name: dragonflye
description: Assemble bacterial isolate genomes from Nanopore reads
keywords:
  - bacterial
  - assembly
  - nanopore
tools:
  - dragonflye:
      description: Microbial assembly pipeline for Nanopore reads
      homepage: https://github.com/rpetit3/dragonflye
      documentation: https://github.com/rpetit3/dragonflye/blob/main/README.md
      licence: ["GPL v2"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - shortreads:
      type: file
      description: |
        Optional. List of FastQ files of short reads (paired-end data) that will be used to polish the draft genome.
      pattern: "*.fastq.gz"
  - longreads:
      type: file
      description: Input Nanopore FASTQ file
      pattern: "*.fastq.gz"
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"
  - contigs:
      type: file
      description: The final assembly produced by Dragonflye
      pattern: "*.fa"
  - log:
      type: file
      description: Full log file for bug reporting
      pattern: "dragonflye.log"
  - raw_contigs:
      type: file
      description: Raw assembly produced by the assembler (Flye, Miniasm, or Raven)
      pattern: "{flye,miniasm,raven}.fasta"
  - txt:
      type: file
      description: Assembly information output by Flye
      pattern: "flye-info.txt"
  - gfa:
      type: file
      description: Assembly graph produced by Miniasm, or Raven
      pattern: "{flye,miniasm,raven}-unpolished.gfa"
authors:
  - "@rpetit3"
maintainers:
  - "@rpetit3"
