name: gatk4_mergevcfs
description: Merges several vcf files
keywords:
  - gatk4
  - merge
  - 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/categories/360002369672s
      doi: 10.1158/1538-7445.AM2017-3590
      licence: ["Apache-2.0"]
      identifier: ""
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}"
  - - meta2:
        type: map
        description: |
          Groovy Map containing reference information
          e.g. [ id:'genome']
    - dict:
        type: file
        description: Optional Sequence Dictionary as input
        pattern: "*.dict"
output:
  - vcf:
      - meta:
          type: file
          description: merged vcf file
          pattern: "*.vcf.gz"
      - "*.vcf.gz":
          type: file
          description: merged vcf file
          pattern: "*.vcf.gz"
  - tbi:
      - meta:
          type: file
          description: index files for the merged vcf files
          pattern: "*.tbi"
      - "*.tbi":
          type: file
          description: index files for the merged vcf files
          pattern: "*.tbi"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@kevinmenden"
maintainers:
  - "@kevinmenden"
