first commit

defaults

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+{   
+    "battenberg_docker":"registry.cn-shanghai.aliyuncs.com/shaolab2023_docker/battenberg_lcl:2.8",
+    "battenberg_cluster":"OnDemand bcs.ps.r.8xlarge img-ubuntu-vpc",
+    "disk_size":"200"
+}

inputs

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+{
+  "{{ project_name }}.battenberg_docker": "{{ battenberg_docker }}",
+  "{{ project_name }}.tumor_id": "{{ tumor_id }}",
+  "{{ project_name }}.tumor_bam": "{{ tumor_bam }}",
+  "{{ project_name }}.normal_id": "{{ normal_id }}",
+  "{{ project_name }}.normal_bam": "{{ normal_bam }}",
+  "{{ project_name }}.battenberg_cluster": "{{ battenberg_cluster }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}"
+}

tasks/battenberg.wdl

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+task battenberg {
+    String tumor_id
+    File tumor_bam
+    String normal_id
+    File normal_bam
+
+    String docker
+    String cluster
+    String disk_size
+
+    command <<<
+
+        set -o pipefail
+        set -e
+        samtools view -h ${normal_bam} |sed 's/chr//g'|samtools view  -bS > ./${normal_id}.sorted.deduped.nochr.bam
+        samtools view -h ${tumor_bam} |sed 's/chr//g'|samtools view  -bS > ./${tumor_id}.sorted.deduped.nochr.bam
+        samtools index  ./${normal_id}.sorted.deduped.nochr.bam
+        samtools index  ./${tumor_id}.sorted.deduped.nochr.bam
+        cp /opt/battenberg_reference/battenberg_wgs.R ./
+        Rscript ./battenberg_wgs.R -t ${tumor_id} -n ${normal_id} --nb ${normal_id}.sorted.deduped.nochr.bam --tb  ${tumor_id}.sorted.deduped.nochr.bam --cpu 1 --sex female -o ./
+         
+    >>>
+
+    runtime {
+        docker : docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        File subclones = "${tumor_id}_subclones.txt"
+        File rho = "${tumor_id}_rho_and_psi.txt"
+        File average_png = "${tumor_id}_BattenbergProfile_average.png"
+        File subclones_png = "${tumor_id}_subclones.png"
+        File distance_png = "${tumor_id}_distance.png"
+        File tumor_png = "${tumor_id}.tumour.png"
+        File germline_png = "${tumor_id}.germline.png"
+        File coverage_png = "${tumor_id}_coverage.png"
+        File alleleratio_png = "${tumor_id}_alleleratio.png"
+        
+    }
+
+}
+
+

workflow.wdl

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