Nextflow Registry | nf-core/vt/normalize@0.0.0-0c7146d

nf-core/vt/normalize @ 0.0.0-0c7146d

normalizes variants in a VCF file

normalization vcf snps indels

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @nvnieuwk

Maintainers: @nvnieuwk

normalizes variants in a VCF file

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

include { VT_NORMALIZE } from 'nf-core/vt/normalize'

MIT License

Process

`Name`	`VT_NORMALIZE`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`vcf` file	The VCF file to normalize `*.vcf(.gz)?`
`tbi` file	The tabix index of the VCF file when bgzipped `*.tbi`
`intervals` file	The intervals of the variants of normalize `*.bed`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. `[ id:'test', single_end:false ]`
`fasta` file	The reference fasta file `*.{fasta,fn,fna,fa}`

#3 tuple

`meta3` map	Groovy Map containing reference index information e.g. `[ id:'test', single_end:false ]`
`fai` file	The index of the reference fasta file (OPTIONAL) `*.fai`

Output 3 channels

#1 fai tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`${fasta}.fai` file	The created index of the reference fasta file (only when the fai wasn't supplied) `*.fai`

#2 vcf tuple

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

#3 versions

`versions.yml` file	File containing software versions `versions.yml`

Tool	Description	Homepage
vt	A tool set for short variant discovery in genetic sequence data	https://genome.sph.umich.edu/wiki/Vt

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:23:16 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fvt%2Fnormalize/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/vt/normalize/blobs/sha256:33dac74201000a1af05986029f37814cf9bdd65287a086c398e2abc4307fe08e
Size	3.0 KB
Checksum	sha256:33dac74201000a1af05986029f37814cf9bdd65287a086c398e2abc4307fe08e
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:23:16 (UTC)		1	3.0 KB	-