cnv/tasks/cn_mops.wdl

task CNV {
	String TumorBam
	String NormalBam
	String TumorSampleID
	String bed_file
	String workDir
	String outputDir
	String docker
	String disk_size
	String cluster_config
	
	command <<<
		Rscript cn.mops.R --Tumor=${TumorBam} --Normal=${NormalBam} --TumorID==${TumorSampleID} --bed_file=${bed_file} --workDir=${workDir} --outputDir=${outputDir}
	>>>

	runtime {
		docker: docker
    	cluster: cluster_config
    	systemDisk: "cloud_ssd 40"
    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
	}
	output {
		File sorted_bam = "${TumorSampleID}.cn.mops.res.txt"
	}
}