......

tasks/multiqc.wdl

@@ -7,7 +7,7 @@ task multiqc {
 	Array[File] txt2
 
 	Array[File] bamqc_zip
-	Array[File] RNAseqqc_zip
+	Array[File] rnaseq_zip
 
 	String docker
 	String cluster_config
@@ -27,7 +27,8 @@ task multiqc {
 		do
 		  tar -zxvf $i -C /cromwell_root/tmp/bamqc
 		done
-		for i in ${sep=" " RNAseqqc_zip}
+		
+		for i in ${sep=" " rnaseq_zip}
 		do
 		  tar -zxvf $i -C /cromwell_root/tmp/rnaqc
 		done

workflow.wdl

@@ -37,6 +37,9 @@ workflow {{ project_name }} {
 	String samtools_cluster
 	String stringtie_docker
 	String stringtie_cluster
+	String multiqc_cluster_config
+	String multiqc_docker
+	String multiqc_disk_size
 	Int trim_front1 
 	Int trim_tail1 
 	Int max_len1