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matplotlib temp file

bugSomething isn't workingSomething isn't working

Status: Open.

#305 In nf-core/cutandrun;

· sunta3iouxos opened on Dec 4, 2025

duplicates are always removed

bugSomething isn't workingSomething isn't working

Status: Open.

#304 In nf-core/cutandrun;

· sunta3iouxos opened on Nov 27, 2025

Pipeline failure if a sample has zero alignments

bugSomething isn't workingSomething isn't working

pipeline_error

Status: Open.

#303 In nf-core/cutandrun;

· HDash opened on Nov 25, 2025

test run TRIMGALORE error

bugSomething isn't workingSomething isn't working

Status: Open.

#301 In nf-core/cutandrun;

· JakobHofvander opened on Oct 23, 2025

TODO list for 3.3.0 release

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#300 In nf-core/cutandrun;

· maxulysse opened on Oct 21, 2025

·  

3.3.0

Consesus peaks

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#298 In nf-core/cutandrun;

· sunta3iouxos opened on Oct 10, 2025

cutandrun pipeline reflects density across individual reads rather than read pairs (?)

bugSomething isn't workingSomething isn't working

Status: Open.

#297 In nf-core/cutandrun;

· fansalon opened on Oct 1, 2025

NFCORE_CUTANDRUN:CUTANDRUN:FILTER_READS:SAMTOOLS_VIEW

bugSomething isn't workingSomething isn't working

Status: Open.

#295 In nf-core/cutandrun;

· kartikeyasingh1 opened on Aug 28, 2025

<code>find_unique_reads.py</code> keeps lower-scoring duplicates instead of highest MAPQ

bugSomething isn't workingSomething isn't working

Status: Open.

#293 In nf-core/cutandrun;

· HDash opened on Aug 22, 2025

Discrepancy between MACS2 and SEACR-called peaks

bugSomething isn't workingSomething isn't working

Status: Open.

#292 In nf-core/cutandrun;

· mdozmorov opened on Aug 12, 2025

Why is there no FRiP score section in my MultiQC report?

bugSomething isn't workingSomething isn't working

Status: Open.

#291 In nf-core/cutandrun;

· RnapolyMerase1212 opened on Aug 10, 2025

Accept gzipped custom genomes via --gtf and --fasta

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#286 In nf-core/cutandrun;

· smoe opened on May 19, 2025