Nextflow Registry | nf-core/jvarkit/vcfpolyx@0.0.0-6c4ed3a

nf-core/jvarkit/vcfpolyx @ 0.0.0-6c4ed3a

annotate VCF files for poly repeats

vcf bcf annotation repeats

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:26:30 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fjvarkit%2Fvcfpolyx/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/jvarkit/vcfpolyx/blobs/sha256:feb877932be2f1dd8a85aeaf2babf7dbd0c36e48809f5f1edf745820f8cb425c
Size	3.3 KB
Checksum	sha256:feb877932be2f1dd8a85aeaf2babf7dbd0c36e48809f5f1edf745820f8cb425c
Downloads	3

Version	Date	Status	Downloads	Size