first commit

README.md

+### ecDNA Structure Reconstruction
+
+This APP developed for ecDNA structure construction 
+
+**Accepted data**
+
+* sorted deduped bam file and corresponding bam index file
+
+### Getting Started
+
+```
+# Activate the choppy environment
+$ open-choppy-env
+
+# Install the APP
+$ choppy install YaqingLiu/variant-calling [-f]
+
+# List the parameters
+$ choppy samples YaqingLiu/variant-calling-latest [--no-default]
+
+# Submit you task with the `samples.csv file` and `project name`
+$ choppy batch YaqingLiu/variant-calling-latest samples.csv -p Project [-l project:Label]
+
+# Query the status of all tasks in the project
+$ choppy query -L project:Label | grep "status"
+```
+

defaults

+{
+  "prepareaadocker": "registry-internal.cn-shanghai.aliyuncs.com/pgx-docker-registry/prepareaa",
+  "disk_size": "200",
+  "SMALLcluster_config": "OnDemand bcs.ps.g.xlarge img-ubuntu-vpc",
+  "BIGcluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc"
+}
+
+

inputs

+{
+ 
+  "{{ project_name }}.dedup_bamindex": "{{ dedup_bamindex }}",
+  "{{ project_name }}.prepareaadocker": "{{ prepareaadocker }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.sample_name": "{{ sample_name }}",
+  "{{ project_name }}.dedup_bam": "{{ dedup_bam }}",
+  "{{ project_name }}.BIGcluster_config": "{{ BIGcluster_config }}"
+
+}

tasks/prepareaa.wdl

+task prepareaa {
+
+  File dedup_bam
+  File dedup_bamindex
+  
+  String sample_name
+  String docker
+  String cluster_config
+  String disk_size
+  command <<<
+    set -o pipefail
+    set -e  
+    /home/programs/PrepareAA-master/PrepareAA.py -s ${sample_name} -t 15 --cnvkit_dir /home/programs/cnvkit.py --sorted_bam ${dedup_bam} --run_AA --ref GRCh38 -o /home/output/
+    }
+  
+  >>>
+
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  output {
+    Array[File]  prepareaa_result= glob("/home/output")
+    
+  }
+}

workflow.wdl

+import "./tasks/prepareaa.wdl" as prepareaa
+
+workflow  project_name  {
+
+    File dedup_bam
+    File dedup_bamindex
+  
+    String sample_name
+    String prepareaadocker
+    String BIGcluster_config
+    String disk_size
+
+
+
+    call prepareaa.prepareaa as prepareaa {
+        input:
+        sample_name=sample_name,
+        dedup_bam=dedup_bam,
+        dedup_bamindex=dedup_bamindex,
+        docker=prepareaadocker,
+        cluster_config=BIGcluster_config,
+        disk_size=disk_size
+    }
+}