bedtools-multicov/tasks/bedtools.wdl

task bedtools {

	Array[File] bam
	Array[File] bai
	File bed_file

	String docker
	String cluster_config
	String disk_size

	command <<<
	    set -e -o pipefail
		path=$(dirname ${bam})
		mv ${sep=' ' bai} $path
		bedtools multicov -bams ${sep=' ' bam} -bed ${bed_file} > revread_count.txt 

	>>>

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

	output {
		File read_count = "revread_count.txt"
	}
}