name: gatk4_selectvariants
description: Select a subset of variants from a VCF file
keywords:
  - gatk
  - gatk4
  - selectvariants
  - vcf
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/articles/360036362532-SelectVariants
      tool_dev_url: https://github.com/broadinstitute/gatk
      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: VCF(.gz) file
      pattern: "*.{vcf,vcf.gz}"
  - vcf_idx:
      type: list
      description: VCF file index
      pattern: "*.{idx,tbi}"
  - intervals:
      type: file
      description: One or more genomic intervals over which to operate
      pattern: ".intervals"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - vcf:
      type: file
      description: Compressed VCF file
      pattern: "*.selectvariants.vcf.gz"
  - vcf_tbi:
      type: list
      description: VCF file index
      pattern: "*.{idx,tbi}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@mjcipriano"
  - "@ramprasadn"
