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

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

Filter variants

filter gatk4 variantfiltration vcf

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @kevinmenden @ramprasadn

Maintainers: @kevinmenden @ramprasadn

Filter variants

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

include { GATK4_VARIANTFILTRATION } from 'nf-core/gatk4/variantfiltration'

MIT License

Process

`Name`	`GATK4_VARIANTFILTRATION`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`vcf` list	List of VCF(.gz) files `*.{vcf,vcf.gz}`
`tbi` list	List of VCF file indexes `*.{tbi}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fasta` file	Fasta file of reference genome `*.fasta`

#3 tuple

`meta3` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fai` file	Index of fasta file `*.fasta.fai`

#4 tuple

`meta4` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`dict` file	Sequence dictionary of fastea file `*.dict`

#5 tuple

`meta5` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`gzi` file	Genome index file only needed when the genome file was compressed with the BGZF algorithm. `*.gzi`

Output 3 channels

#1 tbi tuple

`meta` file	Compressed VCF file `*.vcf.gz`
`*.tbi` file	Index of VCF file `*.vcf.gz.tbi`

#2 vcf tuple

`meta` file	Compressed VCF file `*.vcf.gz`
`*.vcf.gz` file	Compressed 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	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

Downlo
Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:20:42 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fvariantfiltration/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gatk4/variantfiltration/blobs/sha256:a352bf92a253da5f6df0442c96c9af0dccb14e8e2dfbc2e66ff00fb192bdd2dc
Size	3.2 KB
Checksum	sha256:a352bf92a253da5f6df0442c96c9af0dccb14e8e2dfbc2e66ff00fb192bdd2dc