name: tbprofiler_profile
description: A tool to detect resistance and lineages of M. tuberculosis genomes
keywords:
  - Mycobacterium tuberculosis
  - resistance
  - serotype
tools:
  - tbprofiler:
      description: Profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from WGS data
      homepage: https://github.com/jodyphelan/TBProfiler
      documentation: https://jodyphelan.gitbook.io/tb-profiler/
      tool_dev_url: https://github.com/jodyphelan/TBProfiler
      doi: "10.1186/s13073-019-0650-x"
      licence: ['GPL v3']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: FASTQ file
      pattern: "*.{fastq.gz,fq.gz}"

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"
  - bam:
      type: file
      description: BAM file with alignment details
      pattern: "*.bam"
  - csv:
      type: file
      description: Optional CSV formated result file of resistance and strain type
      pattern: "*.csv"
  - json:
      type: file
      description: JSON formated result file of resistance and strain type
      pattern: "*.json"
  - txt:
      type: file
      description: Optional text file of resistance and strain type
      pattern: "*.txt"
  - vcf:
      type: file
      description: VCF with variant info again refernce genomes
      pattern: "*.vcf"

authors:
  - "@rpetit3"