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

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

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

filter gatk4 table vcf

Latest version: 0.0.0-0c7146d

Total downloads: 1

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	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:43:26 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fvariantstotable/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/variantstotable/blobs/sha256:6dc69899add68fd50676c8287a78d83cffb7deb18c05abd394f8db7e9ff9ba0b
Size	3.2 KB
Checksum	sha256:6dc69899add68fd50676c8287a78d83cffb7deb18c05abd394f8db7e9ff9ba0b
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:43:26 (UTC)		1	3.2 K