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README.md

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-# Fastq2Bam
+# wgs_somatic_pipeline_v1
 
-将fastq转换成bam文件，并用qualimap对BAM文件进行质控

defaults

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+    {
+        "normal_in1":"",
+        "normal_in2":"",
+        "tumor_in1":"",
+        "tumor_in2":"",
+        "sample_id":"",
+        "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"
+
+
+    }

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 | 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 }}"
+}

workflow.wdl

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+#Only for BamQC
+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 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
+	Boolean bamqc
+
+
+if (normal_in1 != ""){
+	
+		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
+
+		}
+
+		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
+			}
+
+
+	}
+
+if (tumor_in1 != ""){
+
+		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
+
+		}
+
+		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
+			}
+
+
+
+	}
+
+
+}