revised-cufflinks

tasks/cufflinks.wdl

     }
     
     output {
-      File isoforms_count = "${baseout}/isoforms.fpkm_tracking"
-      File genes_count = "${baseout}/genes.fpkm_tracking"
+      File isoforms_fpkm = "${baseout}/isoforms.fpkm_tracking"
+      File genes_fpkm = "${baseout}/genes.fpkm_tracking"
       File skipped_gtf = "${baseout}/skipped.gtf"
       File transcripts_gtf = "${baseout}/transcripts.gtf"
     }

workflow.wdl

 import "./tasks/fastqc.wdl" as fastqc
 import "./tasks/trimmomatic.wdl" as trimmomatic
 import "./tasks/tophat2.wdl" as tophat2
-import "./tasks/cuffdiff2.wdl" as cuffdiff2
+import "./tasks/cufflinks.wdl" as cufflinks
 
 workflow {{ project_name }} {
 	File read1
 		input: baseout=baseout, read_1P=trimmomatic.read_1p, read_2P=trimmomatic.read_2p, gtf=gtf, genome_directory=genome_directory, idx_prefix=idx_prefix
 	}
 
-	call cuffdiff2.cuffdiff2 as cuffdiff2 {
+	call cufflinks.cufflinks as cufflinks {
 		input: gtf = gtf, bam = tophat2.accepted_hits, genome_directory=genome_directory, idx_prefix=idx_prefix, baseout=baseout
 	}
         
 		File fastq_2p = trimmomatic.read_2p
                 File bam = tophat2.accepted_hits
 		File unmapped_bam = tophat2.unmapped_bam
-                File isoforms_count = cuffdiff2.isoforms_count
-		File genes_count = cuffdiff2.genes_count
-		File cds_count = cuffdiff2.cds_count
-		File isoforms_fpkm = cuffdiff2.isoforms_fpkm
-		File genes_fpkm = cuffdiff2.genes_fpkm
-		File cds_fpkm = cuffdiff2.cds_fpkm
+		File isoforms_fpkm = isoforms.fpkm_tracking
+        File genes_fpkm = genes.fpkm_tracking
+        File skipped_gtf = skipped.gtf
+        File transcripts_gtf = transcripts.gtf
 	}
 }