......

workflow.wdl

@@ -26,5 +26,22 @@ workflow {{ project_name }} {
 	Int length_required
 	Int umi_len
 	Int UMI
-	
+	Int qualified_quality_phred
+	Int length_required1
+	Int disable_quality_filtering
+	Int pen_cansplice
+	Int pen_noncansplice
+	Int min_intronlen
+	Int max_intronlen
+	Int maxins
+	Int minins
+	Int fastqc_disk_size
+	Int fastqscreen_disk_size
+	Int qualimapBAMqc_disk_size
+	Int qualimapRNAseq_disk_size
+	Int insert_size
+	Int minimum_length_allowed_for_the_predicted_transcripts
+    	Int Junctions_no_spliced_reads
+   	Float minimum_isoform_abundance
+    	Float maximum_fraction_of_muliplelocationmapped_reads
 }