name: optitype
description: Perform HLA-I typing of sequencing data
keywords:
  - hla-typing
  - ILP
  - HLA-I
tools:
  - optitype:
      description: Precision HLA typing from next-generation sequencing data
      homepage: https://github.com/FRED-2/OptiType
      documentation: https://github.com/FRED-2/OptiType
      doi: "10.1093/bioinformatics/btu548"
      licence: ["BSD-3-Clause"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: BAM file
      pattern: "*.{bam}"
  - bai:
      type: file
      description: BAM index file
      pattern: "*.{bai}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', seq_type:'DNA' ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - output:
      type: file
      description: OptiType Results Folder
      pattern: "${prefix}"
  - pdf:
      type: file
      description: OptiType PDF Plots
      pattern: "*.pdf"

authors:
  - "@apeltzer"
