revised ballgown

tasks/ballgown.wdl

@@ -6,9 +6,9 @@ task ballgown {
     String cluster
 
     command <<<
-      #mkdir /cromwell_root/tmp/
-      #cp -r ${ballgown} /cromwell_root/tmp/
-      Rscript /usr/bin/ballgown.R ${ballgown} ${base}.txt
+      mkdir /cromwell_root/tmp/
+      cp -r ${sep=" " ballgown} /cromwell_root/tmp/ballgown
+      Rscript /usr/bin/ballgown.R /cromwell_root/tmp/ballgown/${base} ${base}.txt
     >>>
     
     runtime {