test14

defaults

 {
   "benchmarking_dir": "oss://pgx-result/renluyao/manuscript_v3.0/reference_datasets_v202103/",
-  "fasta": "GRCh38.d1.vd1.fa",
   "BENCHMARKdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",
-  "dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
   "BEDTOOLSdocker": "registry-internal.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1",
   "disk_size": "500",
   "FASTQCdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:0.11.8",
   "MULTIQCdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/multiqc:v1.8",
   "SMALLcluster_config": "OnDemand bcs.ps.g.xlarge img-ubuntu-vpc",
   "screen_ref_dir": "oss://pgx-reference-data/fastq_screen_reference/",
-  "fastq_1_D5": "",
-  "dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
   "BIGcluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
   "fastq_screen_conf": "oss://pgx-reference-data/fastq_screen_reference/fastq_screen.conf",
   "FASTQSCREENdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0",
   "REPLACE_SENTIEON_DOCKER": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-replaced:1.0",
   "DEEPVARIANT_DOCKER": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/deepvariant:v1.5.0",
   "QUALIMAPdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",
-  "vcf_D5": "",
   "benchmark_region": "oss://pgx-result/renluyao/manuscript_v3.0/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed",
+  "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
+  "fasta": "GRCh38.d1.vd1.fa",
+  "dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
   "db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
+  "dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
   "dbsnp": "dbsnp_146.hg38.vcf",
   "MENDELIANdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/vbt:v1.1",
   "DIYdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.4",
-  "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
   "pl": "ILLUMINA"
 }

inputs

 {
   "{{ project_name }}.benchmarking_dir": "{{ benchmarking_dir }}",
+  "{{ project_name }}.fastq_1_D5": "{{ fastq_1_D5 }}",
+  "{{ project_name }}.fastq_1_D6": "{{ fastq_1_D6 }}",
+  "{{ project_name }}.fastq_1_F7": "{{ fastq_1_F7 }}",
+  "{{ project_name }}.fastq_1_M8": "{{ fastq_1_M8 }}",
+  "{{ project_name }}.fastq_2_D5": "{{ fastq_2_D5 }}",
+  "{{ project_name }}.fastq_2_D6": "{{ fastq_2_D6 }}",
+  "{{ project_name }}.fastq_2_F7": "{{ fastq_2_F7 }}",
+  "{{ project_name }}.fastq_2_M8": "{{ fastq_2_M8 }}",
+  "{{ project_name }}.vcf_D5": "{{ vcf_D5 }}",
+  "{{ project_name }}.vcf_D6": "{{ vcf_D6 }}",
   "{{ project_name }}.vcf_F7": "{{ vcf_F7 }}",
   "{{ project_name }}.vcf_M8": "{{ vcf_M8 }}",
   "{{ project_name }}.fasta": "{{ fasta }}",
   "{{ project_name }}.BENCHMARKdocker": "{{ BENCHMARKdocker }}",
-  "{{ project_name }}.vcf_D6": "{{ vcf_D6 }}",
   "{{ project_name }}.dbsnp_dir": "{{ dbsnp_dir }}",
   "{{ project_name }}.BEDTOOLSdocker": "{{ BEDTOOLSdocker }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.FASTQCdocker": "{{ FASTQCdocker }}",
   "{{ project_name }}.MULTIQCdocker": "{{ MULTIQCdocker }}",
-  "{{ project_name }}.fastq_2_M8": "{{ fastq_2_M8 }}",
   "{{ project_name }}.project": "{{ project_name }}",
   "{{ project_name }}.pl": "{{ pl }}",
-  "{{ project_name }}.fastq_1_M8": "{{ fastq_1_M8 }}",
   "{{ project_name }}.SMALLcluster_config": "{{ SMALLcluster_config }}",
   "{{ project_name }}.screen_ref_dir": "{{ screen_ref_dir }}",
-  "{{ project_name }}.fastq_1_D5": "{{ fastq_1_D5 }}",
   "{{ project_name }}.dbmills_dir": "{{ dbmills_dir }}",
   "{{ project_name }}.BIGcluster_config": "{{ BIGcluster_config }}",
   "{{ project_name }}.fastq_screen_conf": "{{ fastq_screen_conf }}",
-  "{{ project_name }}.fastq_2_D5": "{{ fastq_2_D5 }}",
   "{{ project_name }}.FASTQSCREENdocker": "{{ FASTQSCREENdocker }}",
-  "{{ project_name }}.fastq_2_F7": "{{ fastq_2_F7 }}",
-  "{{ project_name }}.fastq_1_D6": "{{ fastq_1_D6 }}",
-  "{{ project_name }}.fastq_1_F7": "{{ fastq_1_F7 }}",
   "{{ project_name }}.REPLACE_SENTIEON_DOCKER": "{{ REPLACE_SENTIEON_DOCKER }}",
   "{{ project_name }}.DEEPVARIANT_DOCKER": "{{ DEEPVARIANT_DOCKER }}",
   "{{ project_name }}.QUALIMAPdocker": "{{ QUALIMAPdocker }}",
-  "{{ project_name }}.vcf_D5": "{{ vcf_D5 }}",
   "{{ project_name }}.benchmark_region": "{{ benchmark_region }}",
   "{{ project_name }}.db_mills": "{{ db_mills }}",
   "{{ project_name }}.dbsnp": "{{ dbsnp }}",
   "{{ project_name }}.MENDELIANdocker": "{{ MENDELIANdocker }}",
-  "{{ project_name }}.fastq_2_D6": "{{ fastq_2_D6 }}",
   "{{ project_name }}.DIYdocker": "{{ DIYdocker }}",
   "{{ project_name }}.ref_dir": "{{ ref_dir }}"
 }

workflow.wdl

 	String BIGcluster_config
 	String SMALLcluster_config
 
-	# if start with fastq
-	if (fastq_1_D5!= "") {
+	# Fastq is not null, which means starting from fastq
+	if (!defined(fastq_1_D5) && !defined(fastq_2_D5) 
+		&& !defined(fastq_1_D6) && !defined(fastq_2_D6)
+		&& !defined(fastq_1_F7) && !defined(fastq_2_F7)
+		&& !defined(fastq_1_M8) && !defined(fastq_2_M8)) {
 
 		call mapping.mapping as mapping_D5 {
 			input: 
 		# 	cluster_config=SMALLcluster_config,
 		# 	disk_size=disk_size
 		# }
-	}
-
-	# if start with vcf
-	if (vcf_D5!= "") {
+	} 
+	# Fastq is null, check if starts with vcf
+	else if (!defined(vcf_D5) && !defined(vcf_D6) && !defined(vcf_F7) && !defined(vcf_M8) ) {
 		call rename_vcf.rename_vcf as rename_vcf{
 			input:
 			vcf_D5=vcf_D5,