name: unicycler
description: Assembles bacterial genomes
keywords:
  - genome
  - assembly
  - genome assembler
  - small genome
tools:
  - unicycler:
      description: Hybrid assembly pipeline for bacterial genomes
      homepage: https://github.com/rrwick/Unicycler
      documentation: https://github.com/rrwick/Unicycler
      tool_dev_url: https://github.com/rrwick/Unicycler
      doi: 10.1371/journal.pcbi.1005595
      licence: ["GPL v3"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - shortreads:
      type: file
      description: |
        List of input Illumina FastQ files of size 1 and 2 for single-end and paired-end data,
        respectively.
  - longreads:
      type: file
      description: |
        List of input FastQ files of size 1, PacBio or Nanopore long reads.
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"
  - scaffolds:
      type: file
      description: Fasta file containing scaffolds
      pattern: "*.{scaffolds.fa.gz}"
  - gfa:
      type: file
      description: gfa file containing assembly
      pattern: "*.{assembly.gfa.gz}"
  - log:
      type: file
      description: unicycler log file
      pattern: "*.{log}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@JoseEspinosa"
  - "@drpatelh"
  - "@d4straub"