nf-core_modules/modules/sexdeterrmine/main.nf

process SEXDETERRMINE {
    tag "$meta.id"
    label 'process_single'

    conda (params.enable_conda ? "bioconda::sexdeterrmine=1.1.2" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/sexdeterrmine:1.1.2--hdfd78af_1':
        'quay.io/biocontainers/sexdeterrmine:1.1.2--hdfd78af_1' }"

    input:
    tuple val(meta), path(depth)
    path sample_list_file

    output:
    tuple val(meta), path("*.json"), emit: json
    tuple val(meta), path("*.tsv") , emit: tsv
    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 sample_list = sample_list_file ? '-f ${sample_list_file}' : ''
    if ("$depth" == "${prefix}.tsv") error "Input depth and output TSV names are the same, set prefix in module configuration to disambiguate!"

    """
    sexdeterrmine \\
        -I $depth \\
        $sample_list \\
        $args \\
        > ${prefix}.tsv

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        sexdeterrmine: \$(echo \$(sexdeterrmine --version 2>&1))
    END_VERSIONS
    """
}