nf-core_modules/software/gatk4/variantfiltration/main.nf

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

params.options = [:]
def options    = initOptions(params.options)

process GATK4_VARIANTFILTRATION {
    tag "$meta.id"
    label 'process_medium'
    publishDir "${params.outdir}",
        mode: params.publish_dir_mode,
        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }

    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
    } else {
        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
    }

    input:
    tuple val(meta), path(vcf)
    tuple path(fasta), path(fai), path(dict)

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


    script:
    def software = getSoftwareName(task.process)
    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
    """
    gatk VariantFiltration \\
        -R $fasta \\
        -V $vcf \\
        -O ${prefix}.filtered.vcf \\
        $options.args

    gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt
    """
}