revise-tophat2

tasks/tophat2.wdl

@@ -9,7 +9,7 @@ task tophat2 {
    String cluster
 
    command {
-      tophat2 -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 {