debug

defaults

 {
   "benchmarking_dir": "oss://pgx-result/renluyao/manuscript_v3.0/reference_datasets_v202103/",
-  "vcf_F7": "",
   "SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
-  "vcf_M8": "",
   "fasta": "GRCh38.d1.vd1.fa",
   "BENCHMARKdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",
-  "vcf_D6": "",
   "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",
-  "fastq_2_M8": "",
-  "fastq_1_M8": "",
   "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",
-  "fastq_2_D5": "",
   "FASTQSCREENdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0",
-  "fastq_2_F7": "",
   "SENTIEON_LICENSE": "192.168.0.55:8990",
-  "fastq_1_D6": "",
-  "fastq_1_F7": "",
   "SENTIEONdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2019.11.28",
   "QUALIMAPdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",
   "vcf_D5": "",
   "db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
   "dbsnp": "dbsnp_146.hg38.vcf",
   "MENDELIANdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/vbt:v1.1",
-  "fastq_2_D6": "",
   "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/"
 }

inputs

   "{{ project_name }}.fastq_1_D6": "{{ fastq_1_D6 }}",
   "{{ project_name }}.fastq_1_F7": "{{ fastq_1_F7 }}",
   "{{ project_name }}.SENTIEONdocker": "{{ SENTIEONdocker }}",
-  "{{ project_name }}.QUALIMAPdocker": "{{ QUALIMAPdocke }}",
+  "{{ project_name }}.QUALIMAPdocker": "{{ QUALIMAPdocker }}",
   "{{ project_name }}.vcf_D5": "{{ vcf_D5 }}",
   "{{ project_name }}.benchmark_region": "{{ benchmark_region }}",
   "{{ project_name }}.db_mills": "{{ db_mills }}",