nf-core/rnafusion

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RNA-seq analysis pipeline for detection of gene-fusions

Stars: 174
Forks: 125
Open beginner issues: 0
Indexed issues: 24
Avg merge: 1h 17m
Merged PRs (30d): 1

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: good first issue

Beginner friendly Everything

Open All

24 open issues indexed

Error downloading fusion_report Reference Open

bug

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

nf-core/rnafusion#828 · Opened Sep 17, 2026
FusionGDB2 error inside FusionReport reference building Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 42/100

nf-core/rnafusion#823 · 2 comments · Opened Jul 6, 2026
Malformed STAR --outSAMattrRGline due to incorrect whitespace in PL tag Open

bug

Difficulty 1/5 Under an hour Newbie friendliness 82/100

nf-core/rnafusion#822 · Opened Jun 26, 2026
Update `bam_stringtie_merge` with latest fixes from nf-core Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 55/100

nf-core/rnafusion#799 · Opened Apr 16, 2026
Handling samples split over multiple lanes Open

feature-request

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/rnafusion#798 · 1 comment · Opened Apr 14, 2026
Transcript annotations in VCF are lost when data isn't found by FusionInspector Open

bug

Difficulty 5/5 Over a week Newbie friendliness 18/100

nf-core/rnafusion#787 · Opened Jan 19, 2026
Single-end analysis not working Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

nf-core/rnafusion#785 · 2 comments · Opened Dec 30, 2025
create index on "markduplicates" output BAM Open

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

nf-core/rnafusion#784 · 1 comment · Opened Dec 30, 2025
When running a BAM input, ARRIBA_VISUALISATION and FUSIONINSPECTOR modules do not run Open

bug

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

nf-core/rnafusion#780 · 3 comments · 1 reaction · Opened Nov 17, 2025
Process `RNAFUSION:FASTQ_ALIGN_STAR:STAR_ALIGN (test)` terminated with an error exit status (137) Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/rnafusion#777 · 1 comment · Opened Oct 21, 2025
Question about fastp trimming Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/rnafusion#776 · 1 comment · Opened Oct 20, 2025
When using --genomes_base the function exists_not_empty does not work properly Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/rnafusion#774 · Opened Oct 10, 2025
`FUSIONCATCHER` fails with out of memory error Open

bug

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

nf-core/rnafusion#773 · Opened Sep 24, 2025
Reintegrate `QC_WORKFLOW` subworkflow into pipeline after migration to nf-core/subworkflows Open

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

nf-core/rnafusion#755 · Opened Aug 26, 2025
Reintegrate `FUSIONINSPECTOR` subworkflow into pipeline after migration to `nf-core/subworkflows` Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/rnafusion#754 · Opened Aug 26, 2025
Replace `GENCODE_DOWNLOAD` for nf-core `WGET` Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

nf-core/rnafusion#739 · Opened Aug 8, 2025
ctatsplicing reference building triggering Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 25/100

nf-core/rnafusion#704 · Opened Jul 10, 2025
Replace `HGNC_HGNC` module with nf-core `WGET` module Open

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

nf-core/rnafusion#700 · 1 comment · Opened Jul 4, 2025
Gencode release 48 Open

feature-request

Difficulty 2/5 1-3 hours Newbie friendliness 42/100

nf-core/rnafusion#690 · 1 comment · Opened Jul 2, 2025
CTATSPLICING module fails due to lack of clear support for CancerSplicingLib indexing inside container Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/rnafusion#681 · 2 comments · Opened Jun 18, 2025
Create nf-test for STARFUSION_DETECT using a junction file as input Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/rnafusion#593 · Opened Dec 19, 2024
Move local modules to nf-core/modules Open

nf-core/rnafusion#575 · 2 comments · 2 assignees · Opened Dec 6, 2024
Feed fusions separately to fusioninspector Open

feature-request

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

nf-core/rnafusion#517 · Opened Nov 13, 2024
Allow for spike-ins Open

good first issue

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

nf-core/rnafusion#369 · Opened Jun 22, 2023

nf-core/rnafusion

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