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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

Saved input bams for MACS2?

Status: Open.

#285 In nf-core/cutandrun;

· bhanco opened on May 6, 2025

multiqc and dumpsoftwareversions not resumed

bugSomething isn't workingSomething isn't working

Status: Open.

#283 In nf-core/cutandrun;

· mirpedrol opened on Apr 14, 2025

Unexpected Inclusion of Bisulfite_Genome/ Files in Bowtie2 Alignment Step

bugSomething isn't workingSomething isn't working

Status: Open.

#282 In nf-core/cutandrun;

· edogiuili opened on Apr 1, 2025

JSON schema: Cutandrun

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Open.

#280 In nf-core/cutandrun;

· jen-reeve opened on Mar 25, 2025

Could you please share the SVG file of the worflow subway diagram?

Status: Open.

#278 In nf-core/cutandrun;

· yinshiyi opened on Mar 13, 2025

implementation of fastp and implementation of extra trim arguments

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#277 In nf-core/cutandrun;

· sunta3iouxos opened on Mar 11, 2025

Strange error

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#275 In nf-core/cutandrun;

· stela2502 opened on Feb 26, 2025