first commit

defaults

+{   
+    "polysolver_docker":"registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/polysolver:v4.1_hg38",
+    "polysolver_cluster":"OnDemand bcs.b4.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 }}.polysolver_docker": "{{ polysolver_docker }}",
+        "{{ project_name }}.polysolver_cluster": "{{ polysolver_cluster }}",
+	"{{ project_name }}.disk_size": "{{ disk_size }}"
+}

tasks/polysolver.wdl

+task polysolver {
+    String sample_id
+    File normBAM
+    File normBAM_bai
+	
+    String docker
+    String cluster
+    String disk_size
+
+    command <<<
+	
+        set -o pipefail
+        set -e
+        
+        mkdir ${sample_id}
+        cp ${normBAM} ./${sample_id}
+        cp ${normBAM_bai} ./${sample_id}
+
+        for line in `ls ./${sample_id}|sed 's/.bam.*//'|sort|uniq`
+        do
+            line=`ls ./${sample_id}|sed 's/.bam.*//'|sort|uniq`
+            new_name=`echo $line|sed 's/\./_/g'`
+            mv ${sample_id}/$line.bam ${sample_id}/$new_name.bam
+            mv ${sample_id}/$line.bam.bai ${sample_id}/$new_name.bam.bai
+        done
+        
+        normBAM_file=`ls ./${sample_id}/|grep bam|grep -v "TT"|grep -v ".T.sorted"|grep -v "bai"`
+        
+        bash /home/polysolver/scripts/shell_call_hla_type ./${sample_id}/$normBAM_file Asian 1 hg38 STDFQ  0 ./${sample_id}/${sample_id}_hla_type/
+        cut -f 2- ./${sample_id}/${sample_id}_hla_type/winners.hla.txt|sed 's/\s/\n/g' > ./${sample_id}_winners.hlas
+
+     
+
+
+    >>>
+	
+    runtime {
+        docker : docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        File hlas="${sample_id}_winners.hlas"
+    }
+
+}
+
+

workflow.wdl

+import "./tasks/polysolver.wdl" as polysolver
+workflow {{ project_name }} {
+    String sample_id
+    File normBAM
+    File normBAM_bai
+
+    String polysolver_docker
+    String polysolver_cluster
+    String disk_size
+
+        call polysolver.polysolver as polysolver {
+                input:	
+                sample_id=sample_id,
+                normBAM=normBAM,
+                normBAM_bai=normBAM_bai,
+                docker=polysolver_docker,
+                cluster=polysolver_cluster,
+                disk_size=disk_size
+
+        }
+
+
+}