name: gatk4_indexfeaturefile
description: Creates an index for a feature file, e.g. VCF or BED file.
keywords:
  - index
  - feature
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', single_end:false ]
  - feature_file:
      type: file
      description: VCF/BED file
      pattern: "*.{vcf,vcf.gz,bed,bed.gz}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - index:
      type: file
      description: Index for VCF/BED file
      pattern: "*.{tbi,idx}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@santiagorevale"