nf-core_modules/modules/hicap/main.nf

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

    conda (params.enable_conda ? "bioconda::hicap=1.0.3" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/hicap:1.0.3--py_0' :
        'quay.io/biocontainers/hicap:1.0.3--py_0' }"

    input:
    tuple val(meta), path(fasta)
    path database_dir
    path model_fp

    output:
    tuple val(meta), path("*.gbk"), emit: gbk, optional: true
    tuple val(meta), path("*.svg"), emit: svg, optional: true
    tuple val(meta), path("*.tsv"), emit: tsv, optional: true
    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 database_args = database_dir ? "--database_dir ${database_dir}" : ""
    def model_args = model_fp ? "--model_fp ${model_fp}" : ""
    def is_compressed = fasta.getName().endsWith(".gz") ? true : false
    def fasta_name = fasta.getName().replace(".gz", "")
    """
    if [ "$is_compressed" == "true" ]; then
        gzip -c -d $fasta > $fasta_name
    fi
    hicap \\
        --query_fp $fasta_name \\
        $database_args \\
        $model_args \\
        $args \\
        --threads $task.cpus \\
        -o ./

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