fix bug

defaults

@@ -13,11 +13,12 @@
     "bcftools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
     "database": "oss://pgx-reference-data/annovar_hg38/",
     "regions": "oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/agilent_v6_cosmic_hg38.bed",
-    "set_pon": "true",
+    "set_pon": true,
     "cosmic_vcf": "CosmicCodingMuts.hg38.v91.vcf",
     "cosmic_dir": "oss://pgx-reference-data/reference/cosmic/",
     "disk_size": "200",
     "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
-    "set_annovar": "true",
-    "set_vcf2maf": "true"
+    "set_annovar": true,
+    "set_vcf2maf": true,
+    "germline": false
 }

inputs

@@ -25,5 +25,6 @@
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.cluster_config": "{{ cluster_config }}",
   "{{ project_name }}.set_annovar": {{ set_annovar }},
-  "{{ project_name }}.set_vcf2maf": {{ set_vcf2maf }}
+  "{{ project_name }}.set_vcf2maf": {{ set_vcf2maf }},
+  "{{ project_name }}.germline": {{ germline }}
 }

workflow.wdl

@@ -45,6 +45,8 @@ workflow {{ project_name }} {
 	Boolean set_annovar
 	File? database
 	Boolean set_vcf2maf
+	Boolean germline
+
 
 	call mapping.mapping as mapping {
 		input: 
@@ -157,6 +159,25 @@ workflow {{ project_name }} {
 			cluster_config=cluster_config
 		}
 	}
+
+	if (germline) {
+		call Haplotyper.Haplotyper as Haplotyper {
+			input:
+			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+			SENTIEON_LICENSE=SENTIEON_LICENSE,
+			sample=sample,
+			fasta=fasta,
+			ref_dir=ref_dir,
+			recaled_bam=BQSR.recaled_bam,
+			recaled_bam_index=BQSR.recaled_bam_index,
+			dbsnp=dbsnp,
+			dbsnp_dir=dbsnp_dir,
+			regions=regions,
+			docker=docker,
+			disk_size=disk_size,
+			cluster_config=cluster_config
+		}
+	}
 	
 	if (type == "tumor" && defined(normal_recaled_bam)) {
 		call corealigner.corealigner as corealigner {