name: ENSEMBLVEP
description: Ensembl Variant Effect Predictor (VEP)
keywords:
  - annotation
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"]
params:
  - use_cache:
      type: boolean
      description: |
        Enable the usage of containers with cache
        Does not work with conda
  - vep_tag:
      type: value
      description: |
        Specify the tag for the container
        https://hub.docker.com/r/nfcore/vep/tags
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - vcf:
      type: file
      description: |
        vcf to annotate
  - genome:
      type: value
      description: |
        which genome to annotate with
  - species:
      type: value
      description: |
        which species to annotate with
  - cache_version:
      type: value
      description: |
        which version of the cache to annotate with
  - cache:
      type: file
      description: |
        path to VEP cache (optional)
output:
  - vcf:
      type: file
      description: |
        annotated vcf
      pattern: "*.ann.vcf"
  - report:
      type: file
      description: VEP report file
      pattern: "*.html"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@maxulysse"