bedtools-multicov/tasks/bedtools.wdl

task bedtools {

	Array[File] bam
	Array[File] bai
	File bed_file
	
	String docker
	String cluster_config
	String disk_size
	Boolean include_dup

	command <<<
	    set -e -o pipefail
        mkdir -p /cromwell_root/tmp/bedtools
		cp ${sep=' ' bai} /cromwell_root/tmp/bedtools
		cd /cromwell_root/tmp/bedtools
		if ${include_dup}; then
			bedtools multicov -D -bams ${sep=' ' bam} -bed ${bed_file} > /bedtools/revread_count.txt
		else
			bedtools multicov -bams ${sep=' ' bam} -bed ${bed_file} > /bedtools/revread_count.txt
		fi
	>>>

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

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