F

inputs

@@ -0,0 +1,12 @@
+{
+  "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
+  "{{ project_name }}.ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
+  "{{ project_name }}.fastq_1": "{{ read1 }}",
+  "{{ project_name }}.cluster_config": "{{ cluster if cluster != '' else 'OnDemand ecs.sn2ne.2xlarge img-ubuntu-vpc' }}",
+  "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
+  "{{ project_name }}.sample": "{{ sample_name }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}", 
+  "{{ project_name }}.regions": "{{ regions }}",
+  "{{ project_name }}.fastq_2": "{{ read2 }}"
+}
+

tasks/Call_meth.wdl

@@ -0,0 +1,35 @@
+task Haplotyper {
+	
+    File ref_dir
+    
+	File Dedup_bam
+	String sample
+	String docker
+	String cluster_config
+	String disk_size
+
+command <<<
+		set -o pipefail
+		set -e
+		bismark_methylation_extractor -p --no_overlap --comprehensive --report --bedGraph --genome_folder ${ref_dir} ${Dedup_bam}
+	>>>
+	
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File bedGraph = "${sample}_R1_val_1_bismark_bt2_pe.bedGraph.gz"
+		File cov = "${sample}_R1_val_1_bismark_bt2_pe.bismark.cov.gz"
+		File M-bias = "${sample}_R1_val_1_bismark_bt2_pe.M-bias.txt"
+		File splitting_report = "${sample}_R1_val_1_bismark_bt2_pe_splitting_report.txt"
+		File CHG_context = "CHG_context_{sample}_R1_val_1_bismark_bt2_pe.txt"
+		File CHH_context = "CHH_context_{sample}_R1_val_1_bismark_bt2_pe.txt"
+		File CpG_context = "CpG_context_{sample}_R1_val_1_bismark_bt2_pe.txt"
+	}
+}
+
+

tasks/Dedup.wdl

@@ -0,0 +1,34 @@
+task Dedup {
+
+	String sample
+
+	File unsorted_bam
+
+	String docker
+	String cluster_config
+	String disk_size
+
+
+	command <<<
+		set -o pipefail
+		set -e
+		nt=$(nproc)
+		deduplicate_bismark -p --bam ${unsorted_bam}	
+	>>>
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File Dedup_bam = "${sample}_R1_val_1_bismark_bt2_pe.deduplicated.bam"
+	}
+}
+
+
+
+
+
+

tasks/Mapping.wdl

@@ -0,0 +1,29 @@
+task mapping {
+
+    File ref_dir
+	File trim_read1
+	File trim_read2
+
+	String sample
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e	
+		nt=$(nproc)
+		bismark --bowtie2 -p ${nt} --bam  ${ref_dir} -1 ${trim_read1} -2 ${trim_read2}
+
+	>>>
+
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File unsorted_bam = "${sample}_R1_val_1_bismark_bt2_pe.bam"
+	}
+}

tasks/Trim.wdl

@@ -0,0 +1,34 @@
+task TNseq {
+	
+	File fastq_1
+	File fastq_2
+    
+	String docker
+	String cluster_config
+	String sample
+	String disk_size
+
+	
+	
+	command <<<
+		set -o pipefail
+		set -e
+		trim_galore --clip_R1 4 --clip_R2 4 --three_prime_clip_R1 4 --three_prime_clip_R2 4 --paired ${fastq1} ${fastq2}
+		
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File trim_read1 = "${sample}_R1_val_1.fq"
+		File trim_read2 = "${sample}_R2_val_2.fq"
+	}
+
+}
+
+

workflow.wdl

@@ -0,0 +1,60 @@
+import "./tasks/Trim.wdl" as Trim
+import "./tasks/Mapping.wdl" as Meapping
+import "./tasks/Dedup.wdl" as Dedup
+import "./tasks/Call_meth.wdl" as Call_meth
+
+
+workflow {{ project_name }} {
+
+	File fastq_1
+	File fastq_2
+
+	String sample
+	String docker
+	
+
+	String disk_size
+	String cluster_config
+
+    File ref_dir
+
+
+
+	call BQSR.BQSR as BQSR {
+		input:
+		sample=sample,
+		ref_dir=ref_dir,
+		fastq_1=fastq_1,
+		fastq_2=fastq_2,
+		docker=docker,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+	call mapping.mapping as mapping {
+		input: 
+		sample=sample,
+		ref_dir=ref_dir,
+		trim_read1=trim_read1,
+		trim_read2=trim_read2,
+		docker=docker,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+	call Dedup.Dedup as Dedup {
+		input:
+		unsorted_bam=mapping_R1_val_1_bismark_bt2_pe.bam,
+		sample=sample,
+		docker=docker,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+	call Haplotyper.Haplotyper as Haplotyper {
+		input:
+		ref_dir=ref_dir,
+		Dedup_bam=Dedup_R1_val_1_bismark_bt2_pe.deduplicated.bam,
+		sample=sample,
+		docker=docker,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+}