name: vcfanno
description: quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files
keywords:
  - vcf
  - bed
  - annotate
  - variant
tools:
  - vcfanno:
      description: annotate a VCF with other VCFs/BEDs/tabixed files
      homepage: None
      documentation: https://github.com/brentp/vcfanno#vcfanno
      tool_dev_url: https://github.com/brentp/vcfanno
      doi: "10.1186/s13059-016-0973-5"
      licence: ["MIT"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - vcf:
      type: file
      description: query VCF file
      pattern: "*.{vcf.gz}"
  - vcf.tbi:
      type: file
      description: query VCF file index
      pattern: "*.{vcf.gz.tbi}"
  - vcfanno_config:
      type: file
      description: |
        A simple configuration file is used to specify both the source files
        and the set of attributes (in the case of VCF)
        or columns (in the case of BED or other tab-delimited formats)
        that should be added to the query file.
      pattern: "*.{toml}"

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

authors:
  - "@projectoriented"