name: bismark_report description: Collects bismark alignment reports keywords: - bismark - qc - methylation - 5mC - methylseq - bisulphite - report 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 licence: ['GPL-3.0-or-later'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - align_report: type: file description: Bismark alignment reports pattern: "*{report.txt}" - splitting_report: type: file description: Bismark splitting reports pattern: "*{splitting_report.txt}" - dedup_report: type: file description: Bismark deduplication reports pattern: "*.{deduplication_report.txt}" - mbias: type: file description: Text file containing methylation bias information pattern: "*.{txt}" - fasta: type: file description: Input genome fasta file output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - report: type: file description: Bismark reports pattern: "*.{html,txt}" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@phue"