name: svdb_query
description: Query a structural variant database, using a vcf file as query
keywords:
  - structural variants
  - query
  - svdb
tools:
  - svdb:
      description: structural variant database software
      homepage: https://github.com/J35P312/SVDB
      documentation: https://github.com/J35P312/SVDB/blob/master/README.md
      licence: ["MIT"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - in_occs:
      type: list
      description: A list of allele count tags
  - in_frqs:
      type: list
      description: A list of allele frequency tags
  - vcf:
      type: file
      description: query vcf file
      pattern: "*.{vcf,vcf.gz}"
  - vcf_dbs:
      type: file
      description: path to a database vcf, or a comma separated list of vcfs
      pattern: "*.{vcf,vcf.gz}"
  - bedpe_dbs:
      type: file
      description: path to a SV database of the following format chrA-posA-chrB-posB-type-count-frequency, or a comma separated list of files
      pattern: "*.{bedpe}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - out_occs:
      type: list
      description: A list of allele count tags
  - out_frqs:
      type: list
      description: A list of allele frequency tags
  - vcf:
      type: file
      description: Annotated output VCF file
      pattern: "*_query.vcf"

authors:
  - "@ramprasadn"
