name: "motus_profile"
description: Taxonomic meta-omics profiling using universal marker genes
keywords:
  - classify
  - metagenomics
  - fastq
  - taxonomic profiling
tools:
  - "motus":
      description: "Marker gene-based OTU (mOTU) profiling"
      homepage: "https://motu-tool.org/"
      documentation: "https://github.com/motu-tool/mOTUs/wiki"
      tool_dev_url: "https://github.com/motu-tool/mOTUs"
      doi: "10.1038/s41467-019-08844-4"
      licence: "['GPL v3']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
        If input file is the mgc read counts table, the mgc should be set to `true`
        e.g. [ id:'test', single_end:false, mgc:true ]
  - reads:
      type: file
      description: |
        List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data,
        respectively.
        Or the intermediate bam file mapped by bwa to the mOTUs database or
        the output bam file from motus profile.
        Or the intermediate mgc read counts table. Please note if mgc table is input,
        the `mgc` in metadata must be `true`.
      pattern: "*.{fastq,fq,fasta,fa,fastq.gz,fq.gz,fasta.gz,fa.gz,.bam,.tsv,.txt,.mgc}"
  - db:
      type: directory
      description: |
        mOTUs database downloaded by `motus downloadDB`

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"
  - out:
      type: file
      description: Results with taxonomic classification of each read
      pattern: "*.out"
  - bam:
      type: file
      description: Optional intermediate sorted BAM file from BWA
      pattern: "*.{bam}"
  - mgc:
      type: file
      description: Optional intermediate mgc read count table file saved with `-M`.
      pattern: "*.{mgc}"

authors:
  - "@jianhong"