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"