name: "gatk4_denoisereadcounts"
description: Denoises read counts to produce denoised copy ratios
keywords:
  - copyratios
  - denoisereadcounts
  - gatk4
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
      tool_dev_url: "https://github.com/broadinstitute/gatk"
      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', single_end:false ]`
  - counts:
      type: file
      description: Read counts in hdf5 or tsv format.
      pattern: "*.{hdf5,tsv}"
  - pon:
      type: file
      description: Panel of normals file hdf5 or tsv format.
      pattern: "*.{hdf5}"
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"
  - standardized:
      type: file
      description: Standardized copy ratios file.
      pattern: "*.{tsv}"
  - denoised:
      type: file
      description: Denoised copy ratios file
      pattern: "*.{tsv}"
authors:
  - "@ramprasadn"
maintainers:
  - "@ramprasadn"
