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PICARD: demote process_medium → process_low (byte-identical, ~3× throughput)

enhancement

Status: Open.

#1801 In nf-core/rnaseq;

· peachgabba22 opened on Apr 18, 2026

Per-sample MultiQC in --skip_quantification_merge mode waits for all samples to finish

Status: Open.

#1797 In nf-core/rnaseq;

· pinin4fjords opened on Apr 17, 2026

Reorganise usage docs with a user-centric structure

documentation

Status: Open.

#1737 In nf-core/rnaseq;

· pinin4fjords opened on Feb 27, 2026

Support pre-computed bowtie2 rRNA removal index

enhancement

Status: Open.

#1731 In nf-core/rnaseq;

· pinin4fjords opened on Feb 27, 2026

Refactor empty meta map pattern in main.nf

Status: Open.

#1723 In nf-core/rnaseq;

· pinin4fjords opened on Feb 26, 2026

Split prepare_genome subworkflow into smaller subworkflows

Status: Open.

#1721 In nf-core/rnaseq;

· pinin4fjords opened on Feb 26, 2026

More than 1 reference genome

enhancement

Status: Open.

#1695 In nf-core/rnaseq;

· gfill88 opened on Feb 9, 2026

Investigate --alignMatesGapMax for STAR prokaryotic alignment

Status: Open.

#1691 In nf-core/rnaseq;

· pinin4fjords opened on Feb 5, 2026

Sylph Performance Improvement

enhancement

Status: Open.

#1670 In nf-core/rnaseq;

· egreenberg7 opened on Dec 19, 2025

Update StringTie to latest version

enhancement

Status: Open.

#1506 In nf-core/rnaseq;

· rrdavis77 opened on Feb 14, 2025

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