input revised

inputs

@@ -0,0 +1,5 @@
+{
+    "{{ project_name }}.bam": "{{ bam }}",
+    "{{ project_name }}.arcashla.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/tengfei/arcashla:latest",
+    "{{ project_name }}.arcashla.cluster": "OnDemand bcs.a2.large img-ubuntu-vpc"
+}

readme.md

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+> Author: Jun Shang
+>
+> Email: shangjunv@163.com
+>
+> Last Updates: 27/02/2020
+
+#### Requirements
+
+- choppy
+- Ali-Cloud
+
+```
+$ source activate choppy/open-choppy-env
+$ choppy install junshang/arcasHLA
+$ choppy apps
+```
+
+#### quick start
+
+```
+$ choppy samples junshang/arcasHLA-latest > samples.csv
+$ choppy batch junshang/arcasHLA-latest samples.csv -p Your_project_name
+```

tasks/arcashla.wdl

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+task arcashla {
+    File bam
+    String docker
+    String cluster
+
+    command <<<
+       mkdir hla_type
+       /root/arcasHLA/arcasHLA extract ${bam} -o ${base} --paired -t 8 -v
+       /root/arcasHLA/arcasHLA genotype ${base}/${base}.sorted.extracted.1.fq.gz ${base}/${base}.sorted.extracted.2.fq.gz -g A,B,C,DPB1,DQB1,DQA1,DRB1 -o hla_type/${base}.genotype.json -t 8 -v
+    >>>
+
+    runtime {
+       docker: docker
+       cluster: cluster
+       systemDisk: "cloud_ssd 40"
+       dataDisk: "cloud_ssd 200 /cromwell_root/"
+    }
+
+    output {
+      File extracted_1p = "${base}/${base}.sorted.extracted.1.fq.gz"
+      File extracted_2p = "${base}/${base}.sorted.extracted.2.fq.gz"
+      Array[File] hla_type = ["hla_type/${base}.genotype.json", "hla_type/${base}.genes.json", "hla_type/${base}.genotype.log"]
+    }
+
+}
+

workflow.wdl

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+import "./tasks/arcashla.wdl" as arcashla
+
+workflow {{ project_name }} {
+
+	File bam
+
+        call arcashla.arcashla as arcashla {
+               input: bam = bam
+	}
+        
+	
+}
+
+