name: methyldackel_mbias description: Generates methylation bias plots from alignments keywords: - methylation - 5mC - methylseq - bisulphite - methylation bias - mbias - qc - bam - cram tools: - methyldackel: description: | A (mostly) universal methylation extractor for BS-seq experiments. homepage: https://github.com/brentp/bwa-meth documentation: https://github.com/brentp/bwa-meth arxiv: arXiv:1401.1129 input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - fasta: type: file description: Input genome fasta file pattern: "*.{fasta,fa}" - fai: type: file description: FASTA index file pattern: "*.{fai}" - bam: type: file description: BAM/CRAM file pattern: "*.{bam,cram}" - bai: type: file description: BAM/CRAM index file pattern: "*.{bai,crai}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - txt: type: file description: Text file containing methylation bias pattern: "*.{txt}" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@phue"