add qualimap

workflow.wdl

 		read_1P=read1, 
 		read_2P=read2,
 		disk_size= disk_size
-	}
+		}
 
     call samtools.samtools as samtools {
         input: 
 		cluster = samtools_cluster,
 		sam = hisat2.sam,
 		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: 
 		gtf = gtf, 
 		bam = samtools.out_bam,
 		disk_size= disk_size
-	}   
+		}
 
 	call ballgown.ballgown as ballgown {
 		input: 
 		ballgown = stringtie.ballgown,
 		gene_abundance = stringtie.gene_abundance,
 		disk_size= disk_size
-	} 
-	
+		} 
 }