Nextflow Registry | nf-core/macs3/callpeak@0.0.0-6c4ed3a

nf-core/macs3/callpeak @ 0.0.0-6c4ed3a

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: 8

Source: nf-core/modules

Authors: @JoseEspinosa

Maintainers: @JoseEspinosa @Kevin-Brockers

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

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

include { MACS3_CALLPEAK } from 'nf-core/macs3/callpeak'

MIT License

Process

`Name`	`MACS3_CALLPEAK`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample_1', single_end:false ]`
`ipbam` file	The ChIP-seq treatment file
`controlbam` file	The control file

`macs3_gsize` string	Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2,913,022,398), 'mm' for mouse (2,652,783,500), 'ce' for C. elegans (100,286,401) and 'dm' for fruitfly (142,573,017), Default:hs.

Output 6 channels

#1 bdg tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.bdg` file	Optional bedGraph files for input and treatment input samples `*.bdg`

#2 bed tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.bed` file	Optional BED file containing peak summits locations for every peak `*.bed`

#3 xls tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.xls` file	xls file containing annotated peaks `*.xls`

#4 peak tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.{narrowPeak,broadPeak}` file	BED file containing annotated peaks `.gappedPeak,.narrowPeak}`

#5 gapped tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.gappedPeak` file	Optional BED file containing gapped peak `*.gappedPeak`

#6 versions_macs3 tuple

`${task.process}` string	The name of the process
`macs3` string	The name of the tool
`macs3 --version \| sed -e 's/macs3 //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
macs3	Model Based Analysis for ChIP-Seq data	https://macs3-project.github.io/MACS/

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:28:14 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fmacs3%2Fcallpeak/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/macs3/callpeak/blobs/sha256:a9a56d700d673d2c8d69574691dc5673dbda4e2ec3d90a2f8ac8345198475722
Size	3.6 KB
Checksum	sha256:a9a56d700d673d2c8d69574691dc5673dbda4e2ec3d90a2f8ac8345198475722
Downloads	5

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a