first commit

tasks/BQSR.wdl

 
 		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --algo QualCal --plot --before ${sample}_recal_data.table --after ${sample}_recal_data.table.post ${sample}_recal_data.csv
 
-		${SENTIEON_INSTALL_DIR}/bin/sentieon plot bqsr -o ${sample}_bqsrreport.pdf ${sample}_recal_data.csv
+		${SENTIEON_INSTALL_DIR}/bin/sentieon plot QualCal -o ${sample}_bqsrreport.pdf ${sample}_recal_data.csv
 
 	>>>
 

tasks/PON.wdl

 	String SENTIEON_INSTALL_DIR
 	String SENTIEON_LICENSE
 	String sample
+	Boolean PONmode
 
 	File ref_dir
 	String fasta
 		set -e
 		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
 		nt=$(nproc)
-		mkdir -p /cromwell_root/tmp/cosmic/
-		cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/cosmic/
-		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/cosmic/${cosmic_vcf}
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} -i ${normal_recaled_bam} --algo TNhaplotyper --detect_pon --cosmic /cromwell_root/tmp/cosmic/${cosmic_vcf} --dbsnp ${dbsnp_dir}/${dbsnp} ${sample}_pon.vcf
+		if [ ${PONmode} ]; then
+			mkdir -p /cromwell_root/tmp/cosmic/
+			cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/cosmic/
+			${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/cosmic/${cosmic_vcf}
+			${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} -i ${normal_recaled_bam} --algo TNhaplotyper --detect_pon --cosmic /cromwell_root/tmp/cosmic/${cosmic_vcf} --dbsnp ${dbsnp_dir}/${dbsnp} ${sample}_pon.vcf
+		else
+			touch ${sample}_pon.vcf
+		fi
 	>>>
 	
 	runtime {

workflow.wdl

 			cluster_config=cluster_config
 		}
 
-		if (PONmode) {
-			call PON.PON as PON {
-				input:
-				SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-				SENTIEON_LICENSE=SENTIEON_LICENSE,
-				sample=sample[0],
-				fasta=fasta,
-				ref_dir=ref_dir,
-				normal_recaled_bam=normal_BQSR.recaled_bam,
-				normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
-				cosmic_vcf=cosmic_vcf,
-				cosmic_dir=cosmic_dir,
-				dbsnp=dbsnp,
-				dbsnp_dir=dbsnp_dir,
-				docker=sentieon_docker,
-				disk_size=disk_size,
-				cluster_config=cluster_config
-			}
+		call PON.PON as PON {
+			input:
+			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+			SENTIEON_LICENSE=SENTIEON_LICENSE,
+			sample=sample[0],
+			PONmode=PONmode,
+			fasta=fasta,
+			ref_dir=ref_dir,
+			normal_recaled_bam=normal_BQSR.recaled_bam,
+			normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
+			cosmic_vcf=cosmic_vcf,
+			cosmic_dir=cosmic_dir,
+			dbsnp=dbsnp,
+			dbsnp_dir=dbsnp_dir,
+			docker=sentieon_docker,
+			disk_size=disk_size,
+			cluster_config=cluster_config
 		}
-		File pon_vcf=PON.pon_vcf
 	}
 
 	call bcftools.bcftools as bcftools {
 		input:
 		PONmode=PONmode,
-		pon_vcf=pon_vcf,
+		pon_vcf=PON.pon_vcf,
 		docker=bcftools_docker,
 		disk_size=disk_size,
 		cluster_config=cluster_config