add-cluster

tasks/tophat2.wdl

    File gtf
    File genome_directory
    String idx_prefix
-   File read_1P
-   File read_2P
+	File read1
+	File read2
    String baseout
    String docker
    String cluster
 
    command {
-      tophat2 -p 24 -o ${baseout} -G ${gtf} --library-type fr-unstranded --solexa-quals ${genome_directory}/${idx_prefix} ${read_1P} ${read_2P}
+      tophat2 -p 24 -o ${baseout} -G ${gtf} --library-type fr-unstranded --solexa-quals ${genome_directory}/${idx_prefix} ${read1} ${read2}
    }
    
    runtime {