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Pipeline silently skips alignment when strandedness inference fails

Status: Open.

#1693 In nf-core/rnaseq;

· pinin4fjords opened on Feb 6, 2026

Investigate --alignMatesGapMax for STAR prokaryotic alignment

Status: Open.

#1691 In nf-core/rnaseq;

· pinin4fjords opened on Feb 5, 2026

offline mode not working in 3.22.2 unless --igenomes_base is set to a dummy path

bugSomething isn't workingSomething isn't working

Status: Open.

#1690 In nf-core/rnaseq;

· JKing2000 opened on Feb 5, 2026

Add GPU accelerated STAR (Parabricks fq2bam module) as option for aligner

enhancement

Status: Open.

#1678 In nf-core/rnaseq;

· gburnett-nvidia opened on Jan 20, 2026

Sylph Performance Improvement

enhancement

Status: Open.

#1670 In nf-core/rnaseq;

· egreenberg7 opened on Dec 19, 2025

Metro map update

Status: Open.

#1668 In nf-core/rnaseq;

· maxulysse opened on Dec 19, 2025

Improvements for processing prokaryotic datasets using the nf-core/rnaseq pipeline

enhancement

Status: Open.

#1512 In nf-core/rnaseq;

· sebschulz1 opened on Mar 12, 2025

Update StringTie to latest version

enhancement

Status: Open.

#1506 In nf-core/rnaseq;

· rrdavis77 opened on Feb 14, 2025

ERROR Not able to pull image of ('biocontainers/bioconductor-tximeta:1.20.1--r43hdfd78af_0')

awaiting-response-community

bugSomething isn't workingSomething isn't working

Status: Open.

#1457 In nf-core/rnaseq;

· ilariarossoni opened on Nov 26, 2024

Remove need for use of Seqera conda channels

enhancement

Status: Open.

#1431 In nf-core/rnaseq;

· pinin4fjords opened on Oct 23, 2024

3.16.x does not allow numeric sample ids

bugSomething isn't workingSomething isn't working

Status: Open.

#1419 In nf-core/rnaseq;

· idot opened on Oct 17, 2024

SortMeRNA database version

enhancement

Status: Open.

#1354 In nf-core/rnaseq;

· wzheng0520 opened on Aug 16, 2024

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3.23.0