上传文件至 ''

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.large 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
+
+
+    }

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 }}
+
+}

workflow_total_pipeline.wdl

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+#import "./tasks/fastp.wdl" as fastp
+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
+
+
+
+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
+
+	#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
+
+	#config
+    String cluster_config
+    String disk_size
+	Boolean? fastqc
+	Boolean bamqc
+	Boolean Annovar
+
+
+if (normal_in1 != ""){
+
+		call Sentieon_BQSR.Sentieon_BQSR as Sentieon_BQSR_normal{
+			input:
+				ref_dir=ref_fasta_dir,
+				dbsnp_dir=dbsnp_dir,
+				dbmills_dir = dbmills_dir,
+				sample_id=sample_id+'_N',
+				ref_fasta=ref_fasta,
+				dbsnp=dbsnp,
+				db_mills=db_mills,
+				deduped_bam=normal_deduped_bam,
+				deduped_bam_index=normal_deduped_bam_bai,
+				docker=docker_sentieon,
+				cluster_config=cluster_config,
+				disk_size=disk_size,
+				SENTIEON_LICENSE=SENTIEON_LICENSE
+		}
+
+	}
+
+if (tumor_in1 != ""){
+
+		call Sentieon_BQSR.Sentieon_BQSR as Sentieon_BQSR_tumor{
+			input:
+				ref_dir=ref_fasta_dir,
+				dbsnp_dir=dbsnp_dir,
+				dbmills_dir = dbmills_dir,
+				sample_id=sample_id+'_T',
+				ref_fasta=ref_fasta,
+				dbsnp=dbsnp,
+				db_mills=db_mills,
+				deduped_bam=tumor_deduped_bam,
+				deduped_bam_index=tumor_deduped_bam_bai,
+				docker=docker_sentieon,
+				cluster_config=cluster_config,
+				disk_size=disk_size,
+				SENTIEON_LICENSE=SENTIEON_LICENSE
+		}
+
+	}
+
+call TNseq.sentieon_TNseq as sentieon_TNseq{
+	input:
+		sample_id = sample_id,
+		tumor_bam = Sentieon_BQSR_tumor.recaled_bam,
+		tumor_bam_bai = Sentieon_BQSR_tumor.recaled_bam_index,
+		normal_bam = Sentieon_BQSR_normal.recaled_bam,
+		normal_bam_bai = Sentieon_BQSR_normal.recaled_bam_index,
+		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=bcftools_docker,
+	cluster_config=cluster_config,
+	disk_size=disk_size
+}
+
+call TNscope.sentieon_TNscope as sentieon_TNscope{
+	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',
+		tumor_recall_data = Sentieon_BQSR_tumor.recal_table,
+		normal_recall_data = Sentieon_BQSR_normal.recal_table,
+
+		ref_dir = ref_fasta_dir,
+		ref_fasta = ref_fasta,
+		dbsnp_dir = dbsnp_dir,
+		dbsnp = dbsnp,
+		# excute env
+		docker = docker_sentieon,
+		cluster_config = cluster_config,
+		disk_size = disk_size,
+		SENTIEON_LICENSE = SENTIEON_LICENSE
+}
+
+call bcftools.bcftools as TNscope_bcftools {
+	input:
+	vcf=sentieon_TNscope.vcf,
+	fasta=ref_fasta,
+	ref_dir=ref_fasta_dir,
+	docker=bcftools_docker,
+	cluster_config=cluster_config,
+	disk_size=disk_size
+}
+
+call manta_calling.manta_calling as manta_calling{
+	input:
+		tumor_bam = Sentieon_BQSR_tumor.recaled_bam,
+		tumor_bam_bai = Sentieon_BQSR_tumor.recaled_bam_index,
+		normal_bam = Sentieon_BQSR_normal.recaled_bam,
+		normal_bam_bai = Sentieon_BQSR_normal.recaled_bam_index,
+		ref_fasta = ref_fasta,
+		ref_dir = ref_fasta_dir,
+		sample_id = sample_id,
+		docker = docker_manta,
+		cluster_config = cluster_config,
+		disk_size = disk_size
+
+}
+
+call strelka_calling.strelka_calling as strelka_calling{
+	input:
+		tumor_bam = Sentieon_BQSR_tumor.recaled_bam,
+		tumor_bam_bai = Sentieon_BQSR_tumor.recaled_bam_index,
+		normal_bam = Sentieon_BQSR_normal.recaled_bam,
+		normal_bam_bai = Sentieon_BQSR_normal.recaled_bam_index,
+		ref_fasta = ref_fasta,
+		ref_dir = ref_fasta_dir,
+		sample_id = sample_id,
+		manta_indel_vcf = manta_calling.manta_indel_vcf,
+		manta_indel_vcf_index = manta_calling.manta_indel_vcf_index,
+		
+		docker=docker_strelka,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+}
+
+call bcftools_concat.bcftools as bcftools_concat{
+        input:
+            ref_dir=ref_dir,
+            fasta=ref_fasta,
+            vcf_indels=strelka_calling.indel_vcf,
+            vcf_snvs=strelka_calling.snv_vcf,
+            sample_id=sample_id,
+            docker=docker_bcftools,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+
+    }
+
+call bcftools.bcftools as strelka_bcftools {
+	input:
+	vcf=bcftools_concat.vcf,
+	fasta=ref_fasta,
+	ref_dir=ref_fasta_dir,
+	docker=bcftools_docker,
+	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 annovar.ANNOVAR as TNscope_ANNOVAR {
+		input:
+			vcf=TNscope_bcftools.norm_vcf,
+			annovar_database=annovar_database,
+			docker=docker_annovar,
+			cluster_config=cluster_config,
+			disk_size=disk_size
+  }
+
+    call annovar.ANNOVAR as strelka_ANNOVAR {
+		input:
+			vcf=strelka_bcftools.norm_vcf,
+			annovar_database=annovar_database,
+			docker=docker_annovar,
+			cluster_config=cluster_config,
+			disk_size=disk_size
+  }
+}
+
+}