revise-tophat

tasks/tophat2.wdl

@@ -9,7 +9,7 @@ task tophat2 {
    String cluster
 
    command <<<
-      tophat -p 6 -G ${gtf} -o ${baseout} ${genome_directory}/${idx_prefix} ${read1} ${read2}
+      tophat2 -p 6 -G ${gtf} --library-type fr-unstranded --solexa-quals -o ${baseout} ${genome_directory}/${idx_prefix} ${read1} ${read2}
    >>>
    
    runtime {