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

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

Determines the baseline contig ploidy for germline samples given counts data

copy number counts determinegermlinecontigploidy gatk4

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @nvnieuwk

Maintainers: @nvnieuwk

Determines the baseline contig ploidy for germline samples given counts data

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

include { GATK4_DETERMINEGERMLINECONTIGPLOIDY } from 'nf-core/gatk4/determinegermlinecontigploidy'

MIT License

Process

`Name`	`GATK4_DETERMINEGERMLINECONTIGPLOIDY`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`counts` file	One or more count TSV files created with gatk/collectreadcounts `*.tsv`
`bed` file	Optional - A bed file containing the intervals to include in the process `*.bed`
`exclude_beds` file	Optional - One or more bed files containing intervals to exclude from the process `*.bed`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test' ]
`ploidy_model` directory	Optional - A folder containing the ploidy model. When a model is supplied to tool will run in CASE mode. pattern: '*-model/'

`contig_ploidy_table` file	The contig ploidy priors table `*.tsv`

Output 3 channels

#1 calls tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}-calls` directory	A folder containing the calls from the input files `*-calls/`

#2 model tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}-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). `*-model/`

#3 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 18:41:36 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fdeterminegermlinecontigploidy/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/determinegermlinecontigploidy/blobs/sha256:af21f338e9bcf56618c419deaa0b98bafdf7b79c25eb1bc5570e43315c99212c
Size	3.9 KB
Checksum	sha256:af21f338e9bcf56618c419deaa0b98bafdf7b79c25eb1bc5570e43315c99212c
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:41:36 (UTC)		1	3.9 KB	-