metrics

tasks/extract_tables.wdl

@@ -3,13 +3,16 @@ task extract_tables {
 	File fastqc
 	File fastqscreen
 	File hap
+	File aln
+	File quality_yield
+	File wgs_metrics
 
 	String docker
 	String cluster_config
 	String disk_size
 
 	command <<<
-		python /opt/extract_multiqc.py -fastqc_qualimap ${fastqc_qualimap} -fastqc ${fastqc} -fastqscreen ${fastqscreen} -hap ${hap}
+		python /opt/extract_multiqc.py -fastqc_qualimap ${fastqc} -fastqc ${fastqc} -fastqscreen ${fastqscreen} -hap ${hap}
 	>>>
 
 	runtime {