modules/jvarkit_vcffilterjdk

Filtering VCF with dynamically-compiled java expressions

vcfbcffiltervariantjavascript

https://github.com/nf-core/modules/[...]/modules/nf-core/jvarkit/vcffilterjdk

Description

Filtering VCF with dynamically-compiled java expressions

Input

name:type

description

pattern

`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}

`meta2`
`:map`

Groovy Map containing fasta information e.g. [ id:‘test_reference’ ]

`fasta`
`:file`

Fasta reference file

*.fasta

`meta3`
`:map`

Groovy Map containing fasta.fai information e.g. [ id:‘test_reference’ ]

`fai`
`:file`

Fasta file index

*.fasta.fai

`meta4`
`:map`

Groovy Map containing fasta.dict information e.g. [ id:‘test_reference’ ]

`dict`
`:file`

GATK sequence dictionary

*.dict

`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}

`meta6`
`:map`

Groovy Map containing pedigree information e.g. [ id:‘test_reference’ ]

`pedigree`
`:file`

Optional jvarkit pedigree.

*.{tsv,ped,pedigree}

Output

name:type

description

pattern

`vcf`

`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}

`tbi`

`meta`
`:map`

Groovy Map containing VCF information e.g. [ id:‘test’, single_end:false ]

`*.tbi`
`:file`

Alternative VCF file index

*.tbi

`csi`

`meta`
`:map`

Groovy Map containing VCF information e.g. [ id:‘test’, single_end:false ]

`*.csi`
`:file`

Default VCF file index

*.csi

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Tools

jvarkit
MIT License

Java utilities for Bioinformatics.

args_id: $args2

github.com/lindenb/jvarkit jvarkit.readthedocs.io https://github.com/lindenb/jvarkit 10.1093/bioinformatics/btx734

bcftools
MIT

View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF

args_id: $args1$args3

http://samtools.github.io/bcftools/bcftools http://www.htslib.org/doc/bcftools 10.1093/bioinformatics/btp352

modules/jvarkit_vcffilterjdk

Description

Input

`meta`
`:map`

`vcf`
`:file`

`tbi`
`:file`

`regions_file`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`dict`
`:file`

`meta5`
`:map`

`code`
`:file`

`meta6`
`:map`

`pedigree`
`:file`

Output

`vcf`

`meta`
`:map`

`*.${extension}`
`:file`

`tbi`

`meta`
`:map`

`*.tbi`
`:file`

`csi`

`meta`
`:map`

`*.csi`
`:file`

`versions`

`versions.yml`
`:file`

Tools

jvarkit
MIT License

bcftools
MIT

maintainer

get in touch

modules/jvarkit_vcffilterjdk

Description

Input

meta:map

vcf:file

tbi:file

regions_file:file

meta2:map

fasta:file

meta3:map

fai:file

meta4:map

dict:file

meta5:map

code:file

meta6:map

pedigree:file

Output

vcf

meta:map

*.${extension}:file

tbi

meta:map

*.tbi:file

csi

meta:map

*.csi:file

versions

versions.yml:file

Tools

jvarkit MIT License

bcftools MIT

maintainer

get in touch

`meta`
`:map`

`vcf`
`:file`

`tbi`
`:file`

`regions_file`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`dict`
`:file`

`meta5`
`:map`

`code`
`:file`

`meta6`
`:map`

`pedigree`
`:file`

`vcf`

`meta`
`:map`

`*.${extension}`
`:file`

`tbi`

`meta`
`:map`

`*.tbi`
`:file`

`csi`

`meta`
`:map`

`*.csi`
`:file`

`versions`

`versions.yml`
`:file`

jvarkit
MIT License

bcftools
MIT