name: ismapper description: Identify insertion sites positions in bacterial genomes keywords: - fastq - insertion sequences tools: - ismapper: description: A mapping-based tool for identification of the site and orientation of IS insertions in bacterial genomes. homepage: https://github.com/jhawkey/IS_mapper documentation: https://github.com/jhawkey/IS_mapper tool_dev_url: https://github.com/jhawkey/IS_mapper doi: "https://doi.org/10.1186/s12864-015-1860-2" licence: ['BSD'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: type: file description: A set of paired-end FASTQ files pattern: "*.{fastq.gz,fq.gz}" - reference: type: file description: Reference genome in GenBank format pattern: "*.{gbk}" - query: type: file description: Insertion sequences to query in FASTA format pattern: "*.{fasta,fa}" 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" - results: type: directory description: Directory containing ISMapper result files pattern: "*/*" authors: - "@rpetit3"