first commit

inputs

@@ -0,0 +1,16 @@
+{
+  "{{ project_name }}.SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
+  "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
+  "{{ project_name }}.normal_read2": "{{ normal_read2 }}",
+  "{{ project_name }}.tumor_read2": "{{ tumor_read2 }}",
+  "{{ project_name }}.DELLYdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/delly:v0.8.1",
+  "{{ project_name }}.disk_size": "500",
+  "{{ project_name }}.tumor_read1": "{{ tumor_read1 }}",
+  "{{ project_name }}.sample_name": "{{ sample_name }}",
+  "{{ project_name }}.SMALLcluster_config": "OnDemand bcs.a2.xlarge img-ubuntu-vpc",
+  "{{ project_name }}.BCFdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
+  "{{ project_name }}.BIGcluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
+  "{{ project_name }}.normal_read1": "{{ normal_read1 }}",
+  "{{ project_name }}.SENTIEONdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
+  "{{ project_name }}.ref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/"
+}

tasks/bcf2vcf.wdl

@@ -0,0 +1,49 @@
+task bcf2vcf {
+	
+	File ins_bcf
+	File ins_bcf_index
+	File del_bcf
+	File del_bcf_index
+	File dup_bcf
+	File dup_bcf_index
+	File inv_bcf
+	File inv_bcf_index
+	File bnd_bcf
+	File bnd_bcf_index
+
+	String sample_name
+	String docker
+	String disk_size
+	String cluster_config
+	
+
+	command <<<
+
+		set -o pipefail
+		set -e
+		/opt/hall-lab/bcftools-1.9/bin/bcftools view ${ins_bcf} > ${sample_name}.ins.vcf
+		/opt/hall-lab/bcftools-1.9/bin/bcftools view ${del_bcf} > ${sample_name}.del.vcf
+		/opt/hall-lab/bcftools-1.9/bin/bcftools view ${dup_bcf} > ${sample_name}.dup.vcf
+		/opt/hall-lab/bcftools-1.9/bin/bcftools view ${inv_bcf} > ${sample_name}.inv.vcf
+		/opt/hall-lab/bcftools-1.9/bin/bcftools view ${bnd_bcf} > ${sample_name}.bnd.vcf	
+		>>>
+
+		runtime {
+		docker:docker
+    	cluster:cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File ins_vcf = "${sample_name}.ins.vcf"
+		File del_vcf = "${sample_name}.del.vcf"
+		File dup_vcf = "${sample_name}.dup.vcf"
+		File inv_vcf = "${sample_name}.inv.vcf"
+		File bnd_vcf = "${sample_name}.bnd.vcf"
+	}
+}
+
+
+
+

tasks/delly.wdl

@@ -0,0 +1,68 @@
+task delly {
+
+	File tumor_bam
+	File tumor_bam_idx
+	File normal_bam
+	File normal_bam_idx
+	File ref_dir
+	String fasta
+	String sample_name
+	String docker
+	String disk_size
+	String cluster_config
+
+	command <<<
+
+		set -o pipefail
+		set -e
+		echo -e "${sample_name}.tumor\ttumor\n${sample_name}.normal\tnormal" > samples.tsv
+
+		nt=$(nproc)
+		export OMP_NUM_THREADS=$nt
+
+		/opt/delly/src/delly call -n -t DEL -g ${ref_dir}/${fasta} -o ${sample_name}.delly.del.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam}
+
+		/opt/delly/src/delly filter -t DEL -f somatic -o ${sample_name}.delly.del.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.del.somatic.bcf
+
+		/opt/delly/src/delly call -n -t DUP -g ${ref_dir}/${fasta} -o ${sample_name}.delly.dup.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam}
+
+		/opt/delly/src/delly filter -t DUP -f somatic -o ${sample_name}.delly.dup.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.dup.somatic.bcf
+
+		/opt/delly/src/delly call -n -t INS -g ${ref_dir}/${fasta} -o ${sample_name}.delly.ins.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam}
+
+		/opt/delly/src/delly filter -t INS -f somatic -o ${sample_name}.delly.ins.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.ins.somatic.bcf
+
+		/opt/delly/src/delly call -n -t INV -g ${ref_dir}/${fasta} -o ${sample_name}.delly.inv.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam}
+
+		/opt/delly/src/delly filter -t INV -f somatic -o ${sample_name}.delly.inv.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.inv.somatic.bcf
+
+		/opt/delly/src/delly call -n -t BND -g ${ref_dir}/${fasta} -o ${sample_name}.delly.bnd.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam}
+
+		/opt/delly/src/delly filter -t BND -f somatic -o ${sample_name}.delly.bnd.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.bnd.somatic.bcf
+
+		>>>
+
+		runtime {
+		docker:docker
+    	cluster:cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File del_bcf = "${sample_name}.delly.del.somatic.filtered.bcf"
+		File del_bcf_index = "${sample_name}.delly.del.somatic.filtered.bcf.csi"
+		File dup_bcf = "${sample_name}.delly.dup.somatic.filtered.bcf"
+		File dup_bcf_index = "${sample_name}.delly.dup.somatic.filtered.bcf.csi"
+		File ins_bcf = "${sample_name}.delly.ins.somatic.filtered.bcf"
+		File ins_bcf_index = "${sample_name}.delly.ins.somatic.filtered.bcf.csi"
+		File inv_bcf = "${sample_name}.delly.inv.somatic.filtered.bcf"
+		File inv_bcf_index = "${sample_name}.delly.inv.somatic.filtered.bcf.csi"
+		File bnd_bcf = "${sample_name}.delly.bnd.somatic.filtered.bcf"
+		File bnd_bcf_index = "${sample_name}.delly.bnd.somatic.filtered.bcf.csi"
+	}
+}
+
+
+
+

tasks/mapping.wdl

@@ -0,0 +1,34 @@
+task mapping {
+
+    File ref_dir
+    String fasta
+	File fastq_1
+	File fastq_2
+	String type
+	String SENTIEON_INSTALL_DIR
+	String group
+	String sample
+	String pl
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e	
+		export SENTIEON_LICENSE=192.168.0.55:8990
+		nt=$(nproc)
+		${SENTIEON_INSTALL_DIR}/bin/bwa mem -M -R "@RG\tID:${group}.${type}\tSM:${sample}.${type}\tPL:${pl}" -t $nt -K 10000000 ${ref_dir}/${fasta} ${fastq_1} ${fastq_2} | ${SENTIEON_INSTALL_DIR}/bin/sentieon util sort -o ${sample}.sorted.bam -t $nt --sam2bam -i -
+	>>>
+
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File sorted_bam = "${sample}.sorted.bam"
+		File sorted_bam_index = "${sample}.sorted.bam.bai"
+	}
+}

workflow.wdl

@@ -0,0 +1,89 @@
+import "./tasks/mapping.wdl" as mapping
+import "./tasks/delly.wdl" as delly
+import "./tasks/bcf2vcf.wdl" as bcf2vcf
+
+workflow {{ project_name }} {
+	
+	String SENTIEON_INSTALL_DIR
+	String SENTIEONdocker
+	String DELLYdocker
+	String BCFdocker
+
+	File tumor_read1
+	File tumor_read2
+	File normal_read1
+	File normal_read2
+	File ref_dir
+	String fasta
+	String sample_name
+	String disk_size
+
+	String BIGcluster_config
+	String SMALLcluster_config
+
+	call mapping.mapping as tumor_mapping {
+		input: 
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		group=sample_name,
+		sample=sample_name,
+		type="tumor",
+		pl="ILLUMINAL",
+		fasta=fasta,
+		ref_dir=ref_dir,
+		fastq_1=tumor_read1,
+		fastq_2=tumor_read2,
+		docker=SENTIEONdocker,
+		disk_size=disk_size,
+		cluster_config=BIGcluster_config
+	}
+
+	call mapping.mapping as normal_mapping {
+		input: 
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		group=sample_name,
+		sample=sample_name,
+		type="normal",
+		pl="ILLUMINAL",
+		fasta=fasta,
+		ref_dir=ref_dir,
+		fastq_1=normal_read1,
+		fastq_2=normal_read2,
+		docker=SENTIEONdocker,
+		disk_size=disk_size,
+		cluster_config=BIGcluster_config
+	}
+
+	
+	call delly.delly as delly {
+		input: 
+		tumor_bam=tumor_mapping.sorted_bam,
+		tumor_bam_idx=tumor_mapping.sorted_bam_index,
+		normal_bam=normal_mapping.sorted_bam,
+		normal_bam_idx=normal_mapping.sorted_bam_index,
+		ref_dir=ref_dir,
+		fasta=fasta,
+		sample_name=sample_name,
+		docker=DELLYdocker,
+		disk_size=disk_size,
+		cluster_config=SMALLcluster_config
+	}
+
+	call bcf2vcf.bcf2vcf as bcf2vcf {
+		input:
+		ins_bcf=delly.ins_bcf,
+		ins_bcf_index=delly.ins_bcf_index,
+		del_bcf=delly.del_bcf,
+		del_bcf_index=delly.del_bcf_index,
+		dup_bcf=delly.dup_bcf,
+		dup_bcf_index=delly.dup_bcf_index,
+		inv_bcf=delly.inv_bcf,
+		inv_bcf_index=delly.inv_bcf_index,
+		bnd_bcf=delly.bnd_bcf,
+		bnd_bcf_index=delly.bnd_bcf_index,
+		docker=BCFdocker,
+		disk_size=disk_size,
+		cluster_config=SMALLcluster_config,
+		sample_name=sample_name
+	}
+}
+