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MACS3 is reporting that 100 paired reads are needed, even when single end data is used as input

bugSomething isn't workingSomething isn't working

Status: Open.

#524 In nf-core/chipseq;

· MingL196 opened on Jul 9, 2026

Update the aligners (bowtie2, bwa, chromap and star) and associated steps processing steps to use topics channel for software versions.

Status: Open.

#522 In nf-core/chipseq;

· Kevin-Brockers opened on Jul 7, 2026

·  

2.2

Change simple fasq_align_{aligner} subworkflows to fastq_align_dna

Status: Open.

#511 In nf-core/chipseq;

· Kevin-Brockers opened on Apr 30, 2026

PICARD_MERGESAMFILES processes stuck indefinitely, no error logs

Status: Open.

#507 In nf-core/chipseq;

· DaiXiaozan opened on Apr 3, 2026

Change remaining nf-core/modules and nf-core/subworkflow to handle versions topic channels

Status: Open.

Enhancement

#506 In nf-core/chipseq;

· Kevin-Brockers opened on Apr 2, 2026

·  

2.2

Switch local/module GTF2BED to nf-core/module BEDOPS_GTF2BED

enhancement

Status: Open.

#494 In nf-core/chipseq;

· Kevin-Brockers opened on Mar 20, 2026

·  

2.3-enhancements

Clarify genome size error and update usage documentation

bugSomething isn't workingSomething isn't working

Status: Open.

#478 In nf-core/chipseq;

· adthrasher opened on Nov 4, 2025

·  

2.2-bug-fixes

Port bedtools_genomecov from local to nf-core module

improve-behaviourOptimise code without adding functionalityOptimise code without adding functionality

Status: Open.

Task

#469 In nf-core/chipseq;

· FloWuenne opened on Jun 24, 2025

·  

2.3-enhancements

Add minimum_alignment_q_score parameter for MAPQ filtering (similar to nf-core/cutandrun)

enhancement

Status: Open.

#463 In nf-core/chipseq;

· wanisajad opened on May 16, 2025

·  

2.3-enhancements

JSON schema: Chipseq

docsDocumentationDocumentation

Status: Open.

#458 In nf-core/chipseq;

· jen-reeve opened on Mar 25, 2025

·  

2.2

Call peak without chip-seq input control.

enhancement

Status: Open.

#457 In nf-core/chipseq;

· ljw20180420 opened on Mar 21, 2025

·  

2.3-enhancements

Enable the use of CSI bam index

enhancement

Status: Open.

#454 In nf-core/chipseq;

· JoseEspinosa opened on Mar 12, 2025

·  

2.3-enhancements