name: gatk4_combinegvcfs
description: Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file
keywords:
  - gvcf
  - gatk4
  - vcf
  - combinegvcfs
  - Short_Variant_Discovery
tools:
  - gatk4:
      description:
        Genome Analysis Toolkit (GATK4). 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/360037593911-CombineGVCFs
      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: file
      description: Compressed VCF files
      pattern: "*.vcf.gz"
  - vcf_idx:
      type: file
      description: VCF Index file
      pattern: "*.vcf.gz.idx"
  - fasta:
      type: file
      description: The reference fasta file
      pattern: "*.fasta"
  - fai:
      type: file
      description: FASTA index file
      pattern: "*.fasta.fai"
  - dict:
      type: file
      description: FASTA dictionary file
      pattern: "*.dict"
output:
  - gvcf:
      type: file
      description: Compressed Combined GVCF file
      pattern: "*.combined.g.vcf.gz"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@sateeshperi"
  - "@mjcipriano"
  - "@hseabolt"
  - "@maxulysse"