fix bug

tasks/TNscope.wdl

 	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 ""
-	String input_command = if defined(corealigner_bam) then "-i ${corealigner_bam} --tumor_sample ${tumor_name} --normal_sample ${normal_name}" else "-i ${tumor_recaled_bam} --tumor_sample ${tumor_name}"
-	
+		
 	command <<<
 		set -o pipefail
 		set -e
 		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})
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} --algo TNscope ${input_command} --dbsnp ${dbsnp_dir}/${dbsnp} ${pon_command} ${sample}.TNscope.TN.vcf
+		if ${corealigner_bam}; 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
+			${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} -i ${tumor_recaled_bam} --algo TNscope --tumor_sample ${tumor_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${pon_command} ${sample}.TNscope.TN.vcf
+		fi
 		
 	>>>
 

tasks/TNseq.wdl

 	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 ""
-	String input_command = if defined(corealigner_bam) then "-i ${corealigner_bam} --tumor_sample ${tumor_name} --normal_sample ${normal_name}" else "-i ${tumor_recaled_bam} --tumor_sample ${tumor_name}"
-
+	
 	command <<<
 		set -o pipefail
 		set -e
 		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})
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} --algo TNhaplotyper ${input_command} --dbsnp ${dbsnp_dir}/${dbsnp} ${pon_command} ${sample}.TNseq.TN.vcf
 
+		if ${corealigner_bam}; 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
+			${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} -i ${tumor_recaled_bam} --algo TNhaplotyper --tumor_sample ${tumor_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${pon_command} ${sample}.TNseq.TN.vcf
+		fi
 	>>>
 
 	runtime {

tasks/bcftools.wdl

 		set -o pipefail
 		set -e
 		
-		if [ ${set_pon} ]; then
+		if ${set_pon} ; then
 			mkdir -p /cromwell_root/tmp/bcftools/
 			for i in ${sep=" " pon_vcf}
 			do

workflow.wdl

 	File? normal_recaled_bam
 	File? normal_recaled_bam_index
 	String type
-	
+
 	String SENTIEON_INSTALL_DIR
 	String SENTIEON_LICENSE
 	String sentieon_docker
 		}
 	}
 
-	call TNseq.TNseq as TNseq {
-		input:
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		SENTIEON_LICENSE=SENTIEON_LICENSE,
-		fasta=fasta,
-		ref_dir=ref_dir,
-		corealigner_bam=corealigner.corealigner_bam,
-		corealigner_bam_index=corealigner.corealigner_bam_index,
-		tumor_recaled_bam=BQSR.recaled_bam,
-		tumor_recaled_bam_index=BQSR.recaled_bam_index,
-		dbsnp=dbsnp,
-		dbsnp_dir=dbsnp_dir,
-		set_pon=set_pon,
-		pon_vcf=pon_vcf,
-        cosmic_vcf=cosmic_vcf,
-        cosmic_dir=cosmic_dir,
-		tumor_name=sample + "_tumor",
-		normal_name=sample + "_normal",
-		docker=sentieon_docker,
-		sample=sample,
-		disk_size=disk_size,
-		cluster_config=cluster_config
-	}
-    
-	call TNscope.TNscope as TNscope {
-		input:
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		SENTIEON_LICENSE=SENTIEON_LICENSE,
-		fasta=fasta,
-		ref_dir=ref_dir,
-		corealigner_bam=corealigner.corealigner_bam,
-		corealigner_bam_index=corealigner.corealigner_bam_index,
-		tumor_recaled_bam=BQSR.recaled_bam,
-		tumor_recaled_bam_index=BQSR.recaled_bam_index,
-		dbsnp=dbsnp,
-		dbsnp_dir=dbsnp_dir,
-		set_pon=set_pon,
-		pon_vcf=pon_vcf,
-        cosmic_vcf=cosmic_vcf,
-        cosmic_dir=cosmic_dir,
-		tumor_name=sample + "_tumor",
-		normal_name=sample + "_normal",
-		docker=sentieon_docker,
-		sample=sample,
-		disk_size=disk_size,
-		cluster_config=cluster_config
+	if (type == "tumor") {
+		call TNseq.TNseq as TNseq {
+			input:
+			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+			SENTIEON_LICENSE=SENTIEON_LICENSE,
+			fasta=fasta,
+			ref_dir=ref_dir,
+			corealigner_bam=corealigner.corealigner_bam,
+			corealigner_bam_index=corealigner.corealigner_bam_index,
+			tumor_recaled_bam=BQSR.recaled_bam,
+			tumor_recaled_bam_index=BQSR.recaled_bam_index,
+			dbsnp=dbsnp,
+			dbsnp_dir=dbsnp_dir,
+			set_pon=set_pon,
+			pon_vcf=pon_vcf,
+			cosmic_vcf=cosmic_vcf,
+			cosmic_dir=cosmic_dir,
+			tumor_name=sample + "_tumor",
+			normal_name=sample + "_normal",
+			docker=sentieon_docker,
+			sample=sample,
+			disk_size=disk_size,
+			cluster_config=cluster_config
+		}
+	
+		call TNscope.TNscope as TNscope {
+			input:
+			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+			SENTIEON_LICENSE=SENTIEON_LICENSE,
+			fasta=fasta,
+			ref_dir=ref_dir,
+			corealigner_bam=corealigner.corealigner_bam,
+			corealigner_bam_index=corealigner.corealigner_bam_index,
+			tumor_recaled_bam=BQSR.recaled_bam,
+			tumor_recaled_bam_index=BQSR.recaled_bam_index,
+			dbsnp=dbsnp,
+			dbsnp_dir=dbsnp_dir,
+			set_pon=set_pon,
+			pon_vcf=pon_vcf,
+			cosmic_vcf=cosmic_vcf,
+			cosmic_dir=cosmic_dir,
+			tumor_name=sample + "_tumor",
+			normal_name=sample + "_normal",
+			docker=sentieon_docker,
+			sample=sample,
+			disk_size=disk_size,
+			cluster_config=cluster_config
+		}
 	}
-    
+
 	if (set_annovar && defined(TNscope.TNscope_vcf) && defined(TNseq.TNseq_vcf)){
-        call annovar.annovar as annovar {
-            input:
-            docker=annovar_docker,
-            database=database,
-            tnscope_vcf_file=TNscope.TNscope_vcf,
-            tnseq_vcf_file=TNseq.TNseq_vcf,
-            sample=sample,
-            cluster_config=cluster_config,
-            disk_size=disk_size
-        }
+		call annovar.annovar as annovar {
+			input:
+			docker=annovar_docker,
+			database=database,
+			tnscope_vcf_file=TNscope.TNscope_vcf,
+			tnseq_vcf_file=TNseq.TNseq_vcf,
+			sample=sample,
+			cluster_config=cluster_config,
+			disk_size=disk_size
+		}
 
-    	if (set_vcf2maf){
-        	call vcf2maf.vcf2maf as vcf2maf {
-            	input:
-    	        docker=vcf2maf_r_docker,
-        	    multianno_tnscope_txt=annovar.multianno_tnscope_txt,
-            	multianno_tnseq_txt=annovar.multianno_tnseq_txt,
-    	        sample=sample,
-    	        cluster_config=cluster_config,
-    	        disk_size=disk_size
-    	    }
+		if (set_vcf2maf){
+			call vcf2maf.vcf2maf as vcf2maf {
+				input:
+				docker=vcf2maf_r_docker,
+				multianno_tnscope_txt=annovar.multianno_tnscope_txt,
+				multianno_tnseq_txt=annovar.multianno_tnseq_txt,
+				sample=sample,
+				cluster_config=cluster_config,
+				disk_size=disk_size
+			}
 		}
-    }
+	}
 }