---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
name: "ganon_report"
description: Generate a ganon report file from the output of ganon classify
keywords:
  - ganon
  - metagenomics
  - profiling
  - taxonomy
  - k-mer
  - classification
  - report
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 ]
  - rep:
      type: file
      description: Input 'repo' files from ganon classify
      pattern: "*.rep"
  - 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: Output ganon report containing taxonomic profile information. Formatting of contents depends on --output-format.
      pattern: "*.tre"

authors:
  - "@jfy133"
