# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
name: vcf_annotate_snpeff
description: Perform annotation with snpEff and bgzip + tabix index the resulting VCF file
keywords:
  - vcf
  - annotation
  - snpeff
modules:
  - snpeff
  - tabix/bgziptabix
input:
  - ch_vcf:
      description: |
        vcf file
        Structure: [ val(meta), path(vcf) ]
  - val_snpeff_db:
      type: string
      description: db version to use
  - ch_snpeff_cache:
      description: |
        path to root cache folder for snpEff (optional)
        Structure: [ path(cache) ]
output:
  - vcf_tbi:
      description: |
        Compressed vcf file + tabix index
        Structure: [ val(meta), path(vcf), path(tbi) ]
  - reports:
      description: |
        html reports
        Structure: [ path(html) ]
  - versions:
      description: |
        Files containing software versions
        Structure: [ path(versions.yml) ]
authors:
  - "@maxulysse"
