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defaults

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+    {
+        "normal_in1":"",
+        "normal_in2":"",
+        "tumor_in1":"",
+        "tumor_in2":"",
+        "sample_id":"",
+        "Seq_platform":"Illumina",
+        "ref_fasta":"",
+        "ref_fasta_dir":"",
+        "docker_fastp":"registry-vpc.cn-shanghai.aliyuncs.com/easygene/fastp:v0.20.1_cv1",
+        "docker_sentieon":"registry.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":"",
+        "cluster_config":"OnDemand ecs.sn1ne.4xlarge 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",
+        "regions":"",
+        "interval_padding":"",
+        "bamqc":false,
+        "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"
+
+
+    }

inputs

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+{
+"{{ project_name }}.sample_id": "{{ sample_id }}",
+"{{ project_name }}.normal_in1":"{{ normal_in1 }}",
+"{{ project_name }}.normal_in2":"{{ normal_in2 }}",
+"{{ project_name }}.tumor_in1":"{{ tumor_in1 }}",
+"{{ project_name }}.tumor_in2":"{{ tumor_in2 }}",
+"{{ project_name }}.Seq_platform":"{{ Seq_platform }}",
+"{{ project_name }}.ref_fasta":"{{ ref_fasta }}",
+"{{ project_name }}.ref_fasta_dir":"{{ ref_fasta_dir }}",
+"{{ project_name }}.fastqc":"{{ fastqc }}",
+"{{ 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 }}.regions":"{{ regions }}",
+"{{ project_name }}.interval_padding":"{{ interval_padding }}",
+"{{ project_name }}.bamqc":"{{ bamqc }}",
+"{{ 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 }}"
+}

workflow.wdl

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+import "./tasks/fastp.wdl" as fastp
+import "./tasks/fastqTobam.wdl" as fastqTobam
+import "./tasks/qualimap.wdl" as qualimap
+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
+
+
+workflow {{ project_name }} {
+	#sample info
+    File? normal_in1
+    File? normal_in2
+	File? tumor_in1
+	File? tumor_in2
+    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? regions
+    Int? interval_padding
+	File germline_resource
+	File germline_resource_tbi
+
+	#docker
+    String docker_fastp
+	String docker_sentieon
+	String SENTIEON_LICENSE
+	String docker_qualimap
+	String docker_manta
+	String docker_strelka
+
+	#config
+    String cluster_config
+    String disk_size
+	Boolean fastqc=false
+	Boolean bamqc=false
+
+
+if (normal_in1 != ""){
+	
+	if (fastqc){
+		call fastp.fastp as fastp_normal{
+			input:
+				in1=normal_in1,
+				in2=normal_in2,
+				sample_id=sample_id+'_N'
+				docker=docker_fastp,
+				cluster_config=cluster_config,
+				disk_size=disk_size	
+	
+	} 
+
+	if (!fastqc){
+		call fastqTobam.SentieonFastqToBam as SentieonFastqToBam_normal{
+			input:
+				fastq1=normal_in1,
+				fastq2=normal_in2,
+				sample_id=sample_id+'_N',
+				Seq_platform=Seq_platform,
+				ref_fasta=ref_fasta,
+				ref_fasta_dir=ref_fasta_dir,
+				SENTIEON_LICENSE=SENTIEON_LICENSE,
+				docker=docker_sentieon,
+				cluster_config=cluster_config,
+				disk_size=disk_size
+
+		}
+
+		if (bamqc){
+			call qualimap.qualimap as qualimap_normal{
+				 input:
+				 sample_id=sample_id+'_N',
+				 bam_file=SentieonFastqToBam_normal.deduped_bam,
+				 bam_bai=SentieonFastqToBam_normal.deduped_bam_bai,
+				 annot_gff=annot_gff,
+				 docker=docker_qualimap,
+				 cluster_config=cluster_config,
+				 disk_size=disk_size
+			}
+
+
+		}
+
+		call Sentieon_BQSR.Sentieon_BQSR as Sentieon_BQSR_normal{
+			input:
+				ref_dir=ref_fasta_dir,
+				dbsnp_dir=dbsnp_dir,
+				dbmills_dirdbmills_dir,
+				sample_id=sample_id+'_N',
+				ref_fasta=ref_fasta,
+				dbsnp=dbsnp,
+				db_mills=db_mills,
+				deduped_bam=Sentieon_BQSR_normal.deduped_bam,
+				deduped_bam_index=Sentieon_BQSR_normal.deduped_bam_bai,
+				regions=regions,
+				interval_padding=interval_padding,
+				docker=docker_sentieon,
+				cluster_config=cluster_config,
+				disk_size=disk_size,
+				SENTIEON_LICENSE=SENTIEON_LICENSE
+		}
+
+	}
+	}
+
+}
+
+if (tumor_in1 != ""){
+	
+	if (fastqc){
+		call fastp.fastp as fastp_tumor{
+			input:
+				in1=tumor_in1,
+				in2=tumor_in2,
+				sample_id=sample_id+'_T'
+				docker=docker_fastp,
+				cluster_config=cluster_config,
+				disk_size=disk_size	
+	
+	} 
+
+	if (!fastqc){
+		call fastqTobam.SentieonFastqToBam as SentieonFastqToBam_tumor{
+			input:
+				fastq1=tumor_in1,
+				fastq2=tumor_in2,
+				sample_id=sample_id+'_T',
+				Seq_platform=Seq_platform,
+				ref_fasta=ref_fasta,
+				ref_fasta_dir=ref_fasta_dir,
+				SENTIEON_LICENSE=SENTIEON_LICENSE,
+				docker=docker_sentieon,
+				cluster_config=cluster_config,
+				disk_size=disk_size
+
+		}
+
+		if (bamqc){
+			call qualimap.qualimap as qualimap_tumor{
+				 input:
+				 sample_id=sample_id+'_T',
+				 bam_file=SentieonFastqToBam_tumor.deduped_bam,
+				 bam_bai=SentieonFastqToBam_tumor.deduped_bam_bai,
+				 annot_gff=annot_gff,
+				 docker=docker_qualimap,
+				 cluster_config=cluster_config,
+				 disk_size=disk_size
+			}
+
+
+		}
+
+		call Sentieon_BQSR.Sentieon_BQSR as Sentieon_BQSR_tumor{
+			input:
+				ref_dir=ref_fasta_dir,
+				dbsnp_dir=dbsnp_dir,
+				dbmills_dirdbmills_dir,
+				sample_id=sample_id+'_T',
+				ref_fasta=ref_fasta,
+				dbsnp=dbsnp,
+				db_mills=db_mills,
+				deduped_bam=Sentieon_BQSR_tumor.deduped_bam,
+				deduped_bam_index=Sentieon_BQSR_tumor.deduped_bam_bai,
+				regions=regions,
+				interval_padding=interval_padding,
+				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.normal_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 TNscope.sentieon_TNscope as sentieon_TNscope{
+	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.normal_bam_bai,
+		tumor_name = sample_id+'_T',
+		normal_name = sample_id+'_N',
+		tumor_recall_data = Sentieon_BQSR_normal.recaled_bam,
+		normal_recall_data = Sentieon_BQSR_normal.recaled_bam_index,
+
+		ref_dir = ref_fasta_dir,
+		ref_fasta = ref_fasta,
+		regions = regions,
+		interval_padding = interval_padding,
+		dbsnp_dir = dbsnp_dir,
+		dbsnp = dbsnp,
+		# excute env
+		docker = docker_sentieon,
+		cluster_config = cluster_config,
+		disk_size = disk_size,
+		SENTIEON_LICENSE = SENTIEON_LICENSE
+}
+
+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.normal_bam_bai,
+		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{
+		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.normal_bam_bai,
+		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
+}
+
+
+}