revised-cufflinks

tasks/cufflinks.wdl

 task cufflinks {
     File gtf
-    File bam
     File accepted_hits
     File genome_directory
     String idx_prefix
     String docker
 
     command {
-      cufflinks ${gtf} -p 24 -o ${baseout} ${bam}
+      cufflinks ${gtf} -p 24 -o ${baseout} ${baseout}/accepted_hits.bam
 
     runtime {
       dockerTag: docker

workflow.wdl

 	File read2
 	File adapter
 	String baseout
-
 	File gtf
 	File genome_directory
 	String idx_prefix
 	}
 
 	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, genome_directory=genome_directory, idx_prefix=idx_prefix, baseout=baseout
 	}
 }