name: "svtk_standardize"
description: Convert SV calls to a standardized format.
keywords:
  - svtk
  - structural variants
  - SV
  - vcf
  - standardization
tools:
  - "svtk":
      description: "Utilities for consolidating, filtering, resolving, and annotating structural variants."
      homepage: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
      documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
      tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
      doi: ""
      licence: "['MIT']"

input:
  - args:
      type: map
      description: |
        Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters must be set between quotes.
        ```
        {
          [
            "args": "",
            "caller": "delly" // Should be either delly, lumpy, manta, wham or melt
          ]
        }
        ```
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - vcf:
      type: file
      description: A gzipped VCF file to be standardized
      pattern: "*.vcf.gz"
  - fasta_fai:
      type: file
      description: Optional fasta index file that specifies the contigs to be used in the VCF header (defaults to all contigs of GRCh37)
      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"
  - standardized_vcf:
      type: file
      description: A gzipped version of the standardized VCF file
      pattern: "*.std.vcf.gz"

authors:
  - "@nvnieuwk"