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 ]
  - 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
      pattern: "*.{fastq,fq,fasta,fa,fastq.gz,fq.gz,fasta.gz,fa.gz,.bam}"
  - 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}"

authors:
  - "@jianhong"