name: kaiju_kaiju
description: Taxonomic classification of metagenomic sequence data using a protein reference database
keywords:
  - classify
  - metagenomics
  - fastq
  - taxonomic profiling
tools:
  - kaiju:
      description: Fast and sensitive taxonomic classification for metagenomics
      homepage: https://kaiju.binf.ku.dk/
      documentation: https://github.com/bioinformatics-centre/kaiju/blob/master/README.md
      tool_dev_url: https://github.com/bioinformatics-centre/kaiju
      doi: "10.1038/ncomms11257"
      licence: ["GNU GPL v3"]

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/fasta files of size 1 and 2 for single-end and paired-end data,
        respectively.
      pattern: "*.{fastq,fq,fasta,fa,fsa,fas,fna,fastq.gz,fq.gz,fasta.gz,fa.gz,fsa.gz,fas.gz,fna.gz}"
  - db:
      type: files
      description: |
        List containing the database and nodes files for Kaiju
        e.g. [ 'database.fmi', 'nodes.dmp' ]

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"
  - results:
      type: file
      description: Results with taxonomic classification of each read
      pattern: "*.tsv"

authors:
  - "@talnor"
  - "@sofstam"
  - "@jfy133"