Search results

Kallisto index should take into account the "workflow" option

Status: Open.

#491 In nf-core/scrnaseq;

· grst opened on Aug 20, 2025

Parameter validation

quality & consistencyimprove quality and reduce maintenance burdenimprove quality and reduce maintenance burden

Status: Open.

#490 In nf-core/scrnaseq;

· grst opened on Aug 20, 2025

Cannot run cellranger multi with only CRISPR libraries

bugSomething isn't workingSomething isn't working

Status: Open.

#480 In nf-core/scrnaseq;

· dtatarak opened on Jul 22, 2025

GPU profile does not work, CUDA not available

bugSomething isn't workingSomething isn't working

Status: Open.

#476 In nf-core/scrnaseq;

· stevekm opened on Jul 16, 2025

Add include_introns flag for cellranger count

enhancementNew feature or requestNew feature or request

Status: Open.

Enhancement

#475 In nf-core/scrnaseq;

· RoganGrant opened on Jul 10, 2025

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

enhancementNew feature or requestNew feature or request

Status: Open.

#473 In nf-core/scrnaseq;

· Zhenghongc opened on Jul 6, 2025

Make container for ANNDATAR_CONVERT.nf have packages preinstalled on it

bugSomething isn't workingSomething isn't working

Status: Open.

Bug

#470 In nf-core/scrnaseq;

· tzvi909 opened on May 31, 2025

Missing feature types when converting mtx matrix to h5ad

bugSomething isn't workingSomething isn't working

Status: Open.

#468 In nf-core/scrnaseq;

· saraterzo opened on May 9, 2025

Replace custom gtf filter code with nf-core module

quality & consistencyimprove quality and reduce maintenance burdenimprove quality and reduce maintenance burden

Status: Open.

#465 In nf-core/scrnaseq;

· grst opened on Apr 24, 2025

Error running cellrangerarc workflow with 10x Multiome data

bugSomething isn't workingSomething isn't working

Status: Open.

#463 In nf-core/scrnaseq;

· maggiebr0wn opened on Apr 23, 2025

Inquiry about Parameters for snRNA-seq Analysis

Status: Open.

#462 In nf-core/scrnaseq;

· Yaxiong293 opened on Mar 31, 2025

Use different json schemas for different aligners

quality & consistencyimprove quality and reduce maintenance burdenimprove quality and reduce maintenance burden

Status: Open.

#461 In nf-core/scrnaseq;

· grst opened on Mar 31, 2025