1

workflow.wdl

@@ -69,7 +69,7 @@ workflow {{ project_name }} {
 
 		call stringtie.stringtie as stringtie {
 		input: 
-		sample_id=quartet[2],
+		sample_id = quartet[2],
 		gtf = gtf, 
 		bam = samtools.out_bam
 		}
@@ -78,9 +78,10 @@ workflow {{ project_name }} {
 
 	call multiqc.multiqc as multiqc {
 	input:
-	read1_zip=fastqc.read1_zip,
-	read2_zip=fastqc.read2_zip,
-	txt1=fastqscreen.txt1,
-	txt2=fastqscreen.txt2
+	read1_zip = fastqc.read1_zip,
+	read2_zip = fastqc.read2_zip,
+	txt1 = fastqscreen.txt1,
+	txt2 = fastqscreen.txt2,
+	bamqc_zip = qualimapBAMqc.bamqc_zip
 	}
 }