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 """ }