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

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

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

copy number gatk4 postprocessgermlinecnvcalls

Latest version: 0.0.0-0c7146d

Total downloads: 1

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	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:42:52 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fpostprocessgermlinecnvcalls/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/postprocessgermlinecnvcalls/blobs/sha256:1e723537b14f272f996d13cb7d51b19d8a2e7d99ff72397ce43a1686d0388f56
Size	3.9 KB
Checksum	sha256:1e723537b14f272f996d13cb7d51b19d8a2e7d99ff72397ce43a1686d0388f56
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:42:52 (UTC)		1	3.9 KB	-