benchmark_homo_ref_region/tasks/collapseBed.wdl

task collapseBed {
	
	File bed
	String sample
	String docker
	String disk_size
	String cluster_config
	

	command <<<

		cat ${bed} | cut -f1-3 > ${sample}.temp.bed

		/opt/ccdg/bedtools-2.27.1/bin/bedtools merge -i ${sample}.temp.bed > ${sample}.27.homo_ref.consensus.bed

		>>>

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

	output {
		File merged_homo_ref_bed = "${sample}.27.homo_ref.consensus.bed"
	}
}