remove-base

tasks/cuffdiff2.wdl

@@ -1,5 +1,4 @@
 task cuffdiff2 {
-    File bam
     File gtf
     File genome_directory
     String idx_prefix
@@ -15,11 +14,11 @@ task cuffdiff2 {
     }
     
     output {
-      File isoforms_count = "${base}/isoforms.count_tracking"
-      File genes_count = "${base}/genes.count_tracking"
-      File cds_count = "${base}/cds.count_tracking"
-      File isoforms_fpkm = "${base}/isoforms.fpkm_tracking"
-      File genes_fpkm = "${base}/genes.fpkm_tracking"
-      File cds_fpkm = "${base}/cds.fpkm_tracking"
+      File isoforms_count = "${baseout}/isoforms.count_tracking"
+      File genes_count = "${baseout}/genes.count_tracking"
+      File cds_count = "${baseout}/cds.count_tracking"
+      File isoforms_fpkm = "${baseout}/isoforms.fpkm_tracking"
+      File genes_fpkm = "${baseout}/genes.fpkm_tracking"
+      File cds_fpkm = "${baseout}/cds.fpkm_tracking"
     }
 }