name: bedtools_intersect description: Allows one to screen for overlaps between two sets of genomic features. keywords: - bed - intersect 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/intersect.html input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - intervals1: type: file description: BAM/BED/GFF/VCF pattern: "*.{bam|bed|gff|vcf}" - intervals2: type: file description: BAM/BED/GFF/VCF pattern: "*.{bam|bed|gff|vcf}" - extension: type: value description: Extension of the output file. It is set by the user and corresponds to the file format which depends on arguments (e. g., ".bed", ".bam", ".txt", etc.). output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - intersect: type: file description: File containing the description of overlaps found between the two features pattern: "*.${extension}" - version: type: file description: File containing software version pattern: "*.{version.txt}" authors: - "@Emiller88" - "@sruthipsuresh" - "@drpatelh" - "@sidorov-si"