name: gatk4_genotypegvcfs
description: |
  Perform joint genotyping on one or more samples pre-called with HaplotypeCaller.
keywords:
  - joint genotyping
  - genotype
  - gvcf
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"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - gvcf:
      type: file
      description: |
        gVCF(.gz) file or to 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)
  - fasta:
      type: file
      description: Reference fasta file
      pattern: "*.fasta"
  - fai:
      type: file
      description: Reference fasta index file
      pattern: "*.fai"
  - dict:
      type: file
      description: Reference fasta sequence dict file
      pattern: "*.dict"
  - dbsnp:
      type: file
      description: dbSNP VCF file
      pattern: "*.vcf.gz"
  - dbsnp_tbi:
      type: file
      description: dbSNP VCF index file
      pattern: "*.tbi"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - vcf:
      type: file
      description: Genotyped VCF file
      pattern: "*.vcf.gz"
  - tbi:
      type: file
      description: Tbi index for VCF file
      pattern: "*.vcf.gz"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@santiagorevale"
  - "@maxulysse"
