nf-core_modules/modules/ensemblvep/main.nf

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'

params.options = [:]
options = initOptions(params.options)
params.use_cache = false
params.vep_tag = ""

process ENSEMBLVEP {
    label 'process_medium'
    publishDir "${params.outdir}",
        mode: params.publish_dir_mode,
        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }

    conda (params.enable_conda ? "bioconda::ensembl-vep=104.3" : null)
    if (params.use_cache) {
        if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
            container "https://depot.galaxyproject.org/singularity/ensembl-vep:104.3--pl5262h4a94de4_0"
        } else {
            container "quay.io/biocontainers/ensembl-vep:104.3--pl5262h4a94de4_0"
        }
    } else {
        container "nfcore/vep:${params.vep_tag}"
    }

    input:
    tuple val(meta), path(vcf)
    val   genome
    val   species
    val   cache_version
    path  cache

    output:
    tuple val(meta), path("*.ann.vcf"), emit: vcf
    path "*.summary.html"             , emit: report
    path "*.version.txt"              , emit: version

    script:
    def software = getSoftwareName(task.process)
    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
    dir_cache    = params.use_cache ? "\${PWD}/${cache}" : "/.vep"
    """
    mkdir $prefix

    vep \\
        -i $vcf \\
        -o ${prefix}.ann.vcf \\
        $options.args \\
        --assembly $genome \\
        --species $species \\
        --cache \\
        --cache_version $cache_version \\
        --dir_cache $dir_cache \\
        --fork $task.cpus \\
        --format vcf \\
        --stats_file ${prefix}.summary.html

    rm -rf $prefix

    echo \$(vep --help 2>&1) > ${software}.version.txt
    """
}