first commit

defaults

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+{   
+    "battenberg_docker":"registry.cn-shanghai.aliyuncs.com/shaolab2023_docker/battenberg_lcl:3.0",
+    "battenberg_cluster":"OnDemand bcs.es.r.6xlarge img-ubuntu-vpc",
+    "disk_size":"200"
+}

inputs

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+{
+  "{{ project_name }}.battenberg_docker": "{{ battenberg_docker }}",
+  "{{ project_name }}.sample_id": "{{ sample_id }}",
+  "{{ project_name }}.tumor_bam": "{{ tumor_bam }}",
+  "{{ project_name }}.normal_id": "{{ normal_id }}",
+  "{{ project_name }}.normal_bam": "{{ normal_bam }}",
+  "{{ project_name }}.tumor_bam_bai": "{{ tumor_bam_bai }}",
+  "{{ project_name }}.normal_bam_bai": "{{ normal_bam_bai }}",
+  "{{ project_name }}.battenberg_cluster": "{{ battenberg_cluster }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}"
+}

tasks/battenberg.wdl

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+task battenberg {
+    String sample_id
+    File tumor_bam
+    File tumor_bam_bai
+    String normal_id
+    File normal_bam
+    File normal_bam_bai
+
+    String docker
+    String cluster
+    String disk_size
+
+    command <<<
+
+        set -o pipefail
+        set -e
+        cp ${normal_bam} ./${normal_id}.bam
+        cp ${tumor_bam} ./${sample_id}.bam
+        
+        cp ${normal_bam_bai} ./${normal_id}.bam.bai
+        cp ${tumor_bam_bai} ./${sample_id}.bam.bai
+      
+        cp /opt/battenberg_reference/battenberg_wgs.R ./
+        Rscript ./battenberg_wgs.R -t ${sample_id} -n ${normal_id} --nb ./${normal_id}.bam --tb  ./${sample_id}.bam --cpu 4 --sex female -o ./
+        mkdir ${sample_id}_chr_png
+        cp ${sample_id}_subclones_chr*.png ./${sample_id}_chr_png/
+        tar zcvf ./${sample_id}_chr_png.tgz ./${sample_id}_chr_png/
+
+    >>>
+
+    runtime {
+        docker : docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        File subclones = "${sample_id}_subclones.txt"
+        File rho = "${sample_id}_rho_and_psi.txt"
+        File average_png = "${sample_id}_BattenbergProfile_average.png"
+        File subclones_png = "${sample_id}_BattenbergProfile_subclones.png"
+        File distance_png = "${sample_id}_distance.png"
+        File tumor_png = "${sample_id}.tumour.png"
+        File germline_png = "${sample_id}.germline.png"
+        File coverage_png = "${sample_id}_coverage.png"
+        File alleleratio_png = "${sample_id}_alleleratio.png"
+        File chr_png = "${sample_id}_chr_png.tgz"
+    }
+
+}
+
+

workflow.wdl

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+import "./tasks/battenberg.wdl" as battenberg
+workflow {{ project_name }} {
+    String sample_id
+    File tumor_bam
+    String normal_id
+    File normal_bam
+
+    String battenberg_docker
+    String battenberg_cluster
+    String disk_size
+
+        call battenberg.battenberg as battenberg {
+                input:	
+                sample_id=sample_id,
+                tumor_bam=tumor_bam,
+                normal_id=normal_id,
+                normal_bam=normal_bam,
+                docker=battenberg_docker,
+                cluster=battenberg_cluster,
+                disk_size=disk_size
+        }
+
+
+}