name: bismark_deduplicate description: | Removes alignments to the same position in the genome from the Bismark mapping output. 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 ] - bam: type: file description: BAM file containing read alignments pattern: "*.{bam}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: Deduplicated output BAM file containing read alignments pattern: "*.{deduplicated.bam}" - report: type: file description: Bismark deduplication reports pattern: "*.{deduplication_report.txt}" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@phue"