name: "ganon_classify"
description: Classify FASTQ files against ganon database
keywords:
  - ganon
  - metagenomics
  - profiling
  - taxonomy
  - k-mer
  - classification
  - classify
tools:
  - "ganon":
      description: "ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently"
      homepage: "https://github.com/pirovc/ganon"
      documentation: "https://github.com/pirovc/ganon"
      tool_dev_url: "https://github.com/pirovc/ganon"
      doi: "10.1093/bioinformatics/btaa458"
      licence: "['MIT License']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fastqs:
      type: file
      description: Single or paired FASTQ files, optionally gzipped
      pattern: "*.{fq,fq.gz,fastq,fastq.gz}"
  - dbs:
      type: file
      description: Ganon database files from build or build-custom
      pattern: "*.{ibf,tax}"

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"
  - tre:
      type: file
      description: Full ganon report file
      pattern: "*.tre"
  - report:
      type: file
      description: Plain ganon report file with only targets with match
      pattern: "*.rep"
  - lca:
      type: file
      description: Information about the lowest common ancestor match of a given read
      pattern: "*.lca"
  - all:
      type: file
      description: Information of all matches to a given read
      pattern: "*.all"
  - unc:
      type: file
      description: List of all reads without a hit
      pattern: "*.unc"
  - log:
      type: file
      description: Text file containing console output from ganon classify
      pattern: "*.log"

authors:
  - "@jfy133"
