revised-bedtools-task

tasks/bedtools.wdl

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