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"]
      identifier: ""
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:
  - contigs:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.fa":
          type: file
          description: The final assembly produced by Dragonflye
          pattern: "*.fa"
  - log:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - dragonflye.log:
          type: file
          description: Full log file for bug reporting
          pattern: "dragonflye.log"
  - raw_contigs:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "{flye,miniasm,raven}.fasta":
          type: file
          description: Raw assembly produced by the assembler (Flye, Miniasm, or Raven)
          pattern: "{flye,miniasm,raven}.fasta"
  - gfa:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "{flye,miniasm,raven}-unpolished.gfa":
          type: file
          description: Assembly graph produced by Miniasm, or Raven
          pattern: "{flye,miniasm,raven}-unpolished.gfa"
  - txt:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - flye-info.txt:
          type: file
          description: Assembly information output by Flye
          pattern: "flye-info.txt"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@rpetit3"
maintainers:
  - "@rpetit3"
