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

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

Extract fields from a VCF file to a tab-delimited table

filter gatk4 table vcf

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @lindenb

Maintainers: @lindenb

Extract fields from a VCF file to a tab-delimited table

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

include { GATK4_VARIANTSTOTABLE } from 'nf-core/gatk4/variantstotable'

MIT License

Process

`Name`	`GATK4_VARIANTSTOTABLE`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing VCF information. Attribute `gatk_args` can be used to add arguments to gatk. e.g. [ id:'test', gatk_args:'-F CHROM -F POS -F TYPE -GF AD']
`vcf` file	VCF file `*.{vcf,vcf.gz}`
`tbi` file	Index of VCF file. `*.{idx,tbi}`
`arguments_file` file	optional GATK arguments file `*.{txt,list,args,arguments}`
`include_intervals` file	optional GATK region file `*.{bed,bed.gz,interval,interval_list}`
`exclude_intervals` file	optional GATK exclude region file `*.{bed,bed.gz,interval,interval_list}`

#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`

Output 2 channels

#1 table tuple

`meta` file	GATK output `*.tsv`
`*.tsv` file	GATK output `*.tsv`

#2 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 15:20:45 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fvariantstotable/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gatk4/variantstotable/blobs/sha256:a71bc7efa515dfea9b681d28ce351dbdf755e71f69c96044ce07fb4643e08e85
Size	3.2 KB
Checksum	sha256:a71bc7efa515dfea9b681d28ce351dbdf755e71f69c96044ce07fb4643e08e85
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:20:45 (UTC)		3	3.2 KB