first commit

README.md

+# README.md
+
+> Author: Qingwang Chen
+>
+> Email: [qwch20@fudan.edu.cn](mailto:qwch20@fudan.edu.cn)
+>
+> Last Updates: 16/07/2021
+
+#### Requirements
+
+- choppy
+- Ali-Cloud
+- Linux
+
+```
+# 激活choppy环境
+$ source activate choppy (open-choppy-env)
+
+# 第一次安装
+$ choppy install chenqingwang/rtgTools_vcfeval
+# 非第一次安装
+$ choppy install chenqingwang/rtgTools_vcfeval -f 
+
+# 查询已安装APP
+$ choppy apps
+```
+
+#### Quick Start
+
+```
+# 准备 samples.csv 文件
+$ choppy samples chenqingwang/rtgTools_vcfeval-latest > samples.csv
+# 准备无默认参数的samples.csv 文件
+choppy samples --no-default chenqingwang/rtgTools_vcfeval-latest > samples.csv
+
+# 提交任务
+$ choppy batch chenqingwang/rtgTools_vcfeval-latest samples.csv -p Your_project_name -l Your_label
+
+# 查询任务运行状况
+$ choppy query -L Your_label | grep "status"
+
+# 查询失败任务
+$ choppy search -s Failed -p Your_project_name -u chenqingwang --short-format
+
+# 结果文件地址
+$ oss://choppy-cromwell-result/test-choppy/Your_project_name/
+```

defaults

+{   
+    "reference_gtf_file":"oss://pgx-reference-data/GRCh38.d1.vd1/GRCh38.d1.vd1.sdf/",
+    "docker":"registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:3.10.1",
+    "cluster":"OnDemand bcs.a2.large img-ubuntu-vpc",
+    "disk_size":"200"
+    }

inputs

+{
+	"{{ project_name }}.sample_id": "{{ sample_id }}",
+	"{{ project_name }}.vcf1": "{{ vcf1 }}",
+	"{{ project_name }}.vcf2": "{{ vcf2 }}",
+	"{{ project_name }}.SDF": "{{ SDF }}",
+	"{{ project_name }}.docker": "{{ docker }}",
+	"{{ project_name }}.cluster": "{{ cluster }}",
+	"{{ project_name }}.disk_size": "{{ disk_size }}"
+}

tasks/vcfeval.wdl

+task vcfeval {
+    String sample_id
+    File vcf1
+    File vcf2
+    File SDF
+    
+
+    String docker
+    String cluster
+    String disk_size
+
+
+    
+    command <<<
+        set -o pipefail
+        set -e
+
+        mkdir -p ${sample_id}
+
+        /opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b ${vcf1} \
+            -c ${vcf2} \
+            -o ${sample_id}/results \
+            -t ${SDF}
+                  
+        find . -depth > fileList.txt
+    >>>
+
+    runtime {
+        docker: docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+         File fileList = "fileList.txt"
+         File Summary = "summary.txt"
+    }
+}
+

workflow.wdl

+import "./tasks/vcfeval.wdl" as vcfeval
+
+
+workflow {{ project_name }} {
+    String sample_id
+    File vcf1
+    File vcf2
+    File SDF
+    
+
+    String docker
+    String cluster
+    String disk_size	
+
+	call rmats.rmats as rmats {
+		input:
+		vcf1 = vcf1,
+		vcf2 = vcf2,
+		SDF = SDF,
+		sample_id = sample_id,
+		CSTAT = CSTAT,
+		docker = docker,
+		cluster = cluster,
+		disk_size = disk_size
+	}
+}