name: kraken2_run
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
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
output:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - classified:
        type: file
        description: |
            Reads classified to belong to any of the taxa
            on the Kraken2 database.
        pattern: "*{fastq.gz}"
    - unclassified:
        type: file
        description: |
            Reads not classified to belong to any of the taxa
            on the Kraken2 database.
        pattern: "*{fastq.gz}"
    - txt:
        type: file
        description: |
            Kraken2 report containing stats about classified
            and not classifed reads.
        pattern: "*.{report.txt}"
    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"
authors:
    - "@joseespinosa"
    - "@drpatelh"