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

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

Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome.

bed bam genomecov bedtools histogram

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @edmundmiller @sruthipsuresh @drpatelh @sidorov-si @chris-cheshire

Maintainers: @edmundmiller @sruthipsuresh @drpatelh @sidorov-si @chris-cheshire

Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome.

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

include { BEDTOOLS_GENOMECOV } from 'nf-core/bedtools/genomecov'

MIT License

Process

`Name`	`BEDTOOLS_GENOMECOV`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`intervals` file	BAM/BED/GFF/VCF `*.{bam\|bed\|gff\|vcf}`
`scale` integer	Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch

`sizes` file	Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column

`extension` string	Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.

`sort` boolean	Sort the output

Output 2 channels

#1 genomecov tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.${extension}` file	Computed genome coverage file `*.${extension}`

#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 18:26:10 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbedtools%2Fgenomecov/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/bedtools/genomecov/blobs/sha256:f1879bcdec3ba9cfd6b2299ca7ac05491aec97878e4cab1c2236c0dc07bc1cad
Size	3.5 KB
Checksum	sha256:f1879bcdec3ba9cfd6b2299ca7ac05491aec97878e4cab1c2236c0dc07bc1cad
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:26:10 (UTC)		1	3.5 KB	-