first commit

README.md

+# 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.
+
+
+
+
+
+Two steps:
+
+1. Generate the configuration
+
+   ```bash
+   
+   ```
+
+2. Run Strelka 
+
+   ```bash
+   
+   ```
+
+##### Per sample run time
+
+4h30min
+
+##### Reference
+
+1. Strelka User Guide <https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md>
+2. Strelka paper <https://www.nature.com/articles/s41592-018-0051-x>

defaults

+{
+  "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/sentieon-genomics:v2019.11.28",
+  "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
+  "memory": "64"
+}

inputs

+{
+  "{{ project_name }}.fasta": "{{ fasta }}",
+  "{{ project_name }}.tumour_bam_index": "{{ tumour_bam_index }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.normal_bam_index": "{{ normal_bam_index }}",
+  "{{ project_name }}.docker": "{{ docker }}",
+  "{{ project_name }}.tumour_bam": "{{ tumour_bam }}",
+  "{{ project_name }}.cluster_config": "{{ cluster_config }}",
+  "{{ project_name }}.normal_bam": "{{ normal_bam }}",
+  "{{ project_name }}.memory": "{{ memory }}",
+  "{{ project_name }}.sample": "{{ sample }}",
+  "{{ project_name }}.ref_dir": "{{ ref_dir }}"
+}

tasks/manta.wdl

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

workflow.wdl

+import "./tasks/manta.wdl" as manta
+
+
+workflow {{ project_name }} {
+
+    File ref_dir
+	File fasta
+	File normal_bam
+	File normal_bam_index
+	File tumour_bam
+	File tumour_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,
+		normal_bam=normal_bam,
+		normal_bam_index=normal_bam_index,
+		tumour_bam=tumour_bam,
+		tumour_bam_index=tumour_bam_index,
+		memory=memory,
+		sample=sample,
+		docker=docker,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+	}
+