Nextflow Registry | nf-core/gatk4/germlinecnvcaller@0.0.0-0c7146d

nf-core/gatk4/germlinecnvcaller @ 0.0.0-0c7146d

Calls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy.

gatk germline contig ploidy germlinecnvcaller

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @ryanjameskennedy @ViktorHy

Maintainers: @ryanjameskennedy @ViktorHy

Calls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy.

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

include { GATK4_GERMLINECNVCALLER } from 'nf-core/gatk4/germlinecnvcaller'

MIT License

Process

`Name`	`GATK4_GERMLINECNVCALLER`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`tsv` file	One or more count TSV files created with gatk/collectreadcounts `*.tsv`
`intervals` file	Optional - A bed file containing the intervals to include in the process `*.bed`
`ploidy` directory	Directory containing ploidy calls produced by determinegermlinecontigploidy case or cohort mode `*-calls`
`model` directory	Optional - directory containing the model produced by germlinecnvcaller cohort mode `-cnv-model/-model`

Output 4 channels

#1 casecalls tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`-cnv-calls/-calls` directory	Tar gzipped directory containing calls produced by germlinecnvcaller case mode `-cnv-calls/-calls`

#2 cohortcalls tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`-cnv-model/-calls` directory	Tar gzipped directory containing calls produced by germlinecnvcaller case mode `-cnv-model/-calls`

#3 cohortmodel tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`-cnv-model/-model` directory	Optional - Tar gzipped directory containing the model produced by germlinecnvcaller cohort mode `-cnv-model/-model`

#4 versions_gatk4 tuple

`${task.process}` string	The name of the process
`gatk4` string	The name of the tool
`gatk --version \| sed -n '/GATK.v/s/.v//p'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
gatk4	Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.	https://gatk.broadinstitute.org/hc/en-us

Version	0.0.0-0c7146d
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 19:03:22 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fgermlinecnvcaller/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gatk4/germlinecnvcaller/blobs/sha256:4df614ff92ed41eb87e18307df9489a5110a70be0658ecbf03fa20b24b29e3ba
Size	3.9 KB
Checksum	sha256:4df614ff92ed41eb87e18307df9489a5110a70be0658ecbf03fa20b24b29e3ba
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:20:04 (UTC)		3	3.9 KB
0.0.0-0c7146d	08 Apr 2026 19:03:22 (UTC)		3	3.9 KB