update

defaults

@@ -0,0 +1,7 @@
+{
+    "regions": "oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/SureSelect_Human_All_Exon_V6_r2.bed",
+    "disk_size": "100",
+    "cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc",
+    "samtools_docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",
+    "count_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/coverage_count:v3.0"
+}

inputs

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+{
+  "{{ project_name }}.sample_id": "{{ sample_id }}",
+  "{{ project_name }}.bam": "{{ bam }}",
+  "{{ project_name }}.bai": "{{ bai }}",
+  "{{ project_name }}.regions": "{{ regions }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.count_docker": "{{ count_docker }}",
+  "{{ project_name }}.samtools_docker": "{{ samtools_docker }}",
+  "{{ project_name }}.cluster_config": "{{ cluster_config }}"
+}

tasks/count.wdl

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+task count {
+
+    String sample_id
+    File readcount
+    File regions
+    String docker
+    String cluster_config
+    String disk_size
+	
+    command <<<
+        python /count.py -s ${sample_id} -i ${readcount} -c ${regions} -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"
+    }
+}

tasks/depth.wdl

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+task depth {
+	File bam
+	File bai
+	String sample_id
+	File regions
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+		/opt/conda/bin/samtools depth -b ${regions} ${bam} > ${sample_id}.depth
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File bam_depth = "${sample_id}.depth"
+	}
+}

workflow.wdl

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+import "./tasks/depth.wdl" as depth
+import "./tasks/count.wdl" as depth
+
+workflow {{ project_name }} {
+	File bam
+	File bai
+	String sample_id
+	File regions
+	String samtools_docker
+	String count_docker
+	String cluster_config
+	String disk_size
+
+	call depth.depth as depth {
+		input:
+		bam=bam,
+		bai=bai,
+		sample_id=sample_id,
+		regions=regions,
+		docker=samtools_docker,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+
+    call count.count as count {
+        input:
+        readcount=depth.bam_depth,
+        regions=regions,
+        docker=count_docker,
+        disk_size=disk_size,
+        cluster_config=cluster_config,
+        sample_id=sample_id
+    }
+}