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

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

computes both the depth and breadth of coverage of features in file B on the features in file A

bedtools coverage bam bed gff vcf histogram

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @priyanka-surana

Maintainers: @priyanka-surana

computes both the depth and breadth of coverage of features in file B on the features in file A

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

include { BEDTOOLS_COVERAGE } from 'nf-core/bedtools/coverage'

MIT License

Process

`Name`	`BEDTOOLS_COVERAGE`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input_A` file	BAM/BED/GFF/VCF file `*.{bam,bed,gff,vcf}`
`input_B` file	One or more BAM/BED/GFF/VCF file `*.{bam,bed,gff,vcf}`

`genome_file` file	Optional reference genome 2 column file that defines the expected chromosome order in the input files for use with the -sorted option. When `genome_file` is provided, `-sorted` option is added to the command. `*.{fai,txt,chromsizes}`

Output 2 channels

#1 bed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bed` file	File containing coverage of sequence alignments `*.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 powerful toolset for genome arithmetic	https://bedtools.readthedocs.io/en/latest/index.html

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:26:08 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbedtools%2Fcoverage/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/bedtools/coverage/blobs/sha256:4511b35ab54d7084c11959c63a6fa0755524a91c57a79155ecc5e20bbc4133b0
Size	2.7 KB
Checksum	sha256:4511b35ab54d7084c11959c63a6fa0755524a91c57a79155ecc5e20bbc4133b0
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:26:08 (UTC)		1	2.7 KB	-