name: bwameth_align description: Performs alignment of BS-Seq reads using bwameth keywords: - bwameth - alignment - 3-letter genome - map - methylation - 5mC - methylseq - bisulphite - fastq - bam tools: - bwameth: description: | Fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome. homepage: https://github.com/brentp/bwa-meth documentation: https://github.com/brentp/bwa-meth arxiv: arXiv:1401.1129 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: dir description: Directory containing bwameth genome index output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: Output BAM file containing read alignments pattern: "*.{bam}" - version: type: file description: File containing software version pattern: "versions.yml" authors: - "@phue"