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nextflow inspect is not working with 4.1.0 nextflow.config

bugSomething isn't workingSomething isn't working

Status: Open.

#506 In nf-core/scrnaseq;

· kchaung-lilly opened on Nov 12, 2025

Version 4.1.0 fails on AWS

bugSomething isn't workingSomething isn't working

Status: Open.

#503 In nf-core/scrnaseq;

· KallyopeComp opened on Oct 31, 2025

GPU support with docker execution

Status: Open.

#498 In nf-core/scrnaseq;

· ycaniouora opened on Oct 23, 2025

Clarity on support for smart-seq3 data

enhancementNew feature or requestNew feature or request

Status: Open.

#497 In nf-core/scrnaseq;

· campbell-watchmaker opened on Oct 17, 2025

Bug: Typo in cellranger_multi script prevents CRISPR library processing

bugSomething isn't workingSomething isn't working

Status: Open.

#494 In nf-core/scrnaseq;

· enricocannavo opened on Sep 25, 2025

Support additional simpleaf chemistries and orientations

enhancementNew feature or requestNew feature or request

Status: Open.

#493 In nf-core/scrnaseq;

· jeremymsimon opened on Sep 24, 2025

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