first commit

inputs

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+{
+  "{{ project_name }}.sample": "{{ sample }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
+  "{{ project_name }}.annovar_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/annovar:v2018.04",
+  "{{ project_name }}.database": "oss://chinese-quartet/quartet-storage-data/reference_data/annovar_hg38/",
+  "{{ project_name }}.hardfiltration_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/gatk:v2019.01",
+  "{{ project_name }}.vcf_file": "{{ vcf }}",
+  "{{ project_name }}.vcf_index": "{{ vcf_index }}"
+}

tasks/Annovar.wdl

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+task Annovar {
+
+	File vcf_file
+	File database
+	String sample
+	String docker
+	String cluster_config
+	String disk_size
+
+
+	command <<<
+		nt=$(nproc)
+		/installations/annovar/table_annovar.pl ${vcf_file} ${database} -buildver hg38 -out ${sample} -remove -protocol refGene,ensGene,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad30_genome,1000g2015aug_all,clinvar_20190305,gnomad211_genome -operation g,g,f,f,f,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File avinput = "${sample}.avinput"
+		File multianno_txt = "${sample}.hg38_multianno.txt"
+		File multianno_vcf = "${sample}.hg38_multianno.vcf"
+
+	}
+}

tasks/Hardfiltration.wdl

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+task Hardfiltration {
+	
+	File vcf_file
+	File vcf_index
+	String sample
+	String docker
+	String disk_size
+	String cluster_config
+	
+
+	command <<<
+		set -o pipefail
+		set -e
+		java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx32G -jar /gatk/gatk-package-4.1.0.0-local.jar VariantFiltration -V ${vcf_file} -O ${sample}_hc_filtered.vcf --filter-expression "QD<2.0" --filter-name "LowQD" --filter-expression "MQ<40.0" --filter-name "LowMQ" --filter-expression "FS>60.0" --filter-name "FisherStrandBias" --filter-expression "HaplotypeScore>13.0" --filter-name "HighHapScore" --filter-expression "MQRankSum<-12.5" --filter-name "LowMQRankSum" --filter-expression "ReadPosRankSum<-8.0" --filter-name "LowReadPosRankSum" --cluster-size 3 --cluster-window-size 100 --filter-expression "MQ0 >= 4 && ((MQ0/(1.0*DP))>0.1)" --filter-name "HARD_TO_VALIDATE" --filter-expression "DP < 5" --filter-name "LowCoverage" --filter-expression "QUAL < 30.0" --filter-name "VeryLowQual" --filter-expression "QUAL > 30.0 && QUAL < 50.0" --filter-name "LowQual" 
+		cat ${sample}_hc_filtered.vcf |grep "#" > ${sample}_hc_filtered.vcf.header.tmp
+		cat ${sample}_hc_filtered.vcf |grep PASS > ${sample}_hc_filtered.vcf.tmp
+		cat ${sample}_hc_filtered.vcf.header.tmp ${sample}_hc_filtered.vcf.tmp > ${sample}_hc_PASS.vcf
+		>>>
+
+		runtime {
+		docker:docker
+    	cluster:cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File raw_vcf = "${sample}_hc_filtered.vcf"
+		File pass_vcf = "${sample}_hc_PASS.vcf"
+	}
+}
+
+
+
+
+

workflow.wdl

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+import "./tasks/Hardfiltration.wdl" as Hardfiltration
+import "./tasks/Annovar.wdl" as Annovar
+
+workflow {{ project_name }} {
+
+	File vcf_file
+	File database
+	File vcf_index
+	String sample
+	String annovar_docker
+	String hardfiltration_docker
+	String cluster_config
+	String disk_size
+
+	call Hardfiltration.Hardfiltration  as Hardfiltration {
+		input:
+		docker=hardfiltration_docker,
+		sample=sample,
+		vcf_index=vcf_index,
+		disk_size=disk_size,
+		vcf_file=vcf_file,
+		cluster_config=cluster_config
+	}
+	call Annovar.Annovar as Annovar {
+		input:
+		docker=annovar_docker,
+		database=database,
+		vcf_file=Hardfiltration.pass_vcf,
+		sample=sample,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+	
+}