name: bedtools_genomecov description: Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome. keywords: - bed - bam - genomecov tools: - bedtools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html licence: ['MIT'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - intervals: type: file description: BAM/BED/GFF/VCF pattern: "*.{bam|bed|gff|vcf}" - scale: type: value description: Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch - sizes: type: file description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column - extension: type: string description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments. output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - genomecov: type: file description: Computed genome coverage file pattern: "*.${extension}" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@Emiller88" - "@sruthipsuresh" - "@drpatelh" - "@sidorov-si" - "@chris-cheshire"