first commit

defaults

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+{
+  "SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
+  "fasta": "GRCh38.d1.vd1.fa",
+  "dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
+  "disk_size": "800",
+  "docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v202010.02",
+  "cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
+  "dbsnp": "dbsnp_146.hg38.vcf",
+  "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/"
+}

inputs

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+{
+  "{{ project_name }}.SENTIEON_INSTALL_DIR": "{{ SENTIEON_INSTALL_DIR }}",
+  "{{ project_name }}.fasta": "{{ fasta }}",
+  "{{ project_name }}.dbsnp_dir": "{{ dbsnp_dir }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.corealigner_bam": "{{ corealigner_bam }}",
+  "{{ project_name }}.dbmills_dir": "{{ dbmills_dir }}",
+  "{{ project_name }}.cluster_config": "{{ cluster_config }}",
+  "{{ project_name }}.SENTIEON_LICENSE": "{{ SENTIEON_LICENSE }}",
+  "{{ project_name }}.corealigner_bam_index": "{{ corealigner_bam_index }}",
+  "{{ project_name }}.SENTIEONdocker": "{{ SENTIEONdocker }}",
+  "{{ project_name }}.db_mills": "{{ db_mills }}",
+  "{{ project_name }}.sample": "{{ sample }}",
+  "{{ project_name }}.dbsnp": "{{ dbsnp }}",
+  "{{ project_name }}.ref_dir": "{{ ref_dir }}"
+}

tasks/HC.wdl

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+task HC {
+	
+	
+    File ref_dir
+    File dbsnp_dir
+
+	String SENTIEON_INSTALL_DIR
+	String fasta
+	File bam
+	File bam_index
+	String dbsnp
+	String sample
+	String docker
+	String cluster_config
+	String disk_size
+
+command <<<
+		set -o pipefail
+		set -e
+		export SENTIEON_LICENSE=192.168.0.55:8990
+		nt=$(nproc)	
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${bam} --algo Haplotyper -d ${dbsnp_dir}/${dbsnp} ${sample}_hc.vcf
+	>>>
+	
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File vcf = "${sample}_hc.vcf"
+		File vcf_idx = "${sample}_hc.vcf.idx"
+	}
+}
+

workflow.wdl

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