name: kraken2_kraken2
description: Classifies metagenomic sequence data
keywords:
  - classify
  - metagenomics
  - fastq
  - db
tools:
  - kraken2:
      description: |
        Kraken2 is a taxonomic sequence classifier that assigns taxonomic labels to sequence reads
      homepage: https://ccb.jhu.edu/software/kraken2/
      documentation: https://github.com/DerrickWood/kraken2/wiki/Manual
      doi: 10.1186/s13059-019-1891-0
      licence: ["MIT"]
      identifier: biotools:kraken2
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - reads:
        type: file
        description: |
          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
          respectively.
  - - db:
        type: directory
        description: Kraken2 database
  - - save_output_fastqs:
        type: string
        description: |
          If true, optional commands are added to save classified and unclassified reads
          as fastq files
  - - save_reads_assignment:
        type: string
        description: |
          If true, an optional command is added to save a file reporting the taxonomic
          classification of each input read
output:
  - classified_reads_fastq:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.classified{.,_}*":
          type: file
          description: |
            Reads classified as belonging to any of the taxa
            on the Kraken2 database.
          pattern: "*{fastq.gz}"
  - unclassified_reads_fastq:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.unclassified{.,_}*":
          type: file
          description: |
            Reads not classified to any of the taxa
            on the Kraken2 database.
          pattern: "*{fastq.gz}"
  - classified_reads_assignment:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*classifiedreads.txt":
          type: file
          description: |
            Kraken2 output file indicating the taxonomic assignment of
            each input read
  - report:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*report.txt":
          type: file
          description: |
            Kraken2 report containing stats about classified
            and not classifed reads.
          pattern: "*.{report.txt}"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@joseespinosa"
  - "@drpatelh"
maintainers:
  - "@joseespinosa"
  - "@drpatelh"
