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

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

Filtering VCF with dynamically-compiled java expressions

vcf bcf filter variant java script

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @lindenb

Maintainers: @lindenb

Filtering VCF with dynamically-compiled java expressions

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

include { JVARKIT_VCFFILTERJDK } from 'nf-core/jvarkit/vcffilterjdk'

MIT License

Process

`Name`	`JVARKIT_VCFFILTERJDK`

Input 6 channels

#1 tuple

`meta` map	Groovy Map containing VCF information e.g. [ id:'test_reference' ]
`vcf` file	Input VCF/BCF file `*.{vcf,bcf,vcf.gz,bcf.gz}`
`tbi` file	Optional VCF/BCF index file `*.{tbi,csi}`
`regions_file` file	Optional. Restrict to regions listed in a file `*.{bed,bed.gz,txt,tsv}`

#2 tuple

`meta2` map	Groovy Map containing fasta information e.g. [ id:'test_reference' ]
`fasta` file	Fasta reference file `*.fasta`

#3 tuple

`meta3` map	Groovy Map containing fasta.fai information e.g. [ id:'test_reference' ]
`fai` file	Fasta file index `*.fasta.fai`

#4 tuple

`meta4` map	Groovy Map containing fasta.dict information e.g. [ id:'test_reference' ]
`dict` file	GATK sequence dictionary `*.dict`

#5 tuple

`meta5` map	Groovy Map containing code information e.g. [ id:'test_reference' ]
`code` file	File containing custom user code . May be empty if script if provided via `task.ext.args2`. `*.{code,script,txt,tsv,java,js}`

#6 tuple

`meta6` map	Groovy Map containing pedigree information e.g. [ id:'test_reference' ]
`pedigree` file	Optional jvarkit pedigree. `*.{tsv,ped,pedigree}`

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