nf-core_modules/modules/snpeff/main.nf

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

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

process SNPEFF {
    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::snpeff=5.0" : null)
    if (params.use_cache) {
        if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
            container "https://depot.galaxyproject.org/singularity/snpeff:5.0--hdfd78af_1"
        } else {
            container "quay.io/biocontainers/snpeff:5.0--hdfd78af_1"
        }
    } else {
        container "nfcore/snpeff:${params.snpeff_tag}"
    }

    input:
    tuple val(meta), path(vcf)
    val   db
    path  cache

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

    script:
    def software = getSoftwareName(task.process)
    def avail_mem = 6
    if (!task.memory) {
        log.info '[snpEff] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
    } else {
        avail_mem = task.memory.giga
    }
    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
    cache        = params.use_cache ? "-dataDir \${PWD}/${snpeff_cache}" : ""
    """
    snpEff -Xmx${avail_mem}g \\
        $db \\
        $options.args \\
        -csvStats ${prefix}.csv \\
        $cache \\
        $vcf \\
        > ${prefix}.ann.vcf

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