name: "gatk4_postprocessgermlinecnvcalls"
description: Postprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios
keywords:
  - gatk4
  - postprocessgermlinecnvcalls
  - copy number
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/articles/360037593411-PostprocessGermlineCNVCalls
      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 ]
  - ploidy:
      type: directory
      description: |
        Optional - A folder containing the ploidy model.
        When a model is supplied to tool will run in CASE mode.
      pattern: "*-calls/"
  - calls:
      type: directory
      description: A folder containing the calls from the input files
      pattern: "*-cnv-calls/*-calls"
  - model:
      type: directory
      description: |
        A folder containing the model from the input files.
        This will only be created in COHORT mode (when no model is supplied to the process).
      pattern: "*-cnv-model/*-model"

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"
  - denoised:
      type: file
      description: Denoised copy ratio file
      pattern: "*.vcf.gz"
  - segments:
      type: file
      description: Segments VCF file
      pattern: "*.vcf.gz"
  - intervals:
      type: file
      description: Intervals VCF file
      pattern: "*.vcf.gz"

authors:
  - "@ryanjameskennedy"
