revised-bedtools-task

tasks/bedtools.wdl

@@ -9,7 +9,7 @@ task bedtools {
 
 	command <<<
 	    set -e -o pipefail
-		bedtools multicov ${tmp_bam} -bed ${bed_file} > revread_count.txt 
+		cat ~{sep=" " tmp_bam}|bedtools multicov -bed ${bed_file} > revread_count.txt 
 
 	>>>