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"