Nextflow Registry | nf-core/ngsbits/bedcoverage@0.0.0-0c7146d

nf-core/ngsbits/bedcoverage @ 0.0.0-0c7146d

Annotates a BED file with the average coverage of the regions from one or several BAM/CRAM file(s).

bed coverage regions

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @nvnieuwk

Maintainers: @nvnieuwk

Annotates a BED file with the average coverage of the regions from one or several BAM/CRAM file(s).

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

include { NGSBITS_BEDCOVERAGE } from 'nf-core/ngsbits/bedcoverage'

MIT License

Process

`Name`	`NGSBITS_BEDCOVERAGE`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`reads` file	Input BAM/CRAM/SAM file(s), can be one file or a list of files `*.{bam,cram,sam}`
`reads_index` file	The index file(s) from the input BAM/CRAM/SAM file(s) `*.{bai,crai}`
`bed` file	Input BED file containing regions to annotate `*.bed`

#2 tuple

`meta2` map	Groovy Map containing reference fasta information e.g. `[ id:'sample1', single_end:false ]`
`fasta` file	The reference FASTA to use (mandatory when CRAM files are used, otherwise optional) `*.{fasta,fa,fna}`

#3 tuple

`meta3` map	Groovy Map containing reference fasta information e.g. `[ id:'sample1', single_end:false ]`
`fai` file	The index file from the reference FASTA `*.fai`

Output 2 channels

#1 bed tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.bed` file	Output BED file with average coverage of the regions `*.bed`

#2 versions

`versions.yml` file	File containing software versions `versions.yml`

Tool	Description	Homepage
ngsbits	Short-read sequencing tools	https://github.com/imgag/ngs-bits

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:58:53 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fngsbits%2Fbedcoverage/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/ngsbits/bedcoverage/blobs/sha256:7a4c4e8c9978d34c81eb73b02f0df2a1bcabe998cbd05118b6144929dee395e7
Size	2.8 KB
Checksum	sha256:7a4c4e8c9978d34c81eb73b02f0df2a1bcabe998cbd05118b6144929dee395e7
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:58:53 (UTC)		1	2.8 KB	-