pipeline/wdl/hereditary.wdl

task run_hereditary {
    String name
    String output_dir
    String project
    String filter_txt
    command <<<

        if [ ! -d ${output_dir}/hereditary ];then
        mkdir ${output_dir}/hereditary
        fi
        hereditary.py -d $DATABASE/hereditary_database.xlsx -p ${project} -n ${name} -f ${filter_txt} -o ${output_dir}/hereditary
    >>>

    output {
        String run_hereditary_txt = "${output_dir}/hereditary/${name}.hereditary.txt"
    }
}

workflow call_hereditary {

    Boolean run=true

    String name
    String output_dir
    String project
    String filter_txt

    if (run) {
        call run_hereditary {
            input:
                name=name,
                output_dir=output_dir,
                project=project,
                filter_txt=filter_txt
        }
    }

    output {
        String hereditary_txt = "${output_dir}/hereditary/${name}.hereditary.txt"
    }
}