Nextflow Registry | nf-core/jvarkit/wgscoverageplotter@0.0.0-0c7146d

nf-core/jvarkit/wgscoverageplotter @ 0.0.0-0c7146d

Plot whole genome coverage from BAM/CRAM file as SVG

bam cram depth coverage xml svg visualization

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @lindenb

Maintainers: @lindenb

Plot whole genome coverage from BAM/CRAM file as SVG

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

include { JVARKIT_WGSCOVERAGEPLOTTER } from 'nf-core/jvarkit/wgscoverageplotter'

MIT License

Process

`Name`	`JVARKIT_WGSCOVERAGEPLOTTER`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`bam` file	BAM/CRAM file from alignment `*.{bam,cram}`
`bai` file	BAI/CRAI file from alignment `*.{bai,crai}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'test_reference' ]
`fasta` file	The reference fasta file `*.fasta`

#3 tuple

`meta3` map	Groovy Map containing reference fai information e.g. [ id:'test_reference' ]
`fai` file	Index of reference fasta file `fasta.fai`

#4 tuple

`meta4` map	Groovy Map containing reference dict information e.g. [ id:'test_reference' ]
`dict` file	GATK sequence dictionary `*.dict`

Output 2 channels

#1 output tuple

`meta` map	Groovy Map containing Sample information e.g. [ id:'test', single_end:false ]
`*.svg` file	Output SVG file `*.svg`

#2 versions

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

Tool	Description	Homepage
jvarkit	Java utilities for Bioinformatics.	https://github.com/lindenb/jvarkit

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:50:30 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fjvarkit%2Fwgscoverageplotter/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/jvarkit/wgscoverageplotter/blobs/sha256:c4f5a0c5c79555cc8a708bff714faffab60d1d37083d9cc4e30dd3590665d563
Size	2.5 KB
Checksum	sha256:c4f5a0c5c79555cc8a708bff714faffab60d1d37083d9cc4e30dd3590665d563
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:50:30 (UTC)		1	2.5 KB	-