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README.md

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-# TNScope_and_Stralka
+# somatic_SNVs_calling_VIP
 

bcftools_concat.wdl

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+task bcftools {
+  
+  File ref_dir
+  String fasta
+  File vcf_indels
+  File vcf_snvs
+  String sample_id
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    
+    bcftools concat -a ${vcf_indels} ${vcf_snvs} -Oz -o ${sample_id}_stralka.vcf.gz
+    bcftools index -t ${sample_id}_stralka.vcf.gz
+
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File concat_vcf = "${sample_id}_stralka.vcf.gz"
+    File concat_vcf_index = "${sample_id}_stralka.vcf.gz.tbi"
+  }
+}

defaults

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+    {
+        "Seq_platform":"Illumina",
+        "ref_fasta":"GRCh38.d1.vd1.fa",
+        "ref_fasta_dir":"oss://hcc1395/reference_genome/GRCh38.d1.vd1/",
+        "docker_fastp":"registry-vpc.cn-shanghai.aliyuncs.com/easygene/fastp:v0.20.1_cv1",
+		"docker_sentieon":"registry-vpc.cn-shanghai.aliyuncs.com/hcc1395_aliyun/sentieon-genomics:v202112.05",
+        "docker_qualimap":"registry.cn-shanghai.aliyuncs.com/hcc1395_aliyun/qualimap:2.0.0",
+        "docker_manta":"registry.cn-shanghai.aliyuncs.com/hcc1395_aliyun/manta:v1.6.0",
+        "docker_strelka":"registry.cn-shanghai.aliyuncs.com/hcc1395_aliyun/strelka:v2.9.10",
+        "SENTIEON_LICENSE":"172.25.2.5:8990",
+        "cluster_config":"OnDemand ecs.c6.xlarge img-ubuntu-vpc",
+        "disk_size":"500",
+        "fastqc":false,
+        "annot_gff":"oss://hcc1395/reference_genome/gencode.v36.annotation.gff",
+        "dbsnp_dir":"oss://hcc1395/reference_genome/GRCh38.d1.vd1/",
+        "dbmills_dir":"oss://hcc1395/reference_genome/GRCh38.d1.vd1/",
+        "dbsnp":"dbsnp_146.hg38.vcf",
+        "db_mills":"Mills_and_1000G_gold_standard.indels.hg38.vcf",
+        "bamqc":true,
+        "germline_resource":"oss://hcc1395/reference_genome/gnomAD/af-only-gnomad.v3.1.1.vcf.gz",
+        "germline_resource_tbi":"oss://hcc1395/reference_genome/gnomAD/af-only-gnomad.v3.1.1.vcf.gz.tbi",
+        "annovar_database":"oss://hcc1395/reference_genome/annovar/",
+        "docker_bcftools":"registry.cn-shanghai.aliyuncs.com/hcc1395_aliyun/delly:1.1.6",
+        "docker_annovar":"registry.cn-shanghai.aliyuncs.com/hcc1395_aliyun/annovar:v20191024",
+        "Annovar":true,
+		"regions":"",
+        "baseline":"oss://hcc1395/reference_genome/MSIsensor/hg38_reference.list_baseline",
+        "docker_MSIsensor":"registry.cn-shanghai.aliyuncs.com/hcc1395_aliyun/msisensor-pro:1.2.0",
+        "hg38_CDS":"oss://hcc1395/reference_genome/TMB_dir/genecode.v36.CDS_merged.bed",
+        "docker_tmb":"registry.cn-shanghai.aliyuncs.com/hcc1395_aliyun/tmb:1.1.0",
+        "AF_filter":true
+
+    }

inputs

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+{
+"{{ project_name }}.sample_id": "{{ sample_id }}",
+"{{ project_name }}.normal_deduped_bam": "{{ normal_deduped_bam }}",
+"{{ project_name }}.normal_deduped_bam_bai": "{{ normal_deduped_bam_bai }}",
+"{{ project_name }}.tumor_deduped_bam": "{{ tumor_deduped_bam }}",
+"{{ project_name }}.tumor_deduped_bam_bai": "{{ tumor_deduped_bam_bai }}",
+"{{ project_name }}.Seq_platform": "{{ Seq_platform }}",
+"{{ project_name }}.ref_fasta": "{{ ref_fasta }}",
+"{{ project_name }}.ref_fasta_dir": "{{ ref_fasta_dir }}",
+"{{ project_name }}.fastqc": {{ fastqc | tojson }},
+"{{ project_name }}.cluster_config": "{{cluster_config }}",
+"{{ project_name }}.disk_size": "{{ disk_size }}",
+"{{ project_name }}.docker_fastp": "{{ docker_fastp }}",
+"{{ project_name }}.docker_sentieon": "{{ docker_sentieon }}",
+"{{ project_name }}.SENTIEON_LICENSE": "{{ SENTIEON_LICENSE }}",
+"{{ project_name }}.docker_qualimap": "{{ docker_qualimap }}",
+"{{ project_name }}.annot_gff": "{{ annot_gff }}",
+"{{ project_name }}.dbsnp_dir": "{{ dbsnp_dir }}",
+"{{ project_name }}.dbmills_dir": "{{ dbmills_dir }}",
+"{{ project_name }}.dbsnp": "{{ dbsnp }}",
+"{{ project_name }}.db_mills": "{{ db_mills }}",
+"{{ project_name }}.bamqc": {{ bamqc | tojson }},
+"{{ project_name }}.germline_resource": "{{ germline_resource }}",
+"{{ project_name }}.germline_resource_tbi": "{{ germline_resource_tbi }}",
+"{{ project_name }}.docker_manta": "{{ docker_manta }}",
+"{{ project_name }}.docker_strelka": "{{ docker_strelka }}",
+"{{ project_name }}.annovar_database": "{{ annovar_database}}",
+"{{ project_name }}.docker_bcftools":"{{docker_bcftools}}",
+"{{ project_name }}.docker_annovar":"{{docker_annovar}}",
+"{{ project_name }}.Annovar":{{ Annovar | tojson }},
+"{{ project_name }}.AF_filter":{{ AF_filter | tojson }},
+"{{ project_name }}.regions":"{{regions}}",
+"{{ project_name }}.baseline":"{{baseline}}",
+"{{ project_name }}.hg38_CDS":"{{hg38_CDS}}",
+"{{ project_name }}.docker_tmb": "{{ docker_tmb }}",
+"{{ project_name }}.docker_MSIsensor": "{{ docker_MSIsensor }}"
+
+}

workflow.wdl

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+import "./tasks/BQSR.wdl" as Sentieon_BQSR
+import "./tasks/TNseq.wdl" as TNseq
+import "./tasks/TNscope.wdl" as TNscope
+import "./tasks/manta.wdl" as manta_calling
+import "./tasks/strelka.wdl" as strelka_calling
+import "./tasks/bcftools.wdl" as bcftools
+import "./tasks/bcftools_concat.wdl" as bcftools_concat
+import "./tasks/annovar.wdl" as annovar
+import "./tasks/Haplotyper.wdl" as Haplotyper
+import "./tasks/MSIsensor.wdl" as MSIsensor
+import "./tasks/tmb.wdl" as tmb
+
+#VIP客户（只用TNseq进行call）
+workflow {{ project_name }} {
+	#sample info
+    File? normal_deduped_bam
+    File? normal_deduped_bam_bai
+	File? tumor_deduped_bam
+	File? tumor_deduped_bam_bai
+    String sample_id
+	String Seq_platform
+	#reference fasta
+	String ref_fasta
+	File ref_fasta_dir
+	File annot_gff
+    File dbsnp_dir
+    File dbmills_dir
+    String dbsnp
+    String db_mills
+	File germline_resource
+	File germline_resource_tbi
+	File annovar_database
+    File? regions
+    File baseline
+    File hg38_CDS
+
+
+
+	#docker
+    String docker_fastp
+	String docker_sentieon
+	String SENTIEON_LICENSE
+	String docker_qualimap
+	String docker_manta
+	String docker_strelka
+	String docker_bcftools
+	String docker_annovar
+    String docker_tmb
+    String docker_MSIsensor
+
+	#config
+    String cluster_config
+    String disk_size
+	Boolean? fastqc
+	Boolean bamqc
+	Boolean Annovar
+    Boolean AF_filter
+
+
+# call MSIsensor.MSIsensor as MSIsensor {
+#     input:
+#     sample=sample_id,
+#     fasta=ref_fasta,
+#     ref_dir=ref_fasta_dir,
+#     normal_bam=normal_deduped_bam,
+#     normal_bam_index=normal_deduped_bam_bai,
+#     tumor_bam=tumor_deduped_bam,
+#     tumor_bam_index=tumor_deduped_bam_bai,
+#     baseline=baseline,
+#     docker=docker_MSIsensor,
+#     cluster_config=cluster_config,
+#     disk_size=disk_size
+#   }
+
+
+# call Haplotyper.Haplotyper as Haplotyper {
+#       input:
+#         SENTIEON_LICENSE=SENTIEON_LICENSE,
+#         sample=sample_id + '.N',
+#         fasta=ref_fasta,
+#         ref_dir=ref_fasta_dir,
+#         recaled_bam=normal_deduped_bam,
+#         recaled_bam_index=normal_deduped_bam_bai,
+#         dbsnp=dbsnp,
+#         dbsnp_dir=dbsnp_dir,
+#         regions=regions,
+#         docker=docker_sentieon,
+#         disk_size=disk_size,
+#         cluster_config=cluster_config
+#     }
+
+# call bcftools.bcftools as Haplotyper_bcftools {
+#       input:
+#         vcf=Haplotyper.vcf,
+#         fasta=ref_fasta,
+#         ref_dir=ref_fasta_dir,
+#         docker=docker_bcftools,
+#         cluster_config=cluster_config,
+#         disk_size=disk_size
+#     }
+
+call TNseq.sentieon_TNseq as sentieon_TNseq{
+	input:
+		sample_id = sample_id,
+		tumor_bam = tumor_deduped_bam,
+		tumor_bam_bai = tumor_deduped_bam_bai,
+		normal_bam = normal_deduped_bam,
+		normal_bam_bai = normal_deduped_bam_bai,
+		tumor_name = sample_id+'_T',
+		normal_name = sample_id+'_N',
+
+		ref_dir = ref_fasta_dir,
+		ref_fasta = ref_fasta,
+		germline_resource = germline_resource,
+		germline_resource_tbi = germline_resource_tbi,
+
+		docker = docker_sentieon,
+		cluster_config = cluster_config,
+		disk_size = disk_size,
+		SENTIEON_LICENSE = SENTIEON_LICENSE
+}
+
+
+
+call bcftools.bcftools as TNseq_bcftools {
+	input:
+	vcf=sentieon_TNseq.vcf,
+	fasta=ref_fasta,
+	ref_dir=ref_fasta_dir,
+	docker=docker_bcftools,
+	cluster_config=cluster_config,
+	disk_size=disk_size
+}
+
+
+
+if (Annovar){
+	call annovar.ANNOVAR as TNseq_ANNOVAR {
+		input:
+			vcf=TNseq_bcftools.norm_vcf,
+			annovar_database=annovar_database,
+			docker=docker_annovar,
+			cluster_config=cluster_config,
+			disk_size=disk_size
+  }
+
+    # call tmb.TMB as TMB{
+    #     input:
+    #         sample=sample_id,
+    #         hg38_CDS=hg38_CDS,
+    #         regions=regions,
+    #         snpindel_txt=TNseq_ANNOVAR.multianno_txt,
+    #         docker=docker_tmb,
+    #         cluster_config=cluster_config,
+    #         disk_size=disk_size,
+    #         AF_filter=AF_filter
+    # }
+
+    # call annovar.ANNOVAR as Haplotyper_ANNOVAR {
+	# 	input:
+	# 		vcf=Haplotyper_bcftools.norm_vcf,
+	# 		annovar_database=annovar_database,
+	# 		docker=docker_annovar,
+	# 		cluster_config=cluster_config,
+	# 		disk_size=disk_size
+  	# }
+
+
+
+}
+}