revise-cufflinks

tasks/cufflinks.wdl

 task cufflinks {
     File gtf
     File bam
-    File genome_directory
-    String idx_prefix
     String baseout
     String docker
     String cluster
 
     command {
-      cufflinks ${gtf} -p 24 -o ${baseout} ${bam}
+      cufflinks -p 8 -o ${baseout} ${bam}
 
     runtime {
       docker: docker 

workflow.wdl

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