name: ensemblvep_filtervep
description: Filter variants based on Ensembl Variant Effect Predictor (VEP) annotations.
keywords:
  - annotation
  - vcf
  - tab
  - filter
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 ]`
  - input:
      type: file
      description: VCF/TAB file annotated with vep
      pattern: "*.{vcf,tab,tsv,txt}"
  - feature_file:
      type: file
      description: File containing features on separate lines. To be used with --filter option.
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"
  - output:
      type: file
      description: VCF/TAB file
      pattern: "*.{vcf,tab,txt,tsv}"
authors:
  - "@ramprasadn"
maintainers:
  - "@ramprasadn"
