revised-bedtools-task

tasks/bedtools.wdl

@@ -10,7 +10,7 @@ task bedtools {
 
 	command <<<
 	    set -e -o pipefail
-		path=$(dirname ${bam})
+		path=$(dirname ${sep=' ' bam})
 		mv ${sep=' ' bai} $path
 		bedtools multicov -bams ${sep=' ' bam} -bed ${bed_file} > revread_count.txt