name: "whamg"
description: The wham suite consists of two programs, wham and whamg. wham, the original tool, is a very sensitive method with a high false discovery rate. The second program, whamg, is more accurate and better suited for general structural variant (SV) discovery.
keywords:
  - whamg
  - wham
  - vcf
  - bam
  - variant calling
tools:
  - "whamg":
      description: "Structural variant detection and association testing"
      homepage: "https://github.com/zeeev/wham"
      documentation: "https://github.com/zeeev/wham"
      tool_dev_url: "https://github.com/zeeev/wham"
      doi: "https://doi.org/10.1371/journal.pcbi.1004572"
      licence: "['MIT']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: BAM/SAM file
      pattern: "*.{bam,sam}"
  - bai:
      type: file
      description: BAM index file
      pattern: "*.bai"

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"
  - vcf:
      type: file
      description: Compressed VCF file
      pattern: "*.vcf.gz"

authors:
  - "@nvnieuwk"