first commit

defaults

+{   
+    "trec_docker":"registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/trec:6.0",
+    "trec_cluster":"OnDemand bcs.ps.r.xlarge img-ubuntu-vpc",
+    "disk_size":"200"
+}

inputs

+{
+  "{{ project_name }}.trec_docker": "{{ trec_docker }}",
+  "{{ project_name }}.sample_id": "{{ sample_id }}",
+  "{{ project_name }}.tumor_purity": "{{ tumor_purity }}",
+  "{{ project_name }}.TRA_cn": "{{ TRA_cn }}",
+  "{{ project_name }}.tumorBAM": "{{ tumorBAM }}",
+  "{{ project_name }}.tumorBAM_bai": "{{ tumorBAM_bai }}",
+  "{{ project_name }}.trec_cluster": "{{ trec_cluster }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}"
+}

tasks/trec.wdl

+task trec {
+    String sample_id
+    File tumorBAM
+    File tumorBAM_bai
+    String TRA_cn
+    String tumor_purity
+
+    String docker
+    String cluster
+    String disk_size
+
+    command <<<
+
+        set -o pipefail
+        set -e
+        mkdir ./TREC_ana
+        cp ${tumorBAM} ./TREC_ana/
+        cp ${tumorBAM_bai} ./TREC_ana/
+        cd ./TREC_ana
+        cp /software/CBCGA_07604514_Padded_hg38.bed ./
+        bam_name=`ls |grep bam|grep -v bai`
+        echo $bam_name
+        Rscript /software/TREC_script.Rscript --sample_id ${sample_id} \
+           --wes_bed ./CBCGA_07604514_Padded_hg38.bed \
+           --bam ./$bam_name \
+           --tumor_purity ${tumor_purity} \
+           --cn_TRA ${TRA_cn}
+       
+    >>>
+
+    runtime {
+        docker : docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        Array[File] trec_txt = glob("./TREC_ana/*.txt")
+        Array[File] trec_pdf = glob("./TREC_ana/*.pdf")
+    }
+
+}
+
+

workflow.wdl

+import "./tasks/trec.wdl" as trec
+workflow {{ project_name }} {
+    String sample_id
+    File tumorBAM
+    File tumorBAM_bai
+    String TRA_cn
+    String tumor_purity
+
+    String trec_docker
+    String trec_cluster
+    String disk_size
+
+        call trec.trec as trec {
+                input:	
+                sample_id=sample_id,
+                tumorBAM=tumorBAM,
+                tumorBAM_bai=tumorBAM_bai,
+                TRA_cn=TRA_cn,
+                tumor_purity=tumor_purity,
+                docker=trec_docker,
+                cluster=trec_cluster,
+                disk_size=disk_size
+        }
+
+
+}