name: shovill
description: Assemble bacterial isolate genomes from Illumina paired-end reads
keywords:
  - bacterial
  - assembly
  - illumina

tools:
  - shovill:
      description: Microbial assembly pipeline for Illumina paired-end reads
      homepage: https://github.com/tseemann/shovill
      documentation: https://github.com/tseemann/shovill/blob/master/README.md
      licence: ["GPL v2"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: List of input paired-end FastQ files

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"
  - contigs:
      type: file
      description: The final assembly produced by Shovill
      pattern: "contigs.fa"
  - corrections:
      type: file
      description: List of post-assembly corrections made by Shovill
      pattern: "shovill.corrections"
  - log:
      type: file
      description: Full log file for bug reporting
      pattern: "shovill.log"
  - raw_contigs:
      type: file
      description: Raw assembly produced by the assembler (SKESA, SPAdes, MEGAHIT, or Velvet)
      pattern: "{skesa,spades,megahit,velvet}.fasta"
  - gfa:
      type: file
      description: Assembly graph produced by MEGAHIT, SPAdes, or Velvet
      pattern: "contigs.{fastg,gfa,LastGraph}"

authors:
  - "@rpetit3"