dedup

workflow.wdl

@@ -1,8 +1,9 @@
 import "./tasks/mapping.wdl" as mapping
 import "./tasks/delly.wdl" as delly
+import "./tasks/Dedup.wdl" as Dedup
 import "./tasks/bcf2vcf.wdl" as bcf2vcf
 
-workflow {{ project_name }} {
+workflow project_name {
 	
 	String SENTIEON_INSTALL_DIR
 	String SENTIEONdocker
@@ -59,7 +60,7 @@ workflow {{ project_name }} {
 		sorted_bam=tumor_mapping.sorted_bam,
 		sorted_bam_index=tumor_mapping.sorted_bam_index,
 		sample=sample_name,
-		type="tumor"
+		type="tumor",
 		docker=SENTIEONdocker,
 		disk_size=disk_size,
 		cluster_config=BIGcluster_config
@@ -71,7 +72,7 @@ workflow {{ project_name }} {
 		sorted_bam=normal_mapping.sorted_bam,
 		sorted_bam_index=normal_mapping.sorted_bam_index,
 		sample=sample_name,
-		type="normal"
+		type="normal",
 		docker=SENTIEONdocker,
 		disk_size=disk_size,
 		cluster_config=BIGcluster_config