Nextflow Registry | nf-core/ngsbits/bedcoverage@0.0.0-6c4ed3a

nf-core/ngsbits/bedcoverage @ 0.0.0-6c4ed3a

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

bed coverage regions

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:33:07 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fngsbits%2Fbedcoverage/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/ngsbits/bedcoverage/blobs/sha256:b743a4e556306fab9cd9f983eb7e7366d6070c430231e005d1603a02a789a724
Size	2.9 KB
Checksum	sha256:b743a4e556306fab9cd9f983eb7e7366d6070c430231e005d1603a02a789a724
Downloads	4

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:33:07 (UTC)		4	2.9 KB
0.0.0-0c7146d	08 Apr 2026 19:21:20 (UTC)		3	2.9 KB