name: gatk4_genotypegvcfs
description: |
  Perform joint genotyping on one or more samples pre-called with HaplotypeCaller.
keywords:
  - gatk4
  - genotype
  - gvcf
  - joint genotyping
tools:
  - gatk4:
      description: Genome Analysis Toolkit (GATK4)
      homepage: https://gatk.broadinstitute.org/hc/en-us
      documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
      tool_dev_url: https://github.com/broadinstitute/gatk
      doi: "10.1158/1538-7445.AM2017-3590"
      licence: ["BSD-3-clause"]
      identifier: ""
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - input:
        type: file
        description: |
          gVCF(.gz) file or a GenomicsDB
        pattern: "*.{vcf,vcf.gz}"
    - gvcf_index:
        type: file
        description: |
          index of gvcf file, or empty when providing GenomicsDB
        pattern: "*.{idx,tbi}"
    - intervals:
        type: file
        description: Interval file with the genomic regions included in the library
          (optional)
    - intervals_index:
        type: file
        description: Interval index file (optional)
  - - meta2:
        type: map
        description: |
          Groovy Map containing fasta information
          e.g. [ id:'test' ]
    - fasta:
        type: file
        description: Reference fasta file
        pattern: "*.fasta"
  - - meta3:
        type: map
        description: |
          Groovy Map containing fai information
          e.g. [ id:'test' ]
    - fai:
        type: file
        description: Reference fasta index file
        pattern: "*.fai"
  - - meta4:
        type: map
        description: |
          Groovy Map containing dict information
          e.g. [ id:'test' ]
    - dict:
        type: file
        description: Reference fasta sequence dict file
        pattern: "*.dict"
  - - meta5:
        type: map
        description: |
          Groovy Map containing dbsnp information
          e.g. [ id:'test' ]
    - dbsnp:
        type: file
        description: dbSNP VCF file
        pattern: "*.vcf.gz"
  - - meta6:
        type: map
        description: |
          Groovy Map containing dbsnp tbi information
          e.g. [ id:'test' ]
    - dbsnp_tbi:
        type: file
        description: dbSNP VCF index file
        pattern: "*.tbi"
output:
  - vcf:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.vcf.gz":
          type: file
          description: Genotyped VCF file
          pattern: "*.vcf.gz"
  - tbi:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.tbi":
          type: file
          description: Tbi index for VCF file
          pattern: "*.vcf.gz"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@santiagorevale"
  - "@maxulysse"
maintainers:
  - "@santiagorevale"
  - "@maxulysse"
