......

workflow.wdl

@@ -28,7 +28,23 @@ workflow {{ project_name }} {
 		read1=quartet[0], 
 		read2=quartet[1],
 		docker = fastp_docker,
-		cluster = fastp_cluster
+		cluster = fastp_cluster,
+		adapter_sequence = adapter_sequence,
+    		adapter_sequence_r2 = adapter_sequence_r2,
+		umi_loc = umi_loc,
+		trim_front1 = trim_front1,
+		trim_tail1 = trim_tail1, 
+		max_len1  = max_len1,
+		trim_front2  = trim_front2,
+		trim_tail2   = trim_tail2,
+		max_len2  = max_len2,
+		disable_adapter_trimming = disable_adapter_trimming,
+		length_required = length_required,
+		umi_len = umi_len,
+		UMI = UMI,
+		qualified_quality_phred = qualified_quality_phred,
+		length_required1 = length_required1,
+		disable_quality_filtering = disable_quality_filtering
 		}
 	}
 }