first commit

README.md

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+# Strelka2
+
+You don't need to tune the parameters of strelka. It bases on [trained models](<https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/trainingGermlineEmpiricalScore.md>), you may train new models to improve performance.
+
+Why?
+
+
+
+Two steps:
+
+1. Generate the configuration
+
+   ```bash
+   
+   ```
+
+2. Run Strelka 
+
+   ```bash
+   
+   ```
+
+
+
+##### Reference
+
+1. Strelka User Guide <https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md>
+2. 

inputs

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+{
+  "{{ project_name }}.Dedup_bam": "{{ Dedup_bam }}",
+  "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
+  "{{ project_name }}.disk_size": "500",
+  "{{ project_name }}.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/strelka:2.9.10",
+  "{{ project_name }}.cluster_config": "OnDemand ecs.sn1ne.8xlarge img-ubuntu-vpc",
+  "{{ project_name }}.Dedup_bam_index": "{{ Dedup_bam_index }}",
+  "{{ project_name }}.sample": "{{ sample }}",
+  "{{ project_name }}.ref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/"
+}

tasks/strelka.wdl

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+task strelka {
+
+    File ref_dir
+	File fasta
+
+	File Dedup_bam
+	File Dedup_bam_index
+	String sample
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e	
+		nt=$(nproc)
+		configureStrelkaGermlineWorkflow.py --bam ${Dedup_bam} --referenceFasta ${ref_dir}/${fasta} 
+		StrelkaGermlineWorkflow/runWorkflow.py -m local -j $nt
+	>>>
+
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		Array[File] output_files = glob("StrelkaGermlineWorkflow/results/variants/*")
+	}
+}

workflow.wdl

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+import "./tasks/strelka.wdl" as strelka
+
+
+workflow project_name {
+
+    File ref_dir
+	File fasta
+
+	File Dedup_bam
+	File Dedup_bam_index
+	String sample
+	String docker
+	String cluster_config
+	String disk_size
+
+	call strelka.strelka as strelka {
+		input:
+		fasta=fasta,
+		ref_dir=ref_dir,
+		Dedup_bam=Dedup_bam,
+		Dedup_bam_index=Dedup_bam_index,
+		sample=sample,
+		docker=docker,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+	}
+