revise-reference

tasks/tophat2.wdl

@@ -9,10 +9,10 @@ task tophat2 {
    String cluster
 
    command <<<
-      tophat -p 8 -G ${gtf} -o baseout ${genome_directory}/${idx_prefix} ${read1} ${read2}
+      tophat2 -p 8 -G ${gtf} -o ${baseout} ${genome_directory}/${idx_prefix} ${read1} ${read2}
    >>>
    
-   runtime { 
+   runtime {
       docker: docker 
 		cluster: cluster
 		systemDisk: "cloud_ssd 40"