name: picard_sortvcf
description: Sorts vcf files
keywords:
  - sort
  - vcf
  - sortvcf
tools:
  - picard:
      description: Java tools for working with NGS data in the BAM/CRAM/SAM and VCF format
      homepage: https://broadinstitute.github.io/picard/
      documentation: https://broadinstitute.github.io/picard/command-line-overview.html#SortVcf
      licence: ["MIT"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - vcf:
      type: file
      description: VCF file
      pattern: "*.{vcf,vcf.gz}"
  - meta2:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'genome' ]
  - fasta:
      type: file
      description: Reference genome fasta file
      pattern: "*.{fasta,fa}"
  - meta3:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'genome' ]
  - dict:
      type: file
      description: Reference genome dictionary file
      pattern: "*.{dict}"

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: Sorted VCF file
      pattern: "*.{vcf}"

authors:
  - "@ramprasadn"
