name: dragmap_align description: Performs fastq alignment to a reference using DRAGMAP keywords: - alignment - map - fastq - bam - sam tools: - dragmap: description: Dragmap is the Dragen mapper/aligner Open Source Software. homepage: https://github.com/Illumina/dragmap documentation: https://github.com/Illumina/dragmap tool_dev_url: https://github.com/Illumina/dragmap#basic-command-line-usage doi: "" licence: ['GPL v3'] 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. - hashmap: type: file description: DRAGMAP hash table pattern: "Directory containing DRAGMAP hash table *.{cmp,.bin,.txt}" output: - bam: type: file description: Output BAM file containing read alignments pattern: "*.{bam}" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@Emiller88"