first commit

defaults

+{   
+    "lohhla_docker":"registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/lohhla_hg38:v3.6.3",
+    "lohhla_cluster":"OnDemand bcs.ps.r.xlarge img-ubuntu-vpc",
+    "disk_size":"200"
+}

inputs

+{
+    "{{ project_name }}.sample_id": "{{ sample_id }}",
+    "{{ project_name }}.normBAM": "{{ normBAM }}",
+    "{{ project_name }}.normBAM_bai": "{{ normBAM_bai }}",
+    "{{ project_name }}.tumorBAM": "{{ tumorBAM }}",
+    "{{ project_name }}.tumorBAM_bai": "{{ tumorBAM_bai }}",
+    "{{ project_name }}.hlas": "{{ hlas }}",
+    "{{ project_name }}.ascat": "{{ ascat }}",
+    "{{ project_name }}.lohhla_docker": "{{ lohhla_docker }}",
+    "{{ project_name }}.lohhla_cluster": "{{ lohhla_cluster }}",
+    "{{ project_name }}.disk_size": "{{ disk_size }}"
+}

tasks/lohhla.wdl

+task lohhla {
+    String sample_id
+    File normBAM
+    File normBAM_bai
+    File tumorBAM
+    File tumorBAM_bai
+    File hlas
+    File ascat
+
+    String docker
+    String cluster
+    String disk_size
+
+    command <<<
+
+        set -o pipefail
+        set -e
+
+        echo ${sample_id} >a.txt
+        ls ${normBAM}
+        ls ${normBAM_bai}
+        ls ${tumorBAM}
+        ls ${tumorBAM_bai}
+        ls ${hlas}
+        ls ${ascat}
+        
+    >>>
+
+    runtime {
+        docker : docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        Array[File] lohhla_xls = glob("*.txt")
+    }
+
+}
+
+

workflow.wdl

+import "./tasks/lohhla.wdl" as lohhla
+workflow run_lohhla {
+    String sample_id
+    File normBAM
+    File normBAM_bai
+    File tumorBAM
+    File tumorBAM_bai
+    File hlas
+    File ascat
+
+    String lohhla_docker
+    String lohhla_cluster
+    String disk_size
+
+        call lohhla.lohhla as lohhla {
+                input:	
+                sample_id=sample_id,
+                normBAM=normBAM,
+                normBAM_bai=normBAM_bai,
+                tumorBAM=tumorBAM,
+                tumorBAM_bai=tumorBAM_bai,
+                hlas=hlas,
+                ascat=ascat,
+                docker=lohhla_docker
+                cluster=lohhla_cluster,
+                disk_size=disk_size
+
+        }
+
+
+}