revised-cufflinks

workflow.wdl

 	call cufflinks.cufflinks as cufflinks {
 		input: gtf = gtf, bam = tophat2.accepted_hits, genome_directory=genome_directory, idx_prefix=idx_prefix, baseout=baseout
 	}
-        
-	output {
-		Array[File] fastqc_html = fastqc.html
-		Array[File] fastqc_zip = fastqc.zip
-                File fastq_1p = trimmomatic.read_1p
-		File fastq_2p = trimmomatic.read_2p
-                File bam = tophat2.accepted_hits
-		File unmapped_bam = tophat2.unmapped_bam
-		File isoforms_fpkm = isoforms.fpkm_tracking
-        File genes_fpkm = genes.fpkm_tracking
-        File skipped_gtf = skipped.gtf
-        File transcripts_gtf = transcripts.gtf
-	}
 }