name: bismark_genomepreparation description: | Converts a specified reference genome into two different bisulfite converted versions and indexes them for alignments. keywords: - bismark - 3-letter genome - index - methylation - 5mC - methylseq - bisulphite - fasta 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: - fasta: type: file description: Input genome fasta file output: - index: type: dir description: Bismark genome index directory pattern: "BismarkIndex" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@phue"