test: boolean

tasks/TNscope.wdl

 	String dbsnp
 	String disk_size
 
-	String set_pon
+	Boolean set_pon
 	String? cosmic_vcf
 	File? cosmic_dir
 	File? pon_vcf
 	
-	String pon_command = if (set_pon == "true") then "--pon /cromwell_root/tmp/PON/$(basename ${pon_vcf}) --cosmic /cromwell_root/tmp/PON/${cosmic_vcf}" else ""
+	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 <<<

tasks/TNseq.wdl

 	String dbsnp
 	String disk_size
 
-	String set_pon
+	Boolean set_pon
 	String? cosmic_vcf
 	File? cosmic_dir
 	File? pon_vcf
 	
-	String pon_command = if (set_pon == "true") then "--pon /cromwell_root/tmp/PON/$(basename ${pon_vcf}) --cosmic /cromwell_root/tmp/PON/${cosmic_vcf}" else ""
+	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 <<<

tasks/bcftools.wdl

 	String docker
 	String cluster_config
 	String disk_size
-	String set_pon
+	Boolean set_pon
 
 
 	command <<<
 		set -o pipefail
 		set -e
 		
-		if [ ${set_pon} == "true" ] ; then
+		if ${set_pon} ; then
 			mkdir -p /cromwell_root/tmp/bcftools/
 			for i in ${sep=" " pon_vcf}
 			do

workflow.wdl

 	String disk_size
 	String cluster_config
 
-	String set_pon
+	Boolean set_pon
 	File? pon_vcf
 	File? cosmic_dir
 	String? cosmic_vcf
 
-	String set_annovar
+	Boolean set_annovar
 	File? database
-	String set_vcf2maf
-	String germline
+	Boolean set_vcf2maf
+	Boolean germline
 
 
 	call mapping.mapping as mapping {
 		cluster_config=cluster_config
 	}
 
-	if (set_pon == "true" && type == "normal") {
+	if (set_pon && type == "normal") {
 		call PON.PON as PON {
 			input:
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 		}
 	}
 
-	if (germline == "true") {
+	if (germline) {
 		call Haplotyper.Haplotyper as Haplotyper {
 			input:
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 		}
 	}
 
-	if (set_annovar == "true" && defined(TNscope.TNscope_vcf) && defined(TNseq.TNseq_vcf)){
+	if (set_annovar && defined(TNscope.TNscope_vcf) && defined(TNseq.TNseq_vcf)){
 		call annovar.annovar as annovar {
 			input:
 			docker=annovar_docker,
 			disk_size=disk_size
 		}
 
-		if (set_vcf2maf == "true"){
+		if (set_vcf2maf){
 			call vcf2maf.vcf2maf as vcf2maf {
 				input:
 				docker=maftools_docker,