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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 <code>--bga</code> 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. &gt;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

ERROR ~ Error executing process &gt; 'NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)'

bugSomething isn't workingSomething isn't working

Status: Open.

#466 In nf-core/chipseq;

· tbooth opened on Jun 5, 2025

ERROR ~ Error executing process &gt; 'NFCORE_CHIPSEQ:CHIPSEQ:DEEPTOOLS_COMPUTEMATRIX (SPT5_T15_REP1)'

bugSomething isn't workingSomething isn't working

Status: Open.

#465 In nf-core/chipseq;

· tbooth opened on Jun 5, 2025

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

JSON schema: Chipseq

docsDocumentationDocumentation

Status: Open.

#458 In nf-core/chipseq;

· jen-reeve opened on Mar 25, 2025

Call peak without chip-seq input control.

enhancement

Status: Open.

#457 In nf-core/chipseq;

· ljw20180420 opened on Mar 21, 2025

Make skip_preseq the default option

enhancement

Status: Open.

#456 In nf-core/chipseq;

· JoseEspinosa opened on Mar 13, 2025

 ·  

2.2

Make skip_preseq the default option

enhancement

Status: Open.

#455 In nf-core/chipseq;

· JoseEspinosa opened on Mar 13, 2025

Enable the use of CSI bam index

enhancement

Status: Open.

#454 In nf-core/chipseq;

· JoseEspinosa opened on Mar 12, 2025

 ·  

2.2

Can we do chip seq analysis using nextflow without input sample?

enhancement

Status: Open.

#452 In nf-core/chipseq;

· autumnfe79 opened on Mar 6, 2025