Nextflow Registry | nf-core/jvarkit/vcfpolyx@0.0.0-0c7146d

nf-core/jvarkit/vcfpolyx @ 0.0.0-0c7146d

annotate VCF files for poly repeats

vcf bcf annotation repeats

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @lindenb

Maintainers: @lindenb

annotate VCF files for poly repeats

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

include { JVARKIT_VCFPOLYX } from 'nf-core/jvarkit/vcfpolyx'

MIT License

Process

`Name`	`JVARKIT_VCFPOLYX`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing VCF information
`vcf` file	Groovy Map containing reference genome information for vcf `*.{vcf,bcf,vcf.gz,bcf.gz}`
`tbi` file	Alternative VCF file index `*.tbi`
`regions_file` file	Regions file

#2 tuple

`meta2` map	Groovy Map containing fasta information
`fasta` file	Groovy Map containing reference genome information for fai reference fasta file `*.fasta`

#3 tuple

`meta3` map	Groovy Map containing fasta.fai information
`fai` file	Groovy Map containing reference genome information for fai `*.fasta.fai`

#4 tuple

`meta4` map	Groovy Map containing fasta.dict information
`dict` file	Groovy Map containing reference genome information for GATK sequence dictionary `*.dict`

Output 4 channels

#1 csi tuple

`meta` map	Groovy Map containing VCF information e.g. [ id:'test', single_end:false ]
`*.csi` file	Default VCF file index `*.csi`

#2 tbi tuple

`meta` map	Groovy Map containing VCF information e.g. [ id:'test', single_end:false ]
`*.tbi` file	Alternative VCF file index `*.tbi`

#3 vcf tuple

`meta` map	Groovy Map containing VCF information e.g. [ id:'test', single_end:false ]
`*.${extension}` file	VCF filtered output file `*.{vcf,bcf,vcf.gz,bcf.gz}`

#4 versions

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

Tool	Description	Homepage
jvarkit	Java utilities for Bioinformatics.	https://github.com/lindenb/jvarkit
bcftools	View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF	http://samtools.github.io/bcftools/bcftools.html

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:50:28 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fjvarkit%2Fvcfpolyx/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/jvarkit/vcfpolyx/blobs/sha256:efb71c93d6188297f43e198441a703f2bb7d3ef2e15e975416d7bbaf1be5153c
Size	3.3 KB
Checksum	sha256:efb71c93d6188297f43e198441a703f2bb7d3ef2e15e975416d7bbaf1be5153c
Downloads	1

Version	Date	Status	Downloads	Size	Diff