nf-core_modules/modules/snpeff/meta.yml

name: snpEff
description: Genetic variant annotation and functional effect prediction toolbox
keywords:
    - annotation
tools:
    - snpeff:
        description: |
            SnpEff is a variant annotation and effect prediction tool.
            It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).
        homepage: https://pcingola.github.io/SnpEff/
        documentation: https://pcingola.github.io/SnpEff/se_introduction/
        licence: ['MIT']
params:
    - use_cache:
        type: boolean
        description: |
          boolean to enable the usage of containers with cache
          Enable the usage of containers with cache
          Does not work with conda
    - snpeff_tag:
        type: value
        description: |
          Specify the tag for the container
          https://hub.docker.com/r/nfcore/snpeff/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
    - db:
        type: value
        description: |
            which db to annotate with
    - cache:
        type: file
        description: |
            path to snpEff cache (optional)
output:
    - vcf:
        type: file
        description: |
            annotated vcf
        pattern: "*.ann.vcf"
    - report:
        type: file
        description: snpEff report file
        pattern: "*.html"
    - versions:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
authors:
    - "@maxulysse"