revise-cufflinks

tasks/cufflinks.wdl

 task cufflinks {
-    File gtf
     File bam
     String baseout
     String docker
     String cluster
 
     command {
-      cufflinks -p 8 -o ${baseout} ${bam}
+    cufflinks -p 8 -o ${baseout} ${bam}
     }
 
     runtime {
-      docker: docker 
+    docker: docker 
 		cluster: cluster
 		systemDisk: "cloud_ssd 40"
 		dataDisk: "cloud_ssd 200 /cromwell_root/"

tasks/tophat2.wdl

    String docker
    String cluster
 
-   command <<<
+   command {
       tophat2 -p 6 -G ${gtf} --library-type fr-unstranded --solexa-quals -o ${baseout} ${genome_directory}/${idx_prefix} ${read1} ${read2}
-   >>>
+   }
    
    runtime {
       docker: docker 

workflow.wdl

 	}
 
 	call cufflinks.cufflinks as cufflinks {
-		input: gtf = gtf, bam = tophat2.accepted_hits, baseout=baseout
+		input: baseout=baseout, bam=tophat2.accepted_hits
 	}
 }