name: racon
description: Consensus module for raw de novo DNA assembly of long uncorrected reads
keywords:
  - assembly
  - pacbio
  - nanopore
  - polish
tools:
  - racon:
      description: Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.
      homepage: https://github.com/lbcb-sci/racon
      documentation: https://github.com/lbcb-sci/racon
      tool_dev_url: https://github.com/lbcb-sci/racon
      doi: https://doi.org/10.1101/gr.214270.116
      licence: ['MIT']

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 files. Racon expects single end reads
      pattern: "*.{fastq,fastq.gz,fq,fq.gz}"
  - assembly:
      type: file
      description: Genome assembly to be improved
      pattern: "*.{fasta,fa}"
  - paf:
      type: file
      description: Alignment in PAF format
      pattern: "*.paf"

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"
  - improved_assembly:
      type: file
      description: Improved genome assembly
      pattern: "*_assembly_consensus.fasta.gz"

authors:
  - "@avantonder"