Search results

Resource allocations for several tools are excessive

bugSomething isn't workingSomething isn't working

Status: Open.

#310 In nf-core/cutandrun;

· spvensko opened on Apr 15, 2026

Nextflow 25.10.4 fails with Cannot invoke method optional() on null object in TRIMGALORE module (nf-core/cutandrun v3.2.2)

bugSomething isn't workingSomething isn't working

Status: Open.

#309 In nf-core/cutandrun;

· susannbruche opened on Mar 18, 2026

deeptools PCA not transposed

Status: Open.

#308 In nf-core/cutandrun;

· laurie-tonon opened on Mar 3, 2026

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

find_unique_reads.py 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