name: "gatk4_determinegermlinecontigploidy"
description: Determines the baseline contig ploidy for germline samples given counts data
keywords:
  - gatk4
  - determinegermlinecontigploidy
  - counts
  - 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/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 ]
  - meta2:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - counts:
      type: file
      description: One or more count TSV files created with gatk/collectreadcounts
      pattern: "*.tsv"
  - bed:
      type: file
      description: Optional - A bed file containing the intervals to include in the process
      pattern: "*.bed"
  - exclude_beds:
      type: file
      description: Optional - One or more bed files containing intervals to exclude from the process
      pattern: "*.bed"
  - contig_ploidy_table:
      type: file
      description: The contig ploidy priors table
      pattern: "*.tsv"
  - ploidy_model:
      type: directory
      description: |
        Optional - A folder containing the ploidy model.
        When a model is supplied to tool will run in CASE mode.
        pattern: '*-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"
  - calls:
      type: directory
      description: A folder containing the calls from the input files
      pattern: "*-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: "*-model/"

authors:
  - "@nvnieuwk"
