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 ]
  - input:
      type: file
      description: BAM/CRAM file from alignment must be sorted, indexed, and duplicate marked
      pattern: "*.{bam,cram}"
  - bai:
      type: file
      description: Index of the BAM/CRAM file
      pattern: "*.{bai,crai}"
  - exclude_bed:
      type: file
      description: An optional bed file containing regions to exclude from the called VCF
      pattern: "*.bed"
  - fasta:
      type: file
      description: The reference fasta file
      pattern: "*.{fasta,fa}"
  - fai:
      type: file
      description: Index of reference fasta file to identify split-reads
      pattern: "*.fai"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - bcf:
      type: file
      description: Called variants in BCF format
      pattern: "*.{bcf}"
  - csi:
    type: file
    description: A generated csi index that matches the bcf output
    pattern: "*.{bcf.csi}"

authors:
  - "@projectoriented"
  - "@nvnieuwk"