revised-cufflinks

tasks/cufflinks.wdl

@@ -1,5 +1,6 @@
 task cufflinks {
     File gtf
+    File bam
     File accepted_hits
     File genome_directory
     String idx_prefix
@@ -7,7 +8,7 @@ task cufflinks {
     String docker
 
     command {
-      cufflinks ${gtf} -p 24 -o ${baseout} ${accepted_hits}
+      cufflinks ${gtf} -p 24 -o ${baseout} ${bam}
 
     runtime {
       dockerTag: docker