name: bwameth_index description: Performs indexing of c2t converted reference genome keywords: - bwameth - 3-letter genome - index - methylseq - bisulphite - fasta tools: - bwameth: description: | Fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome. 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: - fasta: type: file description: Input genome fasta file output: - index: type: dir description: Directory containing bwameth genome index pattern: "index" - version: type: file description: File containing software version pattern: "*.{version.txt}" authors: - "@phue"