name: ensemblvep_vep
description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through `task.ext.args`.
keywords:
  - annotation
  - vcf
  - json
  - tab
tools:
  - ensemblvep:
      description: |
        VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs
        or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
      homepage: https://www.ensembl.org/info/docs/tools/vep/index.html
      documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html
      licence: ["Apache-2.0"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - vcf:
      type: file
      description: |
        vcf to annotate
  - custom_extra_files:
      type: file
      description: |
        extra sample-specific files to be used with the `--custom` flag to be configured with ext.args
        (optional)
  - genome:
      type: string
      description: |
        which genome to annotate with
  - species:
      type: string
      description: |
        which species to annotate with
  - cache_version:
      type: integer
      description: |
        which version of the cache to annotate with
  - cache:
      type: file
      description: |
        path to VEP cache (optional)
  - meta2:
      type: map
      description: |
        Groovy Map containing fasta reference information
        e.g. [ id:'test' ]
  - fasta:
      type: file
      description: |
        reference FASTA file (optional)
      pattern: "*.{fasta,fa}"
  - extra_files:
      type: file
      description: |
        path to file(s) needed for plugins  (optional)
output:
  - vcf:
      type: file
      description: |
        annotated vcf (optional)
      pattern: "*.ann.vcf.gz"
  - tab:
      type: file
      description: |
        tab file with annotated variants (optional)
      pattern: "*.ann.tab.gz"
  - json:
      type: file
      description: |
        json file with annotated variants (optional)
      pattern: "*.ann.json.gz"
  - report:
      type: file
      description: VEP report file
      pattern: "*.html"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@maxulysse"
  - "@matthdsm"
  - "@nvnieuwk"
maintainers:
  - "@maxulysse"
  - "@matthdsm"
  - "@nvnieuwk"
