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
  - lua
  - toml
tools:
  - vcfanno:
      description: annotate a VCF with other VCFs/BEDs/tabixed files

      documentation: https://github.com/brentp/vcfanno#vcfanno
      tool_dev_url: https://github.com/brentp/vcfanno
      doi: "10.1186/s13059-016-0973-5"
      license: ["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, vcf.gz}"
  - vcf_tabix:
      type: file
      description: tabix index of query VCF - only needed if vcf is compressed
      pattern: "*.vcf.gz.tbi"
  - specific_resources:
      type: map
      description: A list of sample specific reference files defined in toml config, must also include indices if bgzipped.
  - toml:
      type: file
      description: configuration file with reference file basenames
      pattern: "*.toml"
  - lua:
      type: file
      description: Lua file for custom annotations
      pattern: "*.lua"
  - resources:
      type: map
      description: List of reference files defined in toml config, must also include indices if bgzipped.

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"
  - "@matthdsm"
