fix bug: modified judgment condition

tasks/TNscope.wdl

@@ -32,13 +32,15 @@ task TNscope {
 		set -e
 		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
 		nt=$(nproc)
-
-		mkdir -p /cromwell_root/tmp/PON/
-		cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/PON/
-		cp ${pon_vcf} /cromwell_root/tmp/PON/
-		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/${cosmic_vcf}
-		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/$(basename ${pon_vcf})
 		
+		if ${set_pon}; then
+			mkdir -p /cromwell_root/tmp/PON/
+			cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/PON/
+			cp ${pon_vcf} /cromwell_root/tmp/PON/
+			${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/${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 TNscope --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${pon_command} ${sample}.TNscope.TN.vcf
 		else

tasks/TNseq.wdl

@@ -31,12 +31,14 @@ task TNseq {
 		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
 		nt=$(nproc)
 
-		mkdir -p /cromwell_root/tmp/PON/
-		cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/PON/
-		cp ${pon_vcf} /cromwell_root/tmp/PON/
-		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/${cosmic_vcf}
-		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/$(basename ${pon_vcf})
-
+		if ${set_pon}; then
+			mkdir -p /cromwell_root/tmp/PON/
+			cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/PON/
+			cp ${pon_vcf} /cromwell_root/tmp/PON/
+			${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/${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