×

nf-core/macs2/callpeak @ 0.0.0-0c7146d

Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments

alignment atac-seq chip-seq peak-calling
Latest version: 0.0.0-0c7146d
Total downloads: 1
Source: nf-core/modules
Authors: @ntoda03 @JoseEspinosa @jianhong
Maintainers: @ntoda03 @JoseEspinosa @jianhong

Summary

Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments

Get started

Add the following snippet to your workflow script to include this module.

include { MACS2_CALLPEAK } from 'nf-core/macs2/callpeak'

License

MIT License

Process
Name MACS2_CALLPEAK
Input 2 channels
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
ipbam file

The ChIP-seq treatment file
controlbam file

The control file
macs2_gsize string

Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8)
Output 6 channels
#1 bdg tuple
meta file

BED file containing annotated peaks

 *.gappedPeak,*.narrowPeak}
*.bdg file

Optional bedGraph files for input and treatment input samples

 *.bdg
#2 bed tuple
meta file

BED file containing annotated peaks

 *.gappedPeak,*.narrowPeak}
*.bed file

Optional BED file containing peak summits locations for every peak

 *.bed
#3 xls tuple
meta file

BED file containing annotated peaks

 *.gappedPeak,*.narrowPeak}
*.xls file

xls file containing annotated peaks

 *.xls
#4 peak tuple
meta file

BED file containing annotated peaks

 *.gappedPeak,*.narrowPeak}
*.{narrowPeak,broadPeak} file

BED file containing annotated peaks

 *.gappedPeak,*.narrowPeak}
#5 gapped tuple
meta file

BED file containing annotated peaks

 *.gappedPeak,*.narrowPeak}
*.gappedPeak file

Optional BED file containing gapped peak

 *.gappedPeak
#6 versions
versions.yml file

File containing software version

 versions.yml
Tool Description Homepage
macs2 Model Based Analysis for ChIP-Seq data n/a
Version 0.0.0-0c7146d
Commit ID 135d883a43b1a2324b4112cd270cf22e20835533
Release Date 08 Apr 2026 18:52:51 (UTC)
Download URL https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fmacs2%2Fcallpeak/0.0.0-0c7146d/download
OCI Store URL https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/macs2/callpeak/blobs/sha256:208014a37107e24330809ef38105d45ca6b17f0bf06345b03b19a5fc13f48269
Size 3.5 KB
Checksum sha256:208014a37107e24330809ef38105d45ca6b17f0bf06345b03b19a5fc13f48269
Downloads 1
Version Date Status Downloads Size Diff
0.0.0-0c7146d 08 Apr 2026 18:52:51 (UTC) 1 3.5 KB -