name: delly_call description: Call structural variants keywords: - genome - structural - variants - bcf tools: - delly: description: Structural variant discovery by integrated paired-end and split-read analysis homepage: https://github.com/dellytools/delly documentation: https://github.com/dellytools/delly/blob/master/README.md tool_dev_url: None doi: "DOI:10.1093/bioinformatics/bts378" licence: ["BSD-3-clause"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: BAM file from alignment must be sorted, indexed, and duplicate marked pattern: "*.{bam}" - fasta: type: file description: The reference fasta file - fai: type: file description: Index of reference fasta file to identify split-reads output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - version: type: file description: File containing software version pattern: "*.{version.txt}" - bcf: type: file description: BCF format pattern: "*.{bcf}" - csi: type: file description: A generated csi index that matches the bcf output pattern: "*.{bcf.csi}" authors: - "@projectoriented"