name: hicap
description: Identify cap locus serotype and structure in your Haemophilus influenzae assemblies
keywords:
  - fasta
  - serotype
  - Haemophilus influenzae
tools:
  - hicap:
      description: In silico typing of the H. influenzae capsule locus
      homepage: https://github.com/scwatts/hicap
      documentation: https://github.com/scwatts/hicap
      tool_dev_url: https://github.com/scwatts/hicap
      doi: "https://doi.org/10.1128/JCM.00190-19"
      licence: ["GPL v3"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: file
      description: FASTA formatted assembly file
      pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}"
  - database_dir:
      type: directory
      description: Optional - Directory containing locus database
      pattern: "*/*"
  - model_fp:
      type: file
      description: Optional - Prodigal model to use for gene prediction
      pattern: "*.{bin}"

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"
  - gbk:
      type: file
      description: GenBank file and cap locus annotations
      pattern: "*.gbk"
  - svg:
      type: file
      description: Visualization of annotated cap locus
      pattern: "*.svg"
  - tsv:
      type: file
      description: Detailed summary of cap locus annotations
      pattern: "*.tsv"

authors:
  - "@rpetit3"