name: bismark_methylationextractor description: Extracts methylation information for individual cytosines from alignments. keywords: - bismark - consensus - map - methylation - 5mC - methylseq - bisulphite - bam - bedGraph 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}" - 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 ] - bedgraph: type: file description: Bismark output file containing coverage and methylation metrics pattern: "*.{bedGraph.gz}" - methylation_calls: type: file description: Bismark output file containing strand-specific methylation calls pattern: "*.{txt.gz}" - coverage: type: file description: Bismark output file containing coverage metrics pattern: "*.{cov.gz}" - report: type: file description: Bismark splitting reports pattern: "*_{splitting_report.txt}" - mbias: type: file description: Text file containing methylation bias information pattern: "*.{M-bias.txt}" - version: type: file description: File containing software version pattern: "versions.yml" authors: - "@phue"