fix bug: modified judgment condition

defaults

@@ -20,5 +20,6 @@
     "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
     "set_annovar": "true",
     "set_vcf2maf": "true",
-    "germline": "false"
+    "germline": "false",
+    "TN": "true"
 }

inputs

@@ -1,5 +1,6 @@
 {
   "{{ project_name }}.sample_id": "{{ sample_id }}",
+  "{{ project_name }}.TN": {{ TN }},
   "{{ project_name }}.fastq_1": "{{ fastq_1 }}",
   "{{ project_name }}.fastq_2": "{{ fastq_2 }}",
   "{{ project_name }}.normal_recaled_bam": "{{ normal_recaled_bam }}",

tasks/TNscope.wdl

@@ -19,20 +19,21 @@ task TNscope {
 	String dbsnp
 	String disk_size
 
+	Boolean TN
 	Boolean set_pon
 	String? cosmic_vcf
 	File? cosmic_dir
 	File? pon_vcf
 	
 	String pon_command = if set_pon then "--pon /cromwell_root/tmp/PON/$(basename ${pon_vcf}) --cosmic /cromwell_root/tmp/PON/${cosmic_vcf}" else ""
-	Boolean TN = if defined(corealigner_bam) then true else false
+	
 	
 	command <<<
 		set -o pipefail
 		set -e
 		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
 		nt=$(nproc)
-		
+
 		if ${set_pon}; then
 			mkdir -p /cromwell_root/tmp/PON/
 			cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/PON/

tasks/TNseq.wdl

@@ -16,14 +16,14 @@ task TNseq {
 	File tumor_recaled_bam_index
 	String dbsnp
 	String disk_size
-
+	
+	Boolean TN
 	Boolean set_pon
 	String? cosmic_vcf
 	File? cosmic_dir
 	File? pon_vcf
 	
 	String pon_command = if set_pon then "--pon /cromwell_root/tmp/PON/$(basename ${pon_vcf}) --cosmic /cromwell_root/tmp/PON/${cosmic_vcf}" else ""
-	Boolean TN = if defined(corealigner_bam) then true else false
 
 	command <<<
 		set -o pipefail
@@ -38,7 +38,7 @@ task TNseq {
 			${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/${cosmic_vcf}
 			${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/$(basename ${pon_vcf})
 		fi
-		
+
 		if ${TN}; then
 			${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} -i ${corealigner_bam} --algo TNhaplotyper --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${pon_command} ${sample}.TNseq.TN.vcf
 		else

workflow.wdl

@@ -16,6 +16,7 @@ import "./tasks/vcf2maf.wdl" as vcf2maf
 workflow {{ project_name }} {
 	
 	String sample_id
+	Boolean TN
 	File fastq_1
 	File fastq_2
 	File? normal_recaled_bam
@@ -180,7 +181,7 @@ workflow {{ project_name }} {
 		}
 	}
 	
-	if (type == "tumor" && defined(normal_recaled_bam)) {
+	if (type == "tumor" && TN) {
 		call corealigner.corealigner as corealigner {
 			input:
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
@@ -252,7 +253,7 @@ workflow {{ project_name }} {
 		}
 	}
 
-	if (set_annovar && defined(TNscope.TNscope_vcf) && defined(TNseq.TNseq_vcf)){
+	if (set_annovar){
 		call annovar.annovar as annovar {
 			input:
 			docker=annovar_docker,