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
      licence: ['AGPL-3.0-or-later']
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}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@drpatelh"
  - "@kevinmenden"