name: gatk4_createsomaticpanelofnormals
description: Create a panel of normals contraining germline and artifactual sites for use with mutect2.
keywords:
  - gatk4
  - createsomaticpanelofnormals
  - panelofnormals
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

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test']
  - genoomicsdb:
      type: directory
      description: genomicsDB workspace that contains the samples to create the somatic panel of normals with.
      pattern: "*_genomicsDBworkspace"
  - fasta:
      type: file
      description: The reference fasta file
      pattern: "*.fasta"
  - fastaidx:
      type: file
      description: Index of reference fasta file
      pattern: "fasta.fai"
  - dict:
      type: file
      description: GATK sequence dictionary
      pattern: "*.dict"

output:
  - vcf:
      type: file
      description: panel of normal as compressed vcf file
      pattern: "*.vcf.gz"
  - tbi:
      type: file
      description: Index of vcf file
      pattern: "*vcf.gz.tbi"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@GCJMackenzie"