name: yara_mapper description: Align reads to a reference genome using YARA keywords: - align - genome - reference tools: - yara: description: Yara is an exact tool for aligning DNA sequencing reads to reference genomes. homepage: https://github.com/seqan/seqan documentation: https://github.com/seqan/seqan tool_dev_url: https://github.com/seqan/seqan doi: "" licence: ['https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: type: file description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. - index: type: file description: YARA genome index files 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" - bam: type: file description: Sorted BAM file pattern: "*.{bam}" authors: - "@apeltzer"