revised ballgown

tasks/qualimap.wdl

 	File bam
 	File bai
 	File gtf
-	String bamname = basename(bam,".bam")
+	String bamname = basename(bam, ".sorted.bam")
 	String docker
 	String cluster
 	String disk_size

workflow.wdl

 		disk_size= disk_size
 	}
 
-	call qualimap.qualimap as qualimap {
-		input:
-		bam = samtools.out_bam,
-		bai = samtools.out_bam_index,
-		gtf = gtf, 
-		docker = qualimap_docker,
-		cluster = qualimap_cluster,
-		disk_size = disk_size
-		}
+	#call qualimap.qualimap as qualimap {
+	#	input:
+	#	bam = samtools.out_bam,
+	#	bai = samtools.out_bam_index,
+	#	gtf = gtf, 
+	#	docker = qualimap_docker,
+	#	cluster = qualimap_cluster,
+	#	disk_size = disk_size
+	#	}
 
     call stringtie.stringtie as stringtie {
         input: 
 		disk_size= disk_size
 	} 
 	
-}
-
-
+}