name: gatk4_learnreadorientationmodel
description: |
  Uses f1r2 counts collected during mutect2 to Learn the prior probability of read orientation artifacts
keywords:
  - gatk4
  - learnreadorientationmodel
  - readorientationartifacts
  - mutect2
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' ]
  - f1r2:
      type: list
      description: list of f1r2 files to be used as input.
      pattern: "*.f1r2.tar.gz"

output:
  - artifactprior:
      type: file
      description: file containing artifact-priors to be used by filtermutectcalls
      pattern: "*.tar.gz"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@GCJMackenzie"