......

workflow.wdl

@@ -36,4 +36,36 @@ workflow {{ project_name }} {
 	String samtools_docker
 	String samtools_cluster
 	String stringtie_docker
-	}
+	String stringtie_cluster
+	String multiqc_cluster_config
+	String multiqc_docker
+	Int multiqc_disk_size
+	Int trim_front1 
+	Int trim_tail1 
+	Int max_len1 
+	Int trim_front2 
+	Int trim_tail2  
+	Int max_len2 
+	Int disable_adapter_trimming
+	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
+}