Nextflow Registry | nf-core/bedtools/shuffle@0.0.0-0c7146d

nf-core/bedtools/shuffle @ 0.0.0-0c7146d

bedtools shuffle will randomly permute the genomic locations of a feature file among a genome defined in a genome file

bed shuffleBed region fai sizes genome bases

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @itrujnara

Maintainers: @itrujnara

bedtools shuffle will randomly permute the genomic locations of a feature file among a genome defined in a genome file

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

include { BEDTOOLS_SHUFFLE } from 'nf-core/bedtools/shuffle'

MIT License

Process

`Name`	`BEDTOOLS_SHUFFLE`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing interval information e.g. [ id:'test' ]
`intervals` file	Input interval (BED/GFF/VCF) file `*.{bed,gff,gff3,vcf}`

#2 tuple

`meta2` map	Groovy Map containing genome information e.g. [ id:'test' ]
`chrom_sizes` file	Chromosome sizes file `*{.genome,.sizes,.txt,.fai}`

`exclude_file` file	BED file containing regions to exclude `*.{bed}`

`include_file` file	BED file containing regions to include `*.{bed}`

Output 2 channels

#1 bed tuple

`meta` map	Groovy Map containing interval information e.g. `[ id:'sample1' ]`
`*.bed` file	BED file with shuffled intervals `*.{bed}`

#2 versions_bedtools tuple

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

Tool	Description	Homepage
bedtools	A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.	n/a

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:26:33 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbedtools%2Fshuffle/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/bedtools/shuffle/blobs/sha256:ed279bf2443e34560dcfa4f7c4161f141404be473e295a95b07e465ae6911a68
Size	3.1 KB
Checksum	sha256:ed279bf2443e34560dcfa4f7c4161f141404be473e295a95b07e465ae6911a68
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:26:33 (UTC)		1	3.1 KB	-