name: mtnucratio description: A small Java tool to calculate ratios between MT and nuclear sequencing reads in a given BAM file. keywords: - mtnucratio - ratio - reads - bam - mitochondrial to nuclear ratio - mitochondria - statistics tools: - mtnucratio: description: A small tool to determine MT to Nuclear ratios for NGS data. homepage: https://github.com/apeltzer/MTNucRatioCalculator documentation: https://github.com/apeltzer/MTNucRatioCalculator tool_dev_url: https://github.com/apeltzer/MTNucRatioCalculator doi: "10.1186/s13059-016-0918-z" licence: ['GPL v3'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: (coordinate) sorted BAM/SAM file pattern: "*.{bam,sam}" - mt_id: type: string description: Identifier of the contig/chromosome of interest (e.g. chromosome, contig) as in the aligned against reference FASTA file, e.g. mt or chrMT for mitochondria output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - versions: type: file description: File containing software versions pattern: "versions.yml" - mtnucratio: type: file description: Text file containing metrics (mtreads, mt_cov_avg, nucreads, nuc_cov_avg, mt_nuc_ratio) pattern: "*.mtnucratio" - json: type: file description: JSON file, containing metadata map with sample name, tool name and version, and metrics as in txt file pattern: "*.json" authors: - "@louperelo"