name: expansionhunter
description: Estimate repeat sizes using NGS data
keywords:
  - STR
  - repeat_expansions
  - bam
  - cram
  - vcf
  - json
tools:
  - expansionhunter:
      description: A tool for estimating repeat sizes
      homepage: https://github.com/Illumina/ExpansionHunter
      documentation: https://github.com/Illumina/ExpansionHunter/blob/master/docs/01_Introduction.md
      doi: "10.1093/bioinformatics/btz431"
      licence: ["Apache-2.0"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: BAM/CRAM file
      pattern: "*.{bam,cram}"
  - meta2:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'test' ]
  - fasta:
      type: file
      description: Reference genome
      pattern: "*.{fna,fa,fasta}"
  - meta3:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'test' ]
  - fasta:
      type: file
      description: Reference genome index
      pattern: "*.fai"
  - meta4:
      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', gender:'female' ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - vcf:
      type: file
      description: VCF with repeat expansions
      pattern: "*.vcf.gz"
  - json:
      type: file
      description: JSON with repeat expansions
      pattern: "*.json.gz"

authors:
  - "@jemten"
