first commit

defaults

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+{
+    "picard_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/picard:2.20.2",
+    "fasta": "hg19_nochr.fa",
+    "ref_dir": "oss://pgx-reference-data/hg19/",
+    "chain": "hg38ToHg19.over.chain.gz",
+    "chain_dir": "oss://pgx-reference-data/reference/cosmic/",
+    "disk_size": "200",
+    "cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc"
+}

inputs

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+{
+
+  "{{ project_name }}.picard_docker": "{{ picard_docker }}",
+  "{{ project_name }}.fasta": "{{ fasta }}",
+  "{{ project_name }}.ref_dir": "{{ ref_dir }}",
+  "{{ project_name }}.chain": "{{ chain }}",
+  "{{ project_name }}.chain_dir": "{{ chain_dir }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.cluster_config": "{{ cluster_config }}"
+}

tasks/picard.wdl

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+task annovar {
+
+	File vcf
+	String sample
+	String docker
+	String cluster_config
+	String disk_size
+
+
+	command <<<
+		set -o pipefail
+		set -e
+		nt=$(nproc)
+		java -jar /usr/bin/picard/picard.jar LiftoverVcf I = ${vcf} O = ${sample}_picard.vcf CHAIN = ${chain_dir}/${chain} R = ${ref_dir}/${fasta}
+	>>>
+	
+	runtime {
+		docker: docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File picard_vcf = "${sample}_picard.vcf"
+	}
+}

workflow.wdl

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+import "./tasks/PON.wdl" as PON
+import "./tasks/bcftools.wdl" as bcftools
+import "./tasks/TNseq.wdl" as TNseq
+import "./tasks/TNscope.wdl" as TNscope
+import "./tasks/annovar.wdl" as annovar
+import "./tasks/vcf2maf.wdl" as vcf2maf
+
+
+workflow {{ project_name }} {
+
+	File normal_recaled_bam
+	File normal_recaled_bam_index
+	File corealigner_bam
+	File corealigner_bam_index
+
+	String SENTIEON_INSTALL_DIR
+	String SENTIEON_LICENSE
+	String sample
+	String sentieon_docker
+	String annovar_docker
+	String vcf2maf_r_docker
+	String bcftools_docker
+	
+	File ref_dir
+	String fasta
+	File dbmills_dir
+	String db_mills
+	File dbsnp_dir
+	String dbsnp
+	File regions
+	File database
+	String disk_size
+	String cluster_config
+
+	Boolean PONmode
+	File? cosmic_dir
+	String? cosmic_vcf
+
+	Boolean set_annovar
+	Boolean set_vcf2maf
+
+
+	if (PONmode) {
+		call PON.PON as PON {
+			input:
+			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+			SENTIEON_LICENSE=SENTIEON_LICENSE,
+			sample=sample,
+			fasta=fasta,
+			ref_dir=ref_dir,
+			normal_recaled_bam=normal_recaled_bam,
+			normal_recaled_bam_index=normal_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
+		}
+		call bcftools.bcftools as bcftools {
+			input:
+			pon_vcf=PON.pon_vcf,
+			docker=bcftools_docker,
+			disk_size=disk_size,
+			cluster_config=cluster_config
+		}
+	}
+
+
+	call TNseq.TNseq as TNseq {
+		input:
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		SENTIEON_LICENSE=SENTIEON_LICENSE,
+		PONmode=PONmode,
+		fasta=fasta,
+		ref_dir=ref_dir,
+		corealigner_bam=corealigner_bam,
+		corealigner_bam_index=corealigner_bam_index,
+		dbsnp=dbsnp,
+		dbsnp_dir=dbsnp_dir,
+		tumor_name=sample + "tumor",
+		normal_name=sample + "normal",
+		cosmic_vcf=cosmic_vcf,
+		cosmic_dir=cosmic_dir,
+		panel_of_normal_vcf = bcftools.panel_of_normal_vcf,
+		docker=sentieon_docker,
+		sample=sample,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+    
+	call TNscope.TNscope as TNscope {
+		input:
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		SENTIEON_LICENSE=SENTIEON_LICENSE,
+		PONmode=PONmode,
+		fasta=fasta,
+		ref_dir=ref_dir,
+		corealigner_bam=corealigner_bam,
+		corealigner_bam_index=corealigner_bam_index,
+		dbsnp=dbsnp,
+		dbsnp_dir=dbsnp_dir,
+		tumor_name=sample + "tumor",
+		normal_name=sample + "normal",
+		cosmic_vcf=cosmic_vcf,
+		cosmic_dir=cosmic_dir,
+		panel_of_normal_vcf = bcftools.panel_of_normal_vcf,
+		docker=sentieon_docker,
+		sample=sample,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+
+	if (set_annovar){
+		call annovar.annovar as annovar {
+			input:
+			docker=annovar_docker,
+			database=database,
+			tnscope_vcf_file=TNscope.TNscope_vcf,
+			tnseq_vcf_file=TNseq.TNseq_vcf,
+			sample=sample,
+			cluster_config=cluster_config,
+			disk_size=disk_size
+		}
+	}
+	
+	if (set_vcf2maf){
+		call vcf2maf.vcf2maf as vcf2maf {
+			input:
+			docker=vcf2maf_r_docker,
+			multianno_tnscope_txt=annovar.multianno_tnscope_txt,
+			multianno_tnseq_txt=annovar.multianno_tnseq_txt,
+			sample=sample,
+			cluster_config=cluster_config,
+			disk_size=disk_size
+		}
+	}
+}