseq#592 · Filter by author jaredfischbach opened on Oct 3, 2026
  

• ANNDATAR_CONVERT silently loses features containing underscores from the output Seurat RDS

  bug
  nf-core/scrnaseq#591 · Filter by author BenjaminATaylor opened on Oct 2, 2026

• Migrate mtx_to_h5ad module to nf-core

  nf-core/scrnaseq#589 · Filter by author delfiterradas opened on Sep 30, 2026
  

• Modify star_starsolo nf-core module to take GTF input file

  nf-core/scrnaseq#588 · Filter by author delfiterradas opened on Sep 30, 2026
  

• cellranger_multi.py filename checks raise assertion on valid filenames containing "R1"

  bug
  nf-core/scrnaseq#582 · Filter by author nathanweeks opened on Sep 18, 2026
  2

• aws credentials

  bug
  nf-core/scrnaseq#580 · Filter by author mvheetve opened on Sep 17, 2026

• cellrangerarc: CELLRANGERARC_MKGTF output breaks CELLRANGERARC_MKREF on Ensembl 110 GTFs

  bug
  nf-core/scrnaseq#578 · Filter by author sminot opened on Sep 6, 2026

• cellrangerarc: --cellranger_index fails with "Path value cannot be null"

  bug
  nf-core/scrnaseq#576 · Filter by author sminot opened on Sep 6, 2026
  1

  

• Naming issue when creating new reference genome with cellranger-arc

  bug
  nf-core/scrnaseq#574 · Filter by author meisterpeter opened on Aug 11, 2026

• Issue with creating config files for cellranger multi

  bugcellranger-multi
  nf-core/scrnaseq#567 · Filter by author esamorodnitsky opened on Jul 15, 2026
  1

• Add inDrops support

  enhancement
  nf-core/scrnaseq#549 · Filter by author nictru opened on May 26, 2026

• igenomes file loading does not overwite null param values

  bug
  nf-core/scrnaseq#547 · Filter by author tgelafr-pfzr opened on May 21, 2026
  2

  

• --cellranger_index expects a file and not a directory, despite what the documentation says

  bug
  nf-core/scrnaseq#538 · Filter by author dtatarak opened on Mar 19, 2026

• Support for 3-file FASTQ inputs from SRA downloads

  enhancement
  Enhancement

  nf-core/scrnaseq#531 · Filter by author emrunali opened on Mar 12, 2026
  5

  

• CELLRANGER_MKVDJREF and CELLRANGER_MULTI failing in the tests

  bug
  nf-core/scrnaseq#529 · Filter by author delfiterradas opened on Mar 11, 2026
  7

  

• cell type annotation

  enhancement
  nf-core/scrnaseq#528 · Filter by author simroka opened on Mar 10, 2026
  2

• BD Rhapsody support?

  enhancement
  nf-core/scrnaseq#527 · Filter by author simroka opened on Mar 10, 2026
  3

  

• Add cellranger aggr

  cellrangerenhancement
  nf-core/scrnaseq#526 · Filter by author simroka opened on Mar 10, 2026
  

• Add velocyto for cellranger output

  cellrangercellranger-multienhancement
  Enhancement

  nf-core/scrnaseq#525 · Filter by author simroka opened on Mar 10, 2026
  

• simpleaf quant Error in checkAlevinFryInputFiles(mapDir = mapDir, permitDir = permitDir, :

  bug
  nf-core/scrnaseq#518 · Filter by author Manonboo089 opened on Jan 22, 2026
  1

• Support additional simpleaf chemistries and orientations

  enhancement
  nf-core/scrnaseq#493 · Filter by author jeremymsimon opened on Sep 24, 2025
  3

• Kallisto index should take into account the "workflow" option

  bug
  nf-core/scrnaseq#491 · Filter by author grst opened on Aug 20, 2025

• Parameter validation

  quality & consistency
  nf-core/scrnaseq#490 · Filter by author grst opened on Aug 20, 2025

• Add include_introns flag for cellranger count

  enhancement
  Enhancement

  nf-core/scrnaseq#475 · Filter by author RoganGrant opened on Jul 10, 2025
  5

  

• Support for both TCR and BCR (VDJ-T and VDJ-B) inputs

  enhancement
  nf-core/scrnaseq#473 · Filter by author Zhenghongc opened on Jul 6, 2025
  4