name: medaka
description: A tool to create consensus sequences and variant calls from nanopore sequencing data
keywords:
  - assembly
  - polishing
  - nanopore
tools:
  - medaka:
      description: Neural network sequence error correction.
      homepage: https://nanoporetech.github.io/medaka/index.html
      documentation: https://nanoporetech.github.io/medaka/index.html
      tool_dev_url: https://github.com/nanoporetech/medaka
      doi: ""
      licence: ["Mozilla Public License 2.0"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: List of input nanopore fasta/FastQ files
      pattern: "*.{fasta,fa,fastq,fastq.gz,fq,fq.gz}"
  - assembly:
      type: file
      description: Genome assembly
      pattern: "*.{fasta,fa}"

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"
  - assembly:
      type: file
      description: Polished genome assembly
      pattern: "*.fa.gz"

authors:
  - "@avantonder"