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nf-core/macs2/callpeak @ 0.0.0-3fc6d40

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

alignment atac-seq chip-seq peak-calling
Latest version: 0.0.0-6c4ed3a
Total downloads: 10
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 0.0.0-3fc6d40
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 22 Apr 2026 15:19:45 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fmacs2%2Fcallpeak/0.0.0-3fc6d40/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/macs2/callpeak/blobs/sha256:74d3eedcda3583eecf3264d772bfc414d409eb3a21d51c889f453c2120b83e7f
Size 3.5 KB
Checksum sha256:74d3eedcda3583eecf3264d772bfc414d409eb3a21d51c889f453c2120b83e7f
Downloads 3
Version Date Status Downloads Size
0.0.0-6c4ed3a 23 Apr 2026 15:28:13 (UTC) 4 3.5 KB
0.0.0-3fc6d40 22 Apr 2026 15:19:45 (UTC)