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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

Add subworkflow-level tests for rRNA removal

enhancement

Status: Open.

#1732 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

polyA imapct on downstrem alaysis particularly alternative splicing

enhancement

Status: Open.

#1729 In nf-core/rnaseq;

· mahsa2001moradi-prog opened on Feb 27, 2026

Migrate local GTF2BED module to nf-core/modules

Status: Open.

#1726 In nf-core/rnaseq;

· pinin4fjords opened on Feb 26, 2026

Refactor empty meta map pattern in main.nf

Status: Open.

#1723 In nf-core/rnaseq;

· pinin4fjords opened on Feb 26, 2026

Revert component-coupled config pattern to pipeline-level configs

Status: Open.

#1722 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

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

Sylph Performance Improvement

enhancement

Status: Open.

#1670 In nf-core/rnaseq;

· egreenberg7 opened on Dec 19, 2025