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 params: - outdir: type: string description: | The pipeline's output directory. By default, the module will output files into `$params.outdir/` - publish_dir_mode: type: string description: | Value for the Nextflow `publishDir` mode parameter. Available: symlink, rellink, link, copy, copyNoFollow, move. - enable_conda: type: boolean description: | Run the module with Conda using the software specified via the `conda` directive - singularity_pull_docker_container: type: boolean description: | Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead. 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}" - version: type: file description: File containing software version pattern: "*.{version.txt}" authors: - "@phue"