add Count

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+	"python.pythonPath": "/usr/bin/python"
+}

defaults

@@ -5,5 +5,6 @@
     "docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bamreadcount:v0.8.0",
     "cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
     "min_base_quality": "0",
-    "min_mapping_quality": "0"
+    "min_mapping_quality": "0",
+    "count_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/coverage_count:v1.0"
 }

inputs

@@ -9,5 +9,6 @@
   "{{ project_name }}.min_base_quality": "{{ min_base_quality }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.cluster_config": "{{ cluster_config }}",
-  "{{ project_name }}.sample_id": "{{ sample_id }}"
+  "{{ project_name }}.sample_id": "{{ sample_id }}",
+  "{{ project_name }}.count_docker": "{{ count_docker }}"
 }

tasks/Count.wdl

@@ -0,0 +1,24 @@
+task Count {
+
+    String sample_id
+    File readcount
+    File bed
+    String docker
+    String cluster_config
+    String disk_size
+
+    command <<<
+        python /bed/count.py -s ${sample_id} -i ${readcount} -c ${bed} -o ${sample_id}.coverage
+    >>>
+
+    runtime {
+        docker: docker
+        cluster: cluster_config
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        File Count = "${sample_id}.coverage"
+    }
+}

workflow.wdl

@@ -1,4 +1,6 @@
 import "./tasks/BAMReadCount.wdl" as BAMReadCount
+import "./tasks/Count.wdl" as Count
+
 
 workflow {{ project_name }} {
     File ref_dir
@@ -10,6 +12,7 @@ workflow {{ project_name }} {
     String min_base_quality
     String sample_id
     String docker
+    String count_docker
     String cluster_config
     String disk_size
     
@@ -28,4 +31,14 @@ workflow {{ project_name }} {
         cluster_config=cluster_config,
         sample_id=sample_id
     }
+
+    call Count.Count as Count {
+        input:
+        readcount=BAMReadCount.readcount,
+        bed=bed,
+        docker=count_docker,
+        disk_size=disk_size,
+        cluster_config=cluster_config,
+        sample_id=sample_id
+    }
 }