nf-core/cageseq

CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.

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10 open issues indexed

Issue with STAR version that produced segmentation faults. Open

bug

Difficulty 1/5 Under an hour Newbie friendliness 68/100

nf-core/cageseq#111 · 1 reaction · Opened Jul 10, 2026
update param names to nf-core style Open

enhancement

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

nf-core/cageseq#108 · Opened May 12, 2026
input modularities Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 52/100

nf-core/cageseq#104 · Opened Apr 9, 2026
2.0.0 Documentation Open

bug

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

nf-core/cageseq#99 · Opened Mar 19, 2026
Check if we can use nf-schema also for folder input Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 20/100

nf-core/cageseq#97 · Opened Mar 19, 2026
Remove test(_)data directories from repo Open

bug enhancement

nf-core/cageseq#96 · 1 comment · 1 assignee · Opened Mar 19, 2026
Migrate local modules to nf-core template Open

bug

nf-core/cageseq#95 · 2 assignees · Opened Mar 19, 2026
Add nf-test snapshots for the whole pipeline Open

bug

nf-core/cageseq#94 · 1 assignee · Opened Mar 19, 2026
Check dependencies in rmarkdown container Open

nf-core/cageseq#92 · 1 assignee · Opened Mar 19, 2026
Check dependencies in cageR biocontainer Open

nf-core/cageseq#91 · 1 assignee · Opened Mar 19, 2026

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