Nextflow Registry | nf-core/genrich@0.0.0-0b45cc0

nf-core/genrich @ 0.0.0-0b45cc0

Peak-calling for ChIP-seq and ATAC-seq enrichment experiments

peak-calling ChIP-seq ATAC-seq

Latest version: 0.0.0-0b45cc0

Total downloads: 1

Source: nf-core/modules

Authors: @JoseEspinosa @samuelruizperez

Maintainers: @JoseEspinosa @samuelruizperez

Peak-calling for ChIP-seq and ATAC-seq enrichment experiments

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

include { GENRICH } from 'nf-core/genrich'

MIT License

Process

`Name`	`GENRICH`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`treatment_bam` file	Coordinate sorted BAM/SAM file from treatment sample or list of BAM/SAM files from biological replicates `*.{bam,sam}`
`control_bam` file	Coordinate sorted BAM/SAM file from control sample or list of BAM/SAM files from control samples `*.{bam,sam}`

`blacklist_bed` file	Bed file containing genomic intervals to exclude from the analysis `*.{bed}`

Output 6 channels

#1 peak tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.narrowPeak` file	Narrow peak file containing genomic intervals of significant enrichment `*.{narrowPeak}`

#2 duplicates tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.duplicates.txt` file	Text output file containing intervals corresponding to PCR duplicates `*.{intervals.txt}`

#3 bed_intervals tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.intervals.bed` file	Bed file containing annotated intervals `*.{intervals.bed}`

#4 bedgraph_pileup tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.pileup.bedGraph` file	bedGraph file containing pileups and p-values `*.{pileup.bedGraph}`

#5 bedgraph_pvalues tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.pvalues.bedGraph` file	bedGraph file containing p/q values `*.{pvalues.bedGraph}`

#6 versions_genrich tuple

`${task.process}` string	The name of the process
`genrich` string	The name of the tool
`Genrich --version 2>&1 \| head -n1 \| sed 's/Genrich, version //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
genrich	Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated following the assay and produces a file detailing peaks of significant enrichment.	https://github.com/jsh58/Genrich

Version	0.0.0-0b45cc0
Commit ID	0b45cc097cafcd4768e2f79b504333fee85940bc
Release Date	29 Apr 2026 21:15:34 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgenrich/0.0.0-0b45cc0/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/genrich/blobs/sha256:00e04b58d87fa39cf42b7308712533655b734ea4cec3395733b0d13b47276595
Size	3.6 KB
Checksum	sha256:00e04b58d87fa39cf42b7308712533655b734ea4cec3395733b0d13b47276595
Downloads	0

Version	Date