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:
  - 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}"
  - bai:
      type: file
      description: Index of the BAM file
      pattern: "*.bai"
  - bed:
      type: file
      description: BED with the regions of interest
      pattern: "*.bed"
  - fasta:
      type: file
      description: FASTA of the reference genome
      pattern: "*.{fa,fasta}"
  - fasta_fai:
      type: file
      description: The index of the FASTA of the reference genome
      pattern: "*.fai"

output:
  - 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"