maftools/workflow.wdl

import "./tasks/general.wdl" as general
import "./tasks/specific.wdl" as specific

workflow {{ project_name }} {
    File input_file

    call general.general as general {
	input:
            output_dir='general',
            input_file=input_file,
	    docker=docker,
	    cluster_config=cluster_config
    }

    {% if genelist %}
    call specific.specific as specific {
        input:
       	    output_dir='specific',
            input_file=input_file,
            docker=docker,
            cluster_config=cluster_config
    } 
    {% endif %}
}