......

workflow.wdl

@@ -12,14 +12,13 @@ workflow {{ project_name }} {
 	
 	
 	
-	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
+}