first commit

defaults

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+{   
+    "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

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+{
+	"{{ 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

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+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
+        
+        now_path=`pwd`
+        echo $now_path > $now_path/test.txt
+        mkdir -p ./ana/${sample_id}/
+        cp ${normBAM} ./ana/${sample_id}/
+        cp ${normBAM_bai} ./ana/${sample_id}/
+        cp ${tumorBAM} ./ana/${sample_id}/
+        cp ${tumorBAM_bai} ./ana/${sample_id}/
+        cp ${hlas} ./ana/
+        cp ${ascat} ./ana/
+
+        for line in `ls ./ana/${sample_id}|sed 's/.bam.*//'|sort|uniq`
+        do
+            new_name=`echo $line|sed 's/\./_/g'`
+            mv ./ana/${sample_id}/$line.bam ./ana/${sample_id}/$new_name.bam
+            mv ./ana/${sample_id}/$line.bam.bai ./ana/${sample_id}/$new_name.bam.bai
+        done
+        normBAM_file=`ls ./ana/${sample_id}/|grep bam|grep -v "TT"|grep -v "bai"|grep -v "_T_sorted"`
+
+        Rscript /software/lohhla_hg38/LOHHLAscript_hg38.R --patientId ${sample_id} \
+           --outputDir $now_path/ana/${sample_id}_output \
+           --normalBAMfile  $now_path/ana/${sample_id}/$normBAM_file \
+           --BAMDir $now_path/ana/${sample_id} \
+           --hlaPath $now_path/ana/${sample_id}_winners.hlas \
+           --HLAfastaLoc /software/lohhla_hg38/data/abc_complete.fasta \
+           --CopyNumLoc $now_path/ana/${sample_id}_ascat.txt \
+           --mappingStep TRUE --minCoverageFilter 10 --fishingStep TRUE --cleanUp FALSE \
+           --gatkDir /software/picard-tools-1.122 \
+           --novoDir /opt/conda/bin \
+           --HLAexonLoc /software/lohhla_hg38/data/hla.dat
+
+       tar -zcvf ./ana/${sample_id}_output.tgz ./ana/${sample_id}_output
+
+    >>>
+	
+    runtime {
+        docker : docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        Array[File] lohhla_xls = glob("./ana/${sample_id}_output/*.xls")
+        Array[File] lohhla_pdf = glob("./ana/${sample_id}_output/Figures/*.pdf")
+        Array[File] lohhla_tgz = glob("./ana/*.tgz")
+    }
+
+}
+
+

workflow.wdl

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+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
+
+        }
+
+
+}