name: Shovill
description: Create a bacterial assembly from paired fastq using shovill
keywords:
    - Genome Assembly
    - Bacterial Isolates
tools:
    - fastqc:
        description: |
            Shovill assembles bacterial isolate genomes from Illumina
            paired-end reads. Shovill uses the SPAdes genome assembler,
            providing pre and post-processing to the SPAdes assembly.
            It also supports SKESA, Velvet and Megahit.
        homepage: https://github.com/tseemann/shovill
        documentation: https://github.com/tseemann/shovill/blob/master/README.md
input:
    -
        - sample_id:
            type: string
            description: Sample identifier
        - reads:
            type: file
            description: pair of fastq files
output:
    -
        - assembly:
            type: file
            description: fasta file
            pattern: ${sample_id}.fasta
authors:
    - "@annacprice"