name: "cadd"
description: CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome.
keywords:
  - cadd
  - annotate
  - variants
tools:
  - "cadd":
      description: "CADD scripts release for offline scoring"
      homepage: "https://cadd.gs.washington.edu/"
      documentation: "https://github.com/kircherlab/CADD-scripts/blob/master/README.md"
      tool_dev_url: "https://github.com/kircherlab/CADD-scripts/"
      doi: "10.1093/nar/gky1016"
      licence: "['Restricted. Free for non-commercial users.']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - vcf:
      type: file
      description: Input file for annotation in vcf or vcf.gz format
      pattern: "*.{vcf,vcf.gz}"
  - annotation_dir:
      type: file
      description: |
        Path to folder containing the vcf files with precomputed CADD scores.
        This folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation.
      pattern: "*.{vcf,vcf.gz}"

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"
  - tsv:
      type: file
      description: Annotated tsv file
      pattern: "*.{tsv,tsv.gz}"

authors:
  - "@ramprasadn"
