name: bismark_align description: Performs alignment of BS-Seq reads using bismark keywords: - bismark - 3-letter genome - map - methylation - 5mC - methylseq - bisulphite - bam tools: - bismark: description: | Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion. homepage: https://github.com/FelixKrueger/Bismark documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 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: Bismark genome index directory pattern: "BismarkIndex" 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}" - unmapped: type: file description: Output FastQ file(s) containing unmapped reads pattern: "*.{fq.gz}" - report: type: file description: Bismark alignment reports pattern: "*{report.txt}" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@phue"