Nextflow Registry | nf-core/gatk4/postprocessgermlinecnvcalls@0.0.0-6c4ed3a

nf-core/gatk4/postprocessgermlinecnvcalls @ 0.0.0-6c4ed3a

Postprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios

copy number gatk4 postprocessgermlinecnvcalls

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @ryanjameskennedy

Maintainers: @ryanjameskennedy

Postprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios

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

include { GATK4_POSTPROCESSGERMLINECNVCALLS } from 'nf-core/gatk4/postprocessgermlinecnvcalls'

MIT License

Process

`Name`	`GATK4_POSTPROCESSGERMLINECNVCALLS`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`calls` directory	A folder containing the calls from the input files `-cnv-calls/-calls`
`model` directory	A folder containing the model from the input files. This will only be created in COHORT mode (when no model is supplied to the process). `-cnv-model/-model`
`ploidy` directory	Optional - A folder containing the ploidy model. When a model is supplied to tool will run in CASE mode. `*-calls/`

Output 4 channels

#1 denoised tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*_denoised.vcf.gz` file	Denoised copy ratio file `*.vcf.gz`

#2 segments tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*_genotyped_segments.vcf.gz` file	Segments VCF file `*.vcf.gz`

#3 intervals tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*_genotyped_intervals.vcf.gz` file	Intervals VCF file `*.vcf.gz`

#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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:20:22 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fpostprocessgermlinecnvcalls/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gatk4/postprocessgermlinecnvcalls/blobs/sha256:06d779d2d4214acdce43f911ae7b45a54b704faa3004ff1b3291a9ded99f4554
Size	3.9 KB
Checksum	sha256:06d779d2d4214acdce43f911ae7b45a54b704faa3004ff1b3291a9ded99f4554
Downloads	4

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:20:22 (UTC)		4	3.9 KB
0.0.0-0c7146d	08 Apr 2026 19:04:30 (UTC)		3	3.9 KB