revised ballgown

tasks/ballgown.wdl

 task ballgown {
-    Array[File] ballgown
     File gene_abundance
     String base = basename(gene_abundance, ".gene.abundance.txt")
+    Array[File] ballgown
     String docker
     String cluster
 
     command <<<
-      mkdir /cromwell_root/tmp/
-      cp -r ${ballgown} /cromwell_root/tmp/
-      Rscript /usr/bin/ballgown.R /cromwell_root/tmp/ballgown/ ${base}.txt
+      #mkdir /cromwell_root/tmp/
+      #cp -r ${ballgown} /cromwell_root/tmp/
+      Rscript /usr/bin/ballgown.R ${ballgown} ${base}.txt
     >>>
     
     runtime {