name: mummer description: MUMmer is a system for rapidly aligning entire genomes keywords: - align - genome - fasta tools: - mummer: description: MUMmer is a system for rapidly aligning entire genomes homepage: http://mummer.sourceforge.net/ documentation: http://mummer.sourceforge.net/ tool_dev_url: http://mummer.sourceforge.net/ doi: https://doi.org/10.1186/gb-2004-5-2-r12 licence: ["The Artistic License"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - ref: type: file description: FASTA file of the reference sequence pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" - query: type: file description: FASTA file of the query sequence pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" 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" - coords: type: file description: File containing coordinates of matches between reference and query sequence pattern: "*.coords" authors: - "@mjcipriano" - "@sateeshperi"