Nextflow Registry | nf-core/picard/liftovervcf@0.0.0-0c7146d

nf-core/picard/liftovervcf @ 0.0.0-0c7146d

Lifts over a VCF file from one reference build to another.

vcf picard liftovervcf

Latest version: 0.0.0-6c4ed3a

Total downloads: 4

Source: nf-core/modules

Authors: @lucpen @ramprasadn

Maintainers: @lucpen @ramprasadn

Lifts over a VCF file from one reference build to another.

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

include { PICARD_LIFTOVERVCF } from 'nf-core/picard/liftovervcf'

MIT License

Process

`Name`	`PICARD_LIFTOVERVCF`

Input 4 channels

#1 tuple

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

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`dict` file	dictionary for fasta file `*.{dict}`

#3 tuple

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

#4 tuple

`meta4` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`chain` file	The liftover chain file

Output 3 channels

#1 vcf_lifted tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.lifted.vcf.gz` file	VCF file containing successfully lifted variants `*.{lifted.vcf.gz}`

#2 vcf_unlifted tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.unlifted.vcf.gz` file	VCF file containing unsuccessfully lifted variants `*.{unlifted.vcf.gz}`

#3 versions_picard tuple

`${task.process}` string	The process the versions were collected from
`picard` string	The tool name
`picard LiftoverVcf --version 2>&1 \| sed -n 's/.*Version://p'` string	The command used to generate the version of the tool

Tool	Description	Homepage
picard	Move annotations from one assembly to another	https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard

Version	0.0.0-0c7146d
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 19:25:49 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fpicard%2Fliftovervcf/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/picard/liftovervcf/blobs/sha256:dbddf85525d60ce70326fe6ad80860ffa7e714a35c2c23fee39bf471491fc919
Size	2.9 KB
Checksum	sha256:dbddf85525d60ce70326fe6ad80860ffa7e714a35c2c23fee39bf471491fc919
Downloads	1

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:36:09 (UTC)		3	3.0 KB
0.0.0-0c7146d	08 Apr 2026 19:25:49 (UTC)		1	2.9 KB