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Add include_introns flag for cellranger count

enhancementNew feature or requestNew feature or request

Status: Open.

Enhancement

#475 In nf-core/scrnaseq;

·RoganGrant openedon 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 openedon 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 openedon 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 openedon 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 openedon 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 openedon Apr 23, 2025

Inquiry about Parameters for snRNA-seq Analysis

Status: Open.

#462 In nf-core/scrnaseq;

·Yaxiong293 openedon 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 openedon Mar 31, 2025

no exit code for CONCAT_H5AD jobs

bugSomething isn't workingSomething isn't working

Status: Open.

#460 In nf-core/scrnaseq;

·nick-youngblut openedon Mar 29, 2025

Support for 10x v3.1 chemistry

enhancementNew feature or requestNew feature or request

Status: Open.

#457 In nf-core/scrnaseq;

·mossjacob openedon Mar 26, 2025

MultiOmeGEX on GCP=> no space left on device

bugSomething isn't workingSomething isn't working

Status: Open.

#456 In nf-core/scrnaseq;

·nick-youngblut openedon Mar 25, 2025

docs on cellranger_index path

enhancementNew feature or requestNew feature or request

Status: Open.

#455 In nf-core/scrnaseq;

·nick-youngblut openedon Mar 25, 2025