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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

Refactor local modules to the current nf-core standard

Status: Open.

#492 In nf-core/chipseq;

· JoseEspinosa opened on Mar 19, 2026

Change CUSTOM_GETCHROMSIZES to SAMTOOLS_FAIDX

Status: Open.

Enhancement

#489 In nf-core/chipseq;

· Kevin-Brockers opened on Mar 13, 2026

Port local modules / subworkflows where possible to nf-core

enhancement

Status: Open.

#486 In nf-core/chipseq;

· Kevin-Brockers opened on Mar 11, 2026

strict syntax - language update

enhancement

Status: Open.

#485 In nf-core/chipseq;

· Kevin-Brockers opened on Mar 11, 2026

Update subworkflows and modules

enhancement

Status: Open.

#484 In nf-core/chipseq;

· Kevin-Brockers opened on Mar 11, 2026

Update pipelines to use topic channels

enhancement

Status: Open.

#483 In nf-core/chipseq;

· Kevin-Brockers opened on Mar 11, 2026

Clarify documentation for antibody

bugSomething isn't workingSomething isn't working

Status: Open.

#479 In nf-core/chipseq;

· adthrasher opened on Nov 4, 2025

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

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

Change bigWig creating to use --bga option

bugSomething isn't workingSomething isn't working

Status: Open.

#468 In nf-core/chipseq;

· FelixKrueger opened on Jun 24, 2025

File name collision when using 1-treatment replicate vs. >1-control replicates, i.e. cannot specify the same sample,replicate pair for each different control replicate

bugSomething isn't workingSomething isn't working

Status: Open.

#467 In nf-core/chipseq;

· a1ultima opened on Jun 16, 2025