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"