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

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

Left align and trim variants using GATK4 LeftAlignAndTrimVariants.

gatk4 leftalignandtrimvariants norm normalize vcf

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @adamrtalbot

Maintainers: @adamrtalbot

Left align and trim variants using GATK4 LeftAlignAndTrimVariants.

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

include { GATK4_LEFTALIGNANDTRIMVARIANTS } from 'nf-core/gatk4/leftalignandtrimvariants'

MIT License

Process

`Name`	`GATK4_LEFTALIGNANDTRIMVARIANTS`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`vcf` file	The vcf file to be normalized e.g. 'file1.vcf.gz'
`tbi` file	Index of the vcf file to be normalized e.g. 'file1.vcf.gz.tbi'
`intervals` file	Bed file with the genomic regions included in the library (optional)

`fasta` file	The reference fasta file `*.fasta`

`fai` file	Index of reference fasta file `*.fasta.fai`

`dict` file	GATK sequence dictionary `*.dict`

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 `*.tbi`

#2 vcf tuple

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

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:42:09 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fleftalignandtrimvariants/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/leftalignandtrimvariants/blobs/sha256:7e2c551771aba8302c78c2c2cd5c8bf96dab1b0a908847d9cec21d972f3291f4
Size	3.2 KB
Checksum	sha256:7e2c551771aba8302c78c2c2cd5c8bf96dab1b0a908847d9cec21d972f3291f4
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:42:09 (UTC)		1	3.2 KB	-