revised-bedtools-task

tasks/bedtools.wdl

         mkdir -p /cromwell_root/tmp/bedtools
 		cp ${sep=' ' bai} /cromwell_root/tmp/bedtools
 		cd /cromwell_root/tmp/bedtools
-		bedtools multicov -bams ${sep=' ' bam} -bed ${bed_file} > ./revread_count.txt
+		bedtools multicov -bams ${sep=' ' bam} -bed ${bed_file} > /bedtools/revread_count.txt
 
 	>>>
 
 	}
 
 	output {
-		File read_count = "./revread_count.txt"
+		File read_count = "/bedtools/revread_count.txt"
 	}
 }