revised-bedtools-task

tasks/bedtools.wdl

@@ -11,7 +11,7 @@ task bedtools {
 	command <<<
 	    set -e -o pipefail
         mkdir -p /cromwell_root/tmp/bedtools
-		mv ${sep=' ' bam} /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