mendelian_vote_summary/tasks/count_mendelian.wdl

task count_mendelian {
	File project_mendelian
	File vote_summary
	File family_vcf
	String family_name = basename(family_vcf,".vcf")
	String docker
	String cluster_config
	String disk_size
	
	command <<<

		python /opt/count_mendelian.py ${project_mendelian} ${vote_summary} ${family_name}.mendelian.count.summary.txt

	>>>

	runtime {
		docker:docker
		cluster: cluster_config
		systemDisk: "cloud_ssd 40"
		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
	}
	output {
		File mendelian_summary = "${family_name}.mendelian.count.summary.txt"
	}
}