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

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

Perform joint genotyping on one or more samples pre-called with HaplotypeCaller.

gatk4 genotype gvcf joint genotyping

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @santiagorevale @maxulysse

Maintainers: @santiagorevale @maxulysse

Perform joint genotyping on one or more samples pre-called with HaplotypeCaller.

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

include { GATK4_GENOTYPEGVCFS } from 'nf-core/gatk4/genotypegvcfs'

MIT License

Process

`Name`	`GATK4_GENOTYPEGVCFS`

Input 6 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input` file	gVCF(.gz) file or a GenomicsDB `*.{vcf,vcf.gz}`
`gvcf_index` file	index of gvcf file, or empty when providing GenomicsDB `*.{idx,tbi}`
`intervals` file	Interval file with the genomic regions included in the library (optional)
`intervals_index` file	Interval index file (optional)

#2 tuple

`meta2` map	Groovy Map containing fasta information e.g. [ id:'test' ]
`fasta` file	Reference fasta file `*.fasta`

#3 tuple

`meta3` map	Groovy Map containing fai information e.g. [ id:'test' ]
`fai` file	Reference fasta index file `*.fai`

#4 tuple

`meta4` map	Groovy Map containing dict information e.g. [ id:'test' ]
`dict` file	Reference fasta sequence dict file `*.dict`

#5 tuple

`meta5` map	Groovy Map containing dbsnp information e.g. [ id:'test' ]
`dbsnp` file	dbSNP VCF file `*.vcf.gz`

#6 tuple

`meta6` map	Groovy Map containing dbsnp tbi information e.g. [ id:'test' ]
`dbsnp_tbi` file	dbSNP VCF index file `*.tbi`

Output 3 channels

#1 tbi tuple

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

#2 vcf tuple

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

#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	Genome Analysis Toolkit (GATK4)	https://gatk.broadinstitute.org/hc/en-us

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:20:03 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fgenotypegvcfs/0.0.0-6c4ed3a/download