fix bug

defaults

@@ -1,23 +1,5 @@
 {
-    "fasta": "hg19_nochr.fa",
-    "ref_dir": "oss://pgx-reference-data/hg19/",
-    "dbsnp": "dbsnp_138.hg19_nochr_sorted.vcf",
-    "dbsnp_dir": "oss://pgx-reference-data/hg19/",
-    "SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
-    "SENTIEON_LICENSE": "192.168.0.55:8990",
-    "dbmills_dir": "oss://pgx-reference-data/hg19/",
-    "db_mills": "Mills_and_1000G_gold_standard.indels.hg19_nochr.vcf",
-    "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2017.11.04",
-    "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",
     "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.bed",
-    "PONmode": true,
-    "cosmic_vcf": "CosmicCodingMuts.hg19.v91.vcf",
-    "cosmic_dir": "oss://pgx-reference-data/reference/cosmic/",
     "disk_size": "200",
-    "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
-    "set_annovar": true,
-    "set_vcf2maf": true
+    "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc"
 }

inputs

@@ -1,25 +1,7 @@
 {
-  "{{ project_name }}.fasta": "{{ fasta }}",
-  "{{ project_name }}.ref_dir": "{{ ref_dir }}",
-  "{{ project_name }}.dbsnp": "{{ dbsnp }}",
-  "{{ project_name }}.dbsnp_dir": "{{ dbsnp_dir }}",
-  "{{ project_name }}.SENTIEON_INSTALL_DIR": "{{ SENTIEON_INSTALL_DIR }}",
-  "{{ project_name }}.SENTIEON_LICENSE": "{{ SENTIEON_LICENSE }}",
-  "{{ project_name }}.dbmills_dir": "{{ dbmills_dir }}",
-  "{{ 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 }}.bcftools_docker": "{{ bcftools_docker }}",
-  "{{ project_name }}.database": "{{ database }}",
-  "{{ project_name }}.BCF": "{{ BCF }}",
-  "{{ project_name }}.regions": "{{ regions }}",
-  "{{ project_name }}.PONmode": "{{ PONmode }}",
-  "{{ project_name }}.cosmic_vcf": "{{ cosmic_vcf }}",
-  "{{ project_name }}.cosmic_dir": "{{ cosmic_dir }}",
+  "{{ project_name }}.BCF": {{ BCF }},
   "{{ 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 }}.cluster_config": "{{ cluster_config }}"
 }