quartet_vcf_qc/tasks/quartet_mendelian.wdl

task quartet_mendelian {
	Array[File] project_mendelian_summary
	String project
	String docker
	String cluster_config
	String disk_size

	command <<<
		for i in ${sep=" " project_mendelian_summary}
		do
		  cat $i |  sed -n '2,3p' >> mendelian.summary
		done
		sed '1i\Family\tReproducibility_D5_D6\tMendelian_Concordance_Quartet' mendelian.summary > ${project}.mendelian.txt

	>>>

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