# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
name: vcf_annotate_ensemblvep
description: Perform annotation with ensemblvep and bgzip + tabix index the resulting VCF file
keywords:
  - vcf
  - annotation
  - ensemblvep
modules:
  - ensemblvep/vep
  - tabix/tabix
input:
  - ch_vcf:
      description: |
        vcf file to annotate
        Structure: [ val(meta), path(vcf), [path(custom_file1), path(custom_file2)... (optionnal)] ]
  - ch_fasta:
      description: |
        Reference genome fasta file (optional)
        Structure: [ val(meta2), path(fasta) ]
  - val_genome:
      type: string
      description: genome to use
  - val_species:
      type: string
      description: species to use
  - val_cache_version:
      type: integer
      description: cache version to use
  - ch_cache:
      description: |
        the root cache folder for ensemblvep (optional)
        Structure: [ val(meta3), path(cache) ]
  - ch_extra_files:
      description: |
        any extra files needed by plugins for ensemblvep (optional)
        Structure: [ path(file1), path(file2)... ]
output:
  - vcf_tbi:
      description: |
        Compressed vcf file + tabix index
        Structure: [ val(meta), path(vcf), path(tbi) ]
  - json:
      description: |
        json file
        Structure: [ val(meta), path(json) ]
  - tab:
      description: |
        tab file
        Structure: [ val(meta), path(tab) ]
  - reports:
      type: file
      description: html reports
      pattern: "*.html"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@maxulysse"
  - "@matthdsm"
  - "@nvnieuwk"
