Nextflow Registry | nf-core/samtools/bedcov@0.0.0-0c7146d

nf-core/samtools/bedcov @ 0.0.0-0c7146d

reports coverage over regions in a supplied BED file

bedcov samtools coverage bed bam cram sam regions

Latest version: 0.0.0-0c7146d

Total downloads: 1

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	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:09:40 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fbedcov/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/samtools/bedcov/blobs/sha256:1a1cfe4fb3c986a39feb0ef4d5006d82c7c3e4cc2bd682169428d0293fa18b2f
Size	2.8 KB
Checksum	sha256:1a1cfe4fb3c986a39feb0ef4d5006d82c7c3e4cc2bd682169428d0293fa18b2f
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:09:40 (UTC)		1	2.8 KB	-