Nextflow Registry | nf-core/sambamba/depth@0.0.0-0c7146d

nf-core/sambamba/depth @ 0.0.0-0c7146d

Outputs a coverage file from bam files

depth coverage sambamba

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @peterpru

Maintainers: @peterpru

Outputs a coverage file from bam files

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

include { SAMBAMBA_DEPTH } from 'nf-core/sambamba/depth'

MIT License

Process

`Name`	`SAMBAMBA_DEPTH`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`bam` file	BAM file `*.{bam}`
`bai` file	BAI file `*.{bai}`

#2 tuple

`meta2` map	Groovy Map containing regions information
`bed` file	bed file `*.{bed}`

`mode` string	Analysis mode can be region, window, base `region\|window\|base`

Output 2 channels

#1 bed tuple

`meta` map	Groovy Map containing sample information
`*.bed` file	bed file `*.bed`

#2 versions_sambamba tuple

`${task.process}` string	The process the versions were collected from
`sambamba` string	The tool name
`sambamba --version 2>&1 \| grep -oPm1 'sambamba \\K[0-9.]+'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
sambamba	Tools for working with SAM/BAM data	https://lomereiter.github.io/sambamba/docs/sambamba-view.html

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:09:24 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsambamba%2Fdepth/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/sambamba/depth/blobs/sha256:0e891b3208b8412e496153b608665eee53e4f78c57ba29420197fded1cd4d695
Size	2.6 KB
Checksum	sha256:0e891b3208b8412e496153b608665eee53e4f78c57ba29420197fded1cd4d695
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:09:24 (UTC)		1	2.6 KB	-