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