name: gatk4_splitintervals
keywords:
  - interval
  - bed
tools:
  - gatk4:
      description: Genome Analysis Toolkit (GATK4)
      homepage: https://gatk.broadinstitute.org/hc/en-us
      documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
      tool_dev_url: https://github.com/broadinstitute/gatk
      doi: "10.1158/1538-7445.AM2017-3590"
      licence: ["BSD-3-clause"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - interval:
      type: file
      description: Interval list or BED
      pattern: "*.{interval,interval_list,bed}"
  - fasta:
      type: file
      description: Reference FASTA
      pattern: "*.{fa,fasta}"
  - fasta_fai:
      type: file
      description: Reference FASTA index
      pattern: "*.fai"
  - dict:
      type: file
      description: Reference sequence dictionary
      pattern: "*.dict"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - bed:
      type: file
      description: A list of scattered interval lists
      pattern: "*.interval_list"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@nvnieuwk"