nf-core_modules/modules/bcftools/norm/main.nf

process BCFTOOLS_NORM {
    tag "$meta.id"
    label 'process_medium'

    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"

    input:
    tuple val(meta), path(vcf), path(tbi)
    path(fasta)

    output:
    tuple val(meta), path("*.gz") , 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}"
    """
    bcftools norm \\
        --fasta-ref ${fasta} \\
        --output ${prefix}.vcf.gz \\
        $args \\
        --threads $task.cpus \\
        ${vcf}

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
    END_VERSIONS
    """

    stub:
    def prefix = task.ext.prefix ?: "${meta.id}"
    """
    touch ${prefix}.vcf.gz

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
    END_VERSIONS
    """
}