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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

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

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

NFCORE_RNASEQ takes values from global scope

Status: Open.

#1339 In nf-core/rnaseq;

· adamrtalbot opened on Jul 9, 2024

Stubs all the way down

enhancement

Status: Open.

#1338 In nf-core/rnaseq;

· maxulysse opened on Jul 9, 2024

Salmon --keepDuplicates by default

enhancement

Status: Open.

#1259 In nf-core/rnaseq;

· adamrtalbot opened on Mar 12, 2024

·  

3.23.0

BBPSPLIT fails cryptically with user errors

bugSomething isn't workingSomething isn't working

Status: Open.

#1130 In nf-core/rnaseq;

· pinin4fjords opened on Nov 22, 2023