name: bedtools_subtract description: Finds overlaps between two sets of regions (A and B), removes the overlaps from A and reports the remaining portion of A. keywords: - bed - gff - vcf - subtract 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/subtract.html licence: ['MIT'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - intervals1: type: file description: BED/GFF/VCF pattern: "*.{bed|gff|vcf}" - intervals2: type: file description: BED/GFF/VCF pattern: "*.{bed|gff|vcf}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bed: type: file description: File containing the difference between the two sets of features patters: "*.bed" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@sidorov-si"