name: minia
description: Minia is a short-read assembler based on a de Bruijn graph
keywords:
  - assembly
tools:
  - minia:
      description: |
        Minia is a short-read assembler based on a de Bruijn graph, capable of assembling
        a human genome on a desktop computer in a day. The output of Minia is a set of contigs.
      homepage: https://github.com/GATB/minia
      documentation: https://github.com/GATB/minia
params:
  - outdir:
      type: string
      description: |
        The pipeline's output directory. By default, the module will
        output files into `$params.outdir/<SOFTWARE>`
  - publish_dir_mode:
      type: string
      description: |
        Value for the Nextflow `publishDir` mode parameter.
        Available: symlink, rellink, link, copy, copyNoFollow, move.
  - enable_conda:
      type: boolean
      description: |
        Run the module with Conda using the software specified
        via the `conda` directive
  - singularity_pull_docker_container:
      type: boolean
      description: |
        Instead of directly downloading Singularity images for use with Singularity,
        force the workflow to pull and convert Docker containers instead.
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: Input reads in FastQ format
      pattern: "*.{fastq.gz, fastq}"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - contigs:
      type: file
      description: The assembled contigs
      pattern: "*.contigs.fa"
  - unitigs:
      type: file
      description: The assembled unitigs
      pattern: "*.unitigs.fa"
  - h5:
      type: file
      description: Minia output h5 file
      pattern: "*{.h5}"
  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"
authors:
  - "@drpatelh"
  - "@kevinmenden"