name: nucmer description: NUCmer is a pipeline for the alignment of multiple closely related nucleotide sequences. keywords: - align - nucleotide tools: - nucmer: description: NUCmer is a pipeline for the alignment of multiple closely related nucleotide sequences. 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" - delta: type: file description: File containing coordinates of matches between reference and query - coords: type: file description: NUCmer1.1 coords output file pattern: "*.{coords}" authors: - "@sateeshperi" - "@mjcipriano"