maftools/tasks/specific.wdl

task specific {
    File input_file
    File output_dir
    File genelist
	
    command <<<
        set -o pipefail
	set -e
        maftools -p specific_gene_as_input ${output_dir} ${input_file} ${genelist}
    >>>

    runtime {
	docker:docker
    	cluster: cluster_config
    	systemDisk: "cloud_ssd 40"
    }

    output {
	File file_summary = "${output_dir}/MAF_summary.png"
	File file_oncoplot = "${output_dir}/Oncoplot.png"
	File file_tt = "${output_dir}/Transition_and_transversion.png.png"
	File file_rainfall = "${output_dir}/Rainfall.png"
	File file_genecloud = "${output_dir}/Genecloud.png"
	File file_interaction = "$output_dir}/Drug_gene_interaction.png"
	File file_pathway = "${output_dir}/Oncogenic_signaling_pathways.png"
    }
}