first commit

inputs

@@ -1,41 +1,16 @@
 {
-  "{{ project_name }}.LCL7merge.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
   "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
-  "{{ project_name }}.LCL6bed_annotation.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
-  "{{ project_name }}.LCL7bed_annotation.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
-  "{{ project_name }}.LCL8bed_annotation.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
-  "{{ project_name }}.LCL7votes.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.1",
-  "{{ project_name }}.LCL6votes.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.1",
   "{{ project_name }}.LCL5VCFrename.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
-  "{{ project_name }}.LCL8mergeInfo.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.1",
   "{{ project_name }}.LCL6mendelian.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/vbt:v1.1",
-  "{{ project_name }}.LCL5mergeInfo.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.1", 
   "{{ project_name }}.mergeSister.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
   "{{ project_name }}.LCL5mendelian.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/vbt:v1.1",
-  "{{ project_name }}.LCL6allInfozipIndex.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
-  "{{ project_name }}.LCL5allInfozipIndex.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
   "{{ project_name }}.disk_size": "150",
-  "{{ project_name }}.LCL7mergeInfo.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.1",
   "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
-  "{{ project_name }}.repeat_bed": "oss://pgx-result/renluyao/manuscript/all.repeat.bed",
-  "{{ project_name }}.LCL6merge.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
-  "{{ project_name }}.LCL6variantsNorm.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
   "{{ project_name }}.LCL6zipIndex.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
-  "{{ project_name }}.LCL7allInfozipIndex.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
-  "{{ project_name }}.LCL5votes.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.1",
-  "{{ project_name }}.LCL6mergeInfo.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.1",
-  "{{ project_name }}.LCL5bed_annotation.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
   "{{ project_name }}.LCL6VCFrename.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
-  "{{ project_name }}.LCL5merge.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
-  "{{ project_name }}.LCL8votes.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.1",
   "{{ project_name }}.reformVCF.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.1",
   "{{ project_name }}.LCL5zipIndex.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
   "{{ project_name }}.cluster_config": "OnDemand bcs.b4.xlarge img-ubuntu-vpc",
-  "{{ project_name }}.LCL8allInfozipIndex.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
-  "{{ project_name }}.LCL7variantsNorm.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
-  "{{ project_name }}.LCL8merge.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
-  "{{ project_name }}.LCL5variantsNorm.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
-  "{{ project_name }}.LCL8variantsNorm.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
   "{{ project_name }}.ref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/"
 }
 

workflow.wdl

@@ -1,4 +1,9 @@
 import "./tasks/mendelian.wdl" as mendelian
+import "./tasks/zipIndex.wdl" as zipIndex
+import "./tasks/VCFrename.wdl" as VCFrename
+import "./tasks/mergeSister.wdl" as mergeSister
+import "./tasks/reformVCF.wdl" as reformVCF
+
 
 workflow {{ project_name }} {
 	File inputSamplesFile