Nextflow Registry | nf-core/samtools/bedcov@0.0.0-6c4ed3a

nf-core/samtools/bedcov @ 0.0.0-6c4ed3a

reports coverage over regions in a supplied BED file

bedcov samtools coverage bed bam cram sam regions

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @ToonRosseel

Maintainers: @ToonRosseel @matthdsm

Summary

reports coverage over regions in a supplied BED file

Get started

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

include { SAMTOOLS_BEDCOV } from 'nf-core/samtools/bedcov'

License

MIT License

Process

`Name`	`SAMTOOLS_BEDCOV`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`input` file	Sorted BAM/CRAM/SAM file `*.{bam,cram,sam}`
`input_index` file	BAM/CRAM index file `*.{bai,crai}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. `[ id:'bed']`
`bed` file	Interval BED file `*.bed`

#3 tuple

`meta3` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fasta` file	Reference genome file `*.{fa,fasta}`
`fasta_index` file	Reference genome index file `*.fai`

Output 2 channels

#1 coverage tuple

meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.tsv file

Reports the total read base count (i.e. the sum of per base read depths) for each genomic region specified in the supplied BED file. The regions are output as they appear in the BED file and are 0-based. Columns 1-3 are chrom/start/end as per the input BED file, followed by N columns of coverages (for N input BAMs), then (if given -d), N columns of bases-at-depth-X, then (if given -c) N columns of read counts.

*.tsv

#2 versions_samtools tuple

`${task.process}` string	The name of the process
`samtools` string	The name of the tool
`samtools version \| sed '1!d;s/.* //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
samtools	Tools for dealing with SAM, BAM and CRAM files	http://www.htslib.org/

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:42:04 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fbedcov/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/samtools/bedcov/blobs/sha256:4bf45a61903da02bf8b0a92682c47b16aaa5958a51b8420f3b969ef7f8b14755
Size	2.8 KB
Checksum	sha256:4bf45a61903da02bf8b0a92682c47b16aaa5958a51b8420f3b969ef7f8b14755
Downloads	4

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:42:04 (UTC)		4	2.8 KB
0.0.0-0c7146d	08 Apr 2026 19:33:19 (UTC)		3	2.8 KB