name: bedtools_bamtobed description: Converts a bam file to a bed12 file. keywords: - bam - bed 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/complement.html licence: ['MIT'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: Input BAM file pattern: "*.{bam}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bed: type: file description: Bed file containing genomic intervals. pattern: "*.{bed}" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@yuukiiwa" - "@drpatelh"