name: gatk4_mergevcfs
description: Merges several vcf files
keywords:
  - vcf
  - merge
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: Two or more VCF files
      pattern: "*.{vcf,vcf.gz}"
  - ref_dict:
      type: file
      description: Optional Sequence Dictionary as input
      pattern: "*.dict"
  - use_ref_dict:
      type: boolean
      description: Specify whether or not to use a given reference dictionary
output:
  - vcf:
      type: file
      description: merged vcf file
      pattern: "*.vcf.gz"
  - tbi:
      type: file
      description: index files for the merged vcf files
      pattern: "*.tbi"

  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@kevinmenden"