name: gatk4_variantfiltration
description: Filter variants
keywords:
  - vcf
  - filter
  - variantfiltration
tools:
  - gatk4:
      description: |
        Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
        with a primary focus on variant discovery and genotyping. Its powerful processing engine
        and high-performance computing features make it capable of taking on projects of any size.
      homepage: https://gatk.broadinstitute.org/hc/en-us
      documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
      doi: 10.1158/1538-7445.AM2017-3590
      licence: ["Apache-2.0"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test']
  - vcf:
      type: list
      description: List of VCF(.gz) files
      pattern: "*.{vcf,vcf.gz}"
  - vcf_tbi:
      type: list
      description: List of VCF file indexes
      pattern: "*.{idx,tbi}"
  - meta2:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'genome' ]
  - fasta:
      type: file
      description: Fasta file of reference genome
      pattern: "*.fasta"
  - meta3:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'genome' ]
  - fai:
      type: file
      description: Index of fasta file
      pattern: "*.fasta.fai"
  - meta4:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'genome' ]
  - dict:
      type: file
      description: Sequence dictionary of fastea file
      pattern: "*.dict"
output:
  - vcf:
      type: file
      description: Compressed VCF file
      pattern: "*.vcf.gz"
  - tbi:
      type: file
      description: Index of VCF file
      pattern: "*.vcf.gz.tbi"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@kevinmenden"
  - "@ramprasadn"
