first commit

defaults

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+{
+    "fasta": "GRCh38.d1.vd1.fa",
+    "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
+    "dbsnp": "dbsnp_146.hg38.vcf",
+    "dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
+    "SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
+    "SENTIEON_LICENSE": "192.168.0.55:8990",
+    "dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
+    "db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
+    "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2019.11.28",
+    "annovar_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/annovar:v2018.04",
+    "maftools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/r-base:4.0.2",
+    "bcftools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
+    "database": "oss://pgx-reference-data/annovar_hg38/",
+    "regions": "oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/SureSelect_Human_All_Exon_V6_r2.bed",
+    "set_pon": "true",
+    "cosmic_vcf": "CosmicCodingMuts.hg38.v91.vcf",
+    "cosmic_dir": "oss://pgx-reference-data/reference/cosmic/",
+    "disk_size": "200",
+    "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
+    "set_annovar": "true",
+    "set_vcf2maf": "true",
+    "germline": "false"
+}

inputs

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+{
+  "{{ project_name }}.sample_id": "{{ sample_id }}",
+  "{{ project_name }}.normal_recaled_bam": "{{ normal_recaled_bam }}",
+  "{{ project_name }}.normal_recaled_bam_index": "{{ normal_recaled_bam_index }}",
+  "{{ project_name }}.fasta": "{{ fasta }}",
+  "{{ project_name }}.ref_dir": "{{ ref_dir }}",
+  "{{ project_name }}.dbsnp": "{{ dbsnp }}",
+  "{{ project_name }}.dbsnp_dir": "{{ dbsnp_dir }}",
+  "{{ project_name }}.SENTIEON_INSTALL_DIR": "{{ SENTIEON_INSTALL_DIR }}",
+  "{{ project_name }}.SENTIEON_LICENSE": "{{ SENTIEON_LICENSE }}",
+  "{{ project_name }}.dbmills_dir": "{{ dbmills_dir }}",
+  "{{ project_name }}.db_mills": "{{ db_mills }}",
+  "{{ project_name }}.sentieon_docker": "{{ sentieon_docker }}",
+  "{{ project_name }}.annovar_docker": "{{ annovar_docker }}",
+  "{{ project_name }}.maftools_docker": "{{ maftools_docker }}",
+  "{{ project_name }}.database": "{{ database }}",
+  "{{ project_name }}.regions": "{{ regions }}",
+  "{{ project_name }}.set_pon": {{ set_pon }},
+  "{{ project_name }}.cosmic_vcf": "{{ cosmic_vcf }}",
+  "{{ project_name }}.cosmic_dir": "{{ cosmic_dir }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.cluster_config": "{{ cluster_config }}",
+  "{{ project_name }}.set_annovar": {{ set_annovar }},
+  "{{ project_name }}.set_vcf2maf": {{ set_vcf2maf }},
+  "{{ project_name }}.germline": {{ germline }}
+}

tasks/PON.wdl

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+task PON {
+
+	String SENTIEON_INSTALL_DIR
+	String SENTIEON_LICENSE
+	String sample
+
+	File ref_dir
+	String fasta
+	File cosmic_dir
+	String cosmic_vcf
+	File dbsnp_dir
+	String dbsnp
+
+	File normal_recaled_bam
+	File normal_recaled_bam_index
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+		set -o pipefail
+		set -e
+		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+		nt=$(nproc)
+		mkdir -p /cromwell_root/tmp/cosmic/
+		cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/cosmic/
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/cosmic/${cosmic_vcf}
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} -i ${normal_recaled_bam} --algo TNhaplotyper --detect_pon --cosmic /cromwell_root/tmp/cosmic/${cosmic_vcf} --dbsnp ${dbsnp_dir}/${dbsnp} ${sample}_pon.vcf
+	>>>
+	
+	runtime {
+		docker: docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"	
+	}
+
+	output {
+		File pon_vcf = "${sample}_pon.vcf"
+	}
+}

workflow.wdl

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+import "./tasks/PON.wdl" as PON
+
+	String SENTIEON_INSTALL_DIR
+	String SENTIEON_LICENSE
+	String sample_id
+
+	File ref_dir
+	String fasta
+	File cosmic_dir
+	String cosmic_vcf
+	File dbsnp_dir
+	String dbsnp
+
+	File normal_recaled_bam
+	File normal_recaled_bam_index
+	String sentieon_docker
+	String cluster_config
+	String disk_size
+	
+workflow {{ project_name }} {
+	call PON.PON as PON {
+		input:
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		SENTIEON_LICENSE=SENTIEON_LICENSE,
+		sample=sample_id,
+		fasta=fasta,
+		ref_dir=ref_dir,
+		normal_recaled_bam=BQSR.recaled_bam,
+		normal_recaled_bam_index=BQSR.recaled_bam_index,
+		cosmic_vcf=cosmic_vcf,
+		cosmic_dir=cosmic_dir,
+		dbsnp=dbsnp,
+		dbsnp_dir=dbsnp_dir,
+		docker=sentieon_docker,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+}