name: "vardictjava"

description: The Java port of the VarDict variant caller
keywords:
  - variant calling
  - VarDict
  - AstraZeneca
tools:
  - "vardictjava":
      description: "Java port of the VarDict variant discovery program"
      homepage: "https://github.com/AstraZeneca-NGS/VarDictJava"
      documentation: "https://github.com/AstraZeneca-NGS/VarDictJava"
      tool_dev_url: "https://github.com/AstraZeneca-NGS/VarDictJava"
      doi: "10.1093/nar/gkw227 "
      licence: "['MIT']"

input:
  # Only when we have meta
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]

  - bam:
      type: file
      description: BAM/SAM file
      pattern: "*.{bam,sam}"
  
  - reference_fasta:
      type: file
      description: FASTA of the reference genome
      pattern: "*.{fa,fasta}"

  - regions_of_interest:
      type: file
      description: BED with the regions of interest
      pattern: "*.bed"

output:
  #Only when we have meta
  - 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"

  - vcf:
      type: file
      description: VCF file output
      pattern: "*.vcf.gz"

authors:
  - "@nvnieuwk"