fix annovar bug

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+	"python.pythonPath": "/usr/bin/python"
+}

defaults

@@ -9,7 +9,7 @@
     "db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
     "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2019.11.28",
     "annovar_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/annovar:v2018.04",
-    "vcf2maf_r_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/r-base:4.0.2",
+    "maftools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/r-base:4.0.2",
     "bcftools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
     "database": "oss://pgx-reference-data/annovar/",
     "regions": "oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/agilent_v6_cosmic_hg38.bed",

inputs

@@ -15,15 +15,15 @@
   "{{ project_name }}.db_mills": "{{ db_mills }}",
   "{{ project_name }}.sentieon_docker": "{{ sentieon_docker }}",
   "{{ project_name }}.annovar_docker": "{{ annovar_docker }}",
-  "{{ project_name }}.vcf2maf_r_docker": "{{ vcf2maf_r_docker }}",
+  "{{ project_name }}.maftools_docker": "{{ maftools_docker }}",
   "{{ project_name }}.database": "{{ database }}",
   "{{ project_name }}.regions": "{{ regions }}",
-  "{{ project_name }}.set_pon": "{{ set_pon }}",
+  "{{ project_name }}.set_pon": {{ set_pon }},
   "{{ project_name }}.pon_vcf": "{{ pon_vcf }}",
   "{{ project_name }}.cosmic_vcf": "{{ cosmic_vcf }}",
   "{{ project_name }}.cosmic_dir": "{{ cosmic_dir }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.cluster_config": "{{ cluster_config }}",
-  "{{ project_name }}.set_annovar": "{{ set_annovar }}",
-  "{{ project_name }}.set_vcf2maf": "{{ set_vcf2maf }}"
+  "{{ project_name }}.set_annovar": {{ set_annovar }},
+  "{{ project_name }}.set_vcf2maf": {{ set_vcf2maf }}
 }

tasks/TNscope.wdl

@@ -25,7 +25,8 @@ task TNscope {
 	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
@@ -37,7 +38,8 @@ task TNscope {
 		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 ${corealigner_bam}; then
+		
+		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
 			${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

tasks/TNseq.wdl

@@ -23,7 +23,8 @@ task TNseq {
 	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
@@ -36,7 +37,7 @@ 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})
 
-		if ${corealigner_bam}; then
+		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
 			${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

tasks/annovar.wdl

@@ -1,7 +1,7 @@
 task annovar {
 
-	File tnscope_vcf_file
-	File tnseq_vcf_file
+	File TNscope_vcf
+	File TNseq_vcf
 	File database
 	String sample
 	String docker
@@ -13,8 +13,8 @@ task annovar {
 		set -o pipefail
 		set -e
 		nt=$(nproc)
-		/installations/annovar/table_annovar.pl ${tnscope_vcf_file} ${database} -buildver hg19 -out ${sample}_tnscope -remove -protocol refGene,cytoBand,genomicSuperDups,snp138,ljb26_all,cosmic78,clinvar_20170130,popfreq_all_20150413,intervar_20170202 -operation g,r,r,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
-		/installations/annovar/table_annovar.pl ${tnseq_vcf_file} ${database} -buildver hg19 -out ${sample}_tnseq -remove -protocol refGene,cytoBand,genomicSuperDups,snp138,ljb26_all,cosmic78,clinvar_20170130,popfreq_all_20150413,intervar_20170202 -operation g,r,r,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
+		/installations/annovar/table_annovar.pl ${TNscope_vcf} ${database} -buildver hg38 -out ${sample}_TNscope -remove -protocol refGene,ensGene,knownGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20200316 -operation g,g,g,r,r,f,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
+		/installations/annovar/table_annovar.pl ${TNseq_vcf} ${database} -buildver hg38 -out ${sample}_TNseq -remove -protocol refGene,ensGene,knownGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20200316 -operation g,g,g,r,r,f,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
 	>>>
 	
 	runtime {
@@ -25,11 +25,11 @@ task annovar {
 	}
 
 	output {
-		File avinput_tnscope = "${sample}_tnscope.avinput"
-		File multianno_tnscope_txt = "${sample}_tnscope.hg19_multianno.txt"
-		File multianno_tnscope_vcf = "${sample}_tnscope.hg19_multianno.vcf"
-		File avinput_tnseq = "${sample}_tnseq.avinput"
-		File multianno_tnseq_txt = "${sample}_tnseq.hg19_multianno.txt"
-		File multianno_tnseq_vcf = "${sample}_tnseq.hg19_multianno.vcf"
+		File avinput_TNscope = "${sample}_TNscope.avinput"
+		File multianno_TNscope_txt = "${sample}_TNscope.hg38_multianno.txt"
+		File multianno_TNscope_vcf = "${sample}_TNscope.hg38_multianno.vcf"
+		File avinput_TNseq = "${sample}_TNseq.avinput"
+		File multianno_TNseq_txt = "${sample}_TNseq.hg38_multianno.txt"
+		File multianno_TNseq_vcf = "${sample}_TNseq.hg38_multianno.vcf"
 	}
 }

tasks/vcf2maf.wdl

@@ -1,15 +1,15 @@
 task vcf2maf {
 
-	File multianno_tnscope_txt
-	File multianno_tnseq_txt
+	File multianno_TNscope_txt
+	File multianno_TNseq_txt
 	String sample
 	String docker
 	String cluster_config
 	String disk_size
 
 	command <<<
-		vcf2maf ${multianno_tnscope_txt} ${sample}_tnscope.MAF
-		vcf2maf ${multianno_tnseq_txt} ${sample}_tnseq.MAF
+		vcf2maf ${multianno_TNscope_txt} ${sample}_TNscope.MAF
+		vcf2maf ${multianno_TNseq_txt} ${sample}_TNseq.MAF
 	>>>
 
 	runtime {
@@ -20,7 +20,7 @@ task vcf2maf {
 	}
 
 	output {
-		File tnscope_maf = "${sample}_tnscope.MAF"
-		File tnseq_maf = "${sample}_tnseq.MAF"
+		File tnscope_maf = "${sample}_TNscope.MAF"
+		File tnseq_maf = "${sample}_TNseq.MAF"
 	}
 }

workflow.wdl

@@ -25,7 +25,7 @@ workflow {{ project_name }} {
 	String SENTIEON_LICENSE
 	String sentieon_docker
 	String annovar_docker
-	String vcf2maf_r_docker
+	String maftools_docker
 	
 	File ref_dir
 	String fasta
@@ -235,8 +235,8 @@ workflow {{ project_name }} {
 			input:
 			docker=annovar_docker,
 			database=database,
-			tnscope_vcf_file=TNscope.TNscope_vcf,
-			tnseq_vcf_file=TNseq.TNseq_vcf,
+			TNscope_vcf=TNscope.TNscope_vcf,
+			TNseq_vcf=TNseq.TNseq_vcf,
 			sample=sample,
 			cluster_config=cluster_config,
 			disk_size=disk_size
@@ -245,9 +245,9 @@ workflow {{ project_name }} {
 		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,
+				docker=maftools_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