revised-bedtools-task

tasks/bedtools.wdl

@@ -10,9 +10,8 @@ task bedtools {
 
 	command <<<
 	    set -e -o pipefail
-		mkdir -p  /cromwell_root/tmp/bedtools
-		cp ${sep=' ' bai} /cromwell_root/tmp/bedtools
-		cd /cromwell_root/tmp/bedtools
+		path=$(dirname ${bam})
+		mv ${sep=' ' bai} $path
 		bedtools multicov -bams ${sep=' ' bam} -bed ${bed_file} > revread_count.txt 
 
 	>>>