name: stranger
description: Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes.
keywords:
  - STR
  - repeat_expansions
  - annotate
  - vcf
tools:
  - stranger:
      description: Annotate VCF files with str variants
      homepage: https://github.com/moonso/stranger
      documentation: https://github.com/moonso/stranger
      tool_dev_url: https://github.com/moonso/stranger
      doi: "10.5281/zenodo.4548873"
      licence: ["MIT"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - vcf:
      type: file
      description: VCF with repeat expansions
      pattern: "*.{vcf.gz,vcf}"
  - meta2:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'test' ]
  - variant_catalog:
      type: file
      description: json file with repeat expansion sites to genotype
      pattern: "*.{json}"

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 with keys STR_STATUS, NormalMax and PathologicMin
      pattern: "*.{vcf.gz}"

authors:
  - "@ljmesi"
