benchmark_homo_ref_region/tasks/gvcf_homo_ref.wdl

task gvcf_homo_ref {
	
	File gvcf
	String sample
	String docker
	String disk_size
	String cluster_config
	

	command <<<

		awk '{ if ($5 == "<NON_REF>") { print } }'  ${gvcf} | sed s'/:/\t/'g | awk '{ if($16 >= 30) { print }}' | cut -f1,2,8 | sed s'/END=//g' > ${sample}.filtered.bed

		/opt/ccdg/bedtools-2.27.1/bin/bedtools merge -i ${sample}.filtered.bed > ${sample}.homo_ref.bed 

		>>>

		runtime {
		docker:docker
    	cluster:cluster_config
    	systemDisk: "cloud_ssd 40"
    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
	}

	output {
		File filtered_bed = "${sample}.filtered.bed"
		File homo_ref_bed = "${sample}.homo_ref.bed"
	}
}