name: "krakenuniq_preloadedkrakenuniq"
description: Classifies metagenomic sequence data using unique k-mer counts
keywords:
  - classify
  - metagenomics
  - kmers
  - fastq
  - db
tools:
  - "krakenuniq":
      description: "Metagenomics classifier with unique k-mer counting for more specific results"
      homepage: https://github.com/fbreitwieser/krakenuniq
      documentation: https://github.com/fbreitwieser/krakenuniq
      doi: 10.1186/s13059-018-1568-0
      licence: ["MIT"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fastqs:
      type: file
      description: List of input FastQ files
  - db:
      type: directory
      description: KrakenUniq database
  - ram_chunk_size:
      type: val
      description: Amount of maximum amount of RAM each chunk of database that should be loaded at any one time
      pattern: "*GB"
  - save_output_fastqs:
      type: boolean
      description: |
        If true, optional commands are added to save classified and unclassified reads
        as fastq files
  - save_reads_assignment:
      type: boolean
      description: |
        If true, an optional command is added to save a file reporting the taxonomic
        classification of each input read
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - classified_reads_fastq:
      type: file
      description: |
        Reads classified as belonging to any of the taxa
        on the KrakenUniq database.
      pattern: "*{fastq.gz}"
  - unclassified_reads_fastq:
      type: file
      description: |
        Reads not classified to any of the taxa
        on the KrakenUniq database.
      pattern: "*{fastq.gz}"
  - classified_assignment:
      type: file
      description: |
        KrakenUniq output file indicating the taxonomic assignment of
        each input read ## DOUBLE CHECK!!
  - report:
      type: file
      description: |
        KrakenUniq report containing stats about classified
        and not classifed reads.
      pattern: "*.{report.txt}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@mjamy"