nf-core_modules/modules/gatk4/reblockgvcf/main.nf

process GATK4_REBLOCKGVCF {
    tag "$meta.id"
    label 'process_low'

    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"

    input:
    tuple val(meta), path(gvcf), path(tbi), path(intervals)
    path fasta
    path fai
    path dict
    path dbsnp
    path dbsnp_tbi

    output:
    tuple val(meta), path("*.rb.g.vcf.gz"), path("*.tbi")  , emit: vcf
    path "versions.yml"                                    , emit: versions

    when:
    task.ext.when == null || task.ext.when

    script:
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
    def dbsnp_command = dbsnp ? "--dbsnp $dbsnp" : ""
    def interval_command = intervals ? "--intervals $intervals" : ""

    def avail_mem = 3
    if (!task.memory) {
        log.info '[GATK ReblockGVCF] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
    } else {
        avail_mem = task.memory.giga
    }
    """
    gatk --java-options "-Xmx${avail_mem}g" ReblockGVCF \\
        --variant $gvcf \\
        --output ${prefix}.rb.g.vcf.gz \\
        --reference $fasta \\
        $dbsnp_command \\
        $interval_command \\
        --tmp-dir . \\
        $args

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
    END_VERSIONS
    """
}