first commit

defaults

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+{
+  "fasta": "GRCh38.d1.vd1.fa",
+  "disk_size": "500",
+  "cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
+  "docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/manta:1.6.0",
+  "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
+  "memory":"50"
+}

inputs

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+{
+  "{{ project_name }}.fasta": "{{ fasta }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.docker": "{{ docker }}",
+  "{{ project_name }}.bam_index": "{{ bam_index }}",
+  "{{ project_name }}.cluster_config": "{{ cluster_config }}",
+  "{{ project_name }}.bam": "{{ bam }}",
+  "{{ project_name }}.memory": "{{ memory }}",
+  "{{ project_name }}.sample": "{{ sample }}",
+  "{{ project_name }}.ref_dir": "{{ ref_dir }}"
+}

tasks/manta.wdl

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+task manta {
+
+    File ref_dir
+	File fasta
+	File bam
+	File bam_index
+	String memory
+	String sample
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+
+		nt=$(nproc)
+		mkdir -p /cromwell_root/tmp
+
+		/opt/manta-1.6.0.centos6_x86_64/bin/configManta.py --bam=${bam} --referenceFasta ${ref_dir}/${fasta} --runDir /cromwell_root/tmp
+
+		/cromwell_root/tmp/runWorkflow.py -j $nt -g ${memory}
+
+		cp /cromwell_root/tmp/results/variants/diploidSV.vcf.gz ${sample}_manta_germlineSV.vcf.gz
+
+
+	>>>
+
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File manta_germline_vcf = "${sample}_manta_germlineSV.vcf.gz"
+	}
+}

workflow.wdl

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+import "./tasks/manta.wdl" as manta
+
+
+workflow {{ project_name }} {
+
+    File ref_dir
+	File fasta
+	File bam
+	File bam_index
+	String memory
+	String sample
+	String docker
+	String cluster_config
+	String disk_size
+
+	call manta.manta as manta {
+		input:
+		fasta=fasta,
+		ref_dir=ref_dir,
+		bam=bam,
+		bam_index=bam_index,
+		memory=memory,
+		sample=sample,
+		docker=docker,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+	}
+