name: "gatk4_germlinecnvcaller"
description: Calls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy.
keywords:
  - gatk
  - gatk4_germlinecnvcaller
  - germline contig ploidy
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', single_end:false ]
  - tsv:
      type: file
      description: One or more count TSV files created with gatk/collectreadcounts
      pattern: "*.tsv"
  - intervals:
      type: file
      description: Optional - A bed file containing the intervals to include in the process
      pattern: "*.bed"
  - model:
      type: directory
      description: Optional - directory containing the model produced by germlinecnvcaller cohort mode
      pattern: "*-cnv-model/*-model"
  - ploidy:
      type: file
      description: Directory containing ploidy calls produced by determinegermlinecontigploidy case or cohort mode
      pattern: "*-calls"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - calls:
      type: file
      description: Tar gzipped directory containing calls produced by germlinecnvcaller case mode
      pattern: "*-cnv-calls/*-calls"
  - model:
      type: directory
      description: Optional - Tar gzipped directory containing the model produced by germlinecnvcaller cohort mode
      pattern: "*-cnv-model/*-model"

authors:
  - "@ryanjameskennedy"
  - "@ViktorHy"
