nf-core/rnaseq

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RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Stars: 1.4k
Forks: 897
Open beginner issues: 0
Indexed issues: 17
Avg merge: 5d 7h
Merged PRs (30d): 7

Dominant language: Nextflow
License: MIT
Last GitHub push: Jul 24, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

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17 open issues indexed

Migrate salmon 1.10.3 -> 2.7.0 (Rust rewrite): validation status and remaining work Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/rnaseq#1921 · Opened Sep 16, 2026
Adopt the docker_arm/singularity_arm container-config profile scheme, retire conf/arm.config Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

nf-core/rnaseq#1920 · 1 comment · 1 reaction · Opened Sep 16, 2026
STAR_ALIGN fails with Transcriptome.cpp:18: could not open input file /geneInfo.tab Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nf-core/rnaseq#1897 · 1 comment · Opened Jul 28, 2026
Reorganise usage docs with a user-centric structure Open

documentation

Difficulty 5/5 Over a week Newbie friendliness 35/100

nf-core/rnaseq#1737 · Opened Feb 27, 2026
More than 1 reference genome Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/rnaseq#1695 · 1 comment · 1 reaction · Opened Feb 9, 2026
Sylph Performance Improvement Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/rnaseq#1670 · 1 reaction · Opened Dec 19, 2025
Update StringTie to latest version Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/rnaseq#1506 · 5 comments · 1 reaction · Opened Feb 14, 2025
NFCORE_RNASEQ takes values from global scope Open

Difficulty 2/5 Half a day Newbie friendliness 55/100

nf-core/rnaseq#1339 · Opened Jul 9, 2024
Stubs all the way down Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 15/100

nf-core/rnaseq#1338 · 1 comment · Opened Jul 9, 2024
Salmon --keepDuplicates by default Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/rnaseq#1259 · 2 comments · 1 reaction · Opened Mar 12, 2024
Explicit subsampling step in rnaseq pipeline Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/rnaseq#1097 · 2 comments · 1 reaction · Opened Oct 17, 2023
Turn off quantification flag Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 38/100

nf-core/rnaseq#1089 · 1 comment · Opened Oct 10, 2023
Parameter for using the --save_reference 'genome' directory Open

awaiting-response-developers enhancement needs-testing

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/rnaseq#998 · 4 comments · 2 reactions · Opened Apr 11, 2023
Use mudskipper to project HISAT2 genomic alignment onto transcriptome Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/rnaseq#822 · 3 comments · Opened May 3, 2022
Output CRAM as default Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 38/100

nf-core/rnaseq#758 · 4 comments · 4 reactions · Opened Jan 31, 2022
Add detected genes into summary table of MultiQC report Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/rnaseq#609 · 1 comment · 1 reaction · Opened Apr 26, 2021
Show good / bad examples in documentation Open

documentation

Difficulty 3/5 3-5 days Newbie friendliness 30/100

nf-core/rnaseq#69 · 6 comments · Opened Aug 20, 2018

nf-core/rnaseq

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