first commit

inputs

@@ -2,9 +2,11 @@
   "{{ project_name }}.SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
   "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
   "{{ project_name }}.disk_size": "500",
-  "{{ project_name }}.gvcf_dir": "{{ gvcf_dir }}",
+  "{{ project_name }}.gvcf_idx_files": "{{ gvcf_idx_files }}",
+  "{{ project_name }}.gvcf_files": "{{ gvcf_files }}",
   "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
   "{{ project_name }}.project": "{{ project }}",
+  "{{ project_name }}.chromo": "{{ chromo }}",
   "{{ project_name }}.cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
   "{{ project_name }}.ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/"
 }

tasks/GVCFtyper_chr3.wdl → tasks/GVCFtyper.wdl

@@ -1,10 +1,12 @@
-task GVCFtyper_chr3 {
+task GVCFtyper {
 	
     File ref_dir
 	String SENTIEON_INSTALL_DIR
 	String fasta
-	File gvcf_dir
+	Array[File] gvcfs
+	Array[File] gvcf_idxs
 	String project
+	String chromo
 	String docker
 	String cluster_config
 	String disk_size
@@ -13,10 +15,8 @@ command <<<
 		set -o pipefail
 		set -e
 		export SENTIEON_LICENSE=192.168.0.55:8990
-		nt=$(nproc)
-		mkdir -p /cromwell_root/tmp
-		cp -r ${gvcf_dir} /cromwell_root/tmp/
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} --algo GVCFtyper ${project}.joint.g.vcf /cromwell_root/tmp/*.chr3.vcf
+		nt=$(nproc)	
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} --algo GVCFtyper ${project}.joint.g.vcf ${sep=" " gvcfs}
 	>>>
 	
 	runtime {
@@ -27,8 +27,8 @@ command <<<
 	}
 
 	output {
-		File gvcf = "${project}.chr3.joint.g.vcf"
-		File gvcf_idx = "${project}.chr3.joint.g.vcf.idx"
+		File gvcf = "${project}.${chromo}joint.g.vcf"
+		File gvcf_idx = "${project}.${chromo}.joint.g.vcf.idx"
 	}
 }
 

tasks/GVCFtyper_chr4.wdl

@@ -1,33 +0,0 @@
-task GVCFtyper_chr4 {
-	
-    File ref_dir
-	String SENTIEON_INSTALL_DIR
-	String fasta
-	File gvcf_dir
-	String project
-	String docker
-	String cluster_config
-	String disk_size
-
-command <<<
-		set -o pipefail
-		set -e
-		export SENTIEON_LICENSE=192.168.0.55:8990
-		nt=$(nproc)
-		mkdir -p /cromwell_root/tmp
-		cp -r ${gvcf_dir} /cromwell_root/tmp/
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} --algo GVCFtyper ${project}.joint.g.vcf /cromwell_root/tmp/*.chr4.vcf
-	>>>
-	
-	runtime {
-		docker:docker
-    	cluster: cluster_config
-    	systemDisk: "cloud_ssd 40"
-    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File gvcf = "${project}.chr4.joint.g.vcf"
-		File gvcf_idx = "${project}.chr4.joint.g.vcf.idx"
-	}
-}

tasks/GVCFtyper_chr7.wdl

@@ -1,33 +0,0 @@
-task GVCFtyper_chr7 {
-	
-    File ref_dir
-	String SENTIEON_INSTALL_DIR
-	String fasta
-	File gvcf_dir
-	String project
-	String docker
-	String cluster_config
-	String disk_size
-
-command <<<
-		set -o pipefail
-		set -e
-		export SENTIEON_LICENSE=192.168.0.55:8990
-		nt=$(nproc)
-		mkdir -p /cromwell_root/tmp
-		cp -r ${gvcf_dir} /cromwell_root/tmp/
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} --algo GVCFtyper ${project}.joint.g.vcf /cromwell_root/tmp/*.chr7.vcf
-	>>>
-	
-	runtime {
-		docker:docker
-    	cluster: cluster_config
-    	systemDisk: "cloud_ssd 40"
-    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File gvcf = "${project}.chr7.joint.g.vcf"
-		File gvcf_idx = "${project}.chr7.joint.g.vcf.idx"
-	}
-}

tasks/GVCFtyper_chr8.wdl

@@ -1,33 +0,0 @@
-task GVCFtyper_chr8 {
-	
-    File ref_dir
-	String SENTIEON_INSTALL_DIR
-	String fasta
-	File gvcf_dir
-	String project
-	String docker
-	String cluster_config
-	String disk_size
-
-command <<<
-		set -o pipefail
-		set -e
-		export SENTIEON_LICENSE=192.168.0.55:8990
-		nt=$(nproc)
-		mkdir -p /cromwell_root/tmp
-		cp -r ${gvcf_dir} /cromwell_root/tmp/
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} --algo GVCFtyper ${project}.joint.g.vcf /cromwell_root/tmp/*.chr8.vcf
-	>>>
-	
-	runtime {
-		docker:docker
-    	cluster: cluster_config
-    	systemDisk: "cloud_ssd 40"
-    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File gvcf = "${project}.chr8.joint.g.vcf"
-		File gvcf_idx = "${project}.chr8.joint.g.vcf.idx"
-	}
-}

tasks/GVCFtyper_chrX.wdl

@@ -1,33 +0,0 @@
-task GVCFtyper_chrX {
-	
-    File ref_dir
-	String SENTIEON_INSTALL_DIR
-	String fasta
-	File gvcf_dir
-	String project
-	String docker
-	String cluster_config
-	String disk_size
-
-command <<<
-		set -o pipefail
-		set -e
-		export SENTIEON_LICENSE=192.168.0.55:8990
-		nt=$(nproc)
-		mkdir -p /cromwell_root/tmp
-		cp -r ${gvcf_dir} /cromwell_root/tmp/
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} --algo GVCFtyper ${project}.joint.g.vcf /cromwell_root/tmp/*.chrX.vcf
-	>>>
-	
-	runtime {
-		docker:docker
-    	cluster: cluster_config
-    	systemDisk: "cloud_ssd 40"
-    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File gvcf = "${project}.chrX.joint.g.vcf"
-		File gvcf_idx = "${project}.chrX.joint.g.vcf.idx"
-	}
-}

workflow.wdl

@@ -1,72 +1,30 @@
-import "./tasks/gVCF_chromo_split.wdl" as gVCF_chromo_split
-import "./tasks/GVCFtyper_chr3.wdl" as GVCFtyper_chr3
-import "./tasks/GVCFtyper_chr4.wdl" as GVCFtyper_chr4
-import "./tasks/GVCFtyper_chr7.wdl" as GVCFtyper_chr7
-import "./tasks/GVCFtyper_chr8.wdl" as GVCFtyper_chr8
-import "./tasks/GVCFtyper_chrX.wdl" as GVCFtyper_chrX
+import "./tasks/GVCFtyper.wdl" as GVCFtyper
 
-workflow {{ project_name }} {
 
-	File gvcf_dir
+workflow project_name {
+
+	File gvcf_files
+	Array[File] gvcfs = read_lines(gvcf_files)
+	File gvcf_idx_files
+	Array[File] gvcf_idxs = read_lines(gvcf_idx_files)
 	String SENTIEON_INSTALL_DIR
 	String docker
 	String project
 	String fasta
+	String chromo
 	File ref_dir
 	String disk_size
 	String cluster_config
 
 
-	call GVCFtyper_chr3.GVCFtyper_chr3 as GVCFtyper_chr3 {
-		input:
-		ref_dir=ref_dir,
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		fasta=fasta,
-		gvcf_dir=gvcf_dir,
-		project=project,
-		docker=docker,
-		cluster_config=cluster_config,
-		disk_size=disk_size
-	}
-	call GVCFtyper_chr4.GVCFtyper_chr4 as GVCFtyper_chr4 {
-		input:
-		ref_dir=ref_dir,
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		fasta=fasta,
-		gvcf_dir=gvcf_dir,
-		project=project,
-		docker=docker,
-		cluster_config=cluster_config,
-		disk_size=disk_size
-	}
-	call GVCFtyper_chr7.GVCFtyper_chr7 as GVCFtyper_chr7 {
-		input:
-		ref_dir=ref_dir,
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		fasta=fasta,
-		gvcf_dir=gvcf_dir,
-		project=project,
-		docker=docker,
-		cluster_config=cluster_config,
-		disk_size=disk_size
-	}
-	call GVCFtyper_chr8.GVCFtyper_chr8 as GVCFtyper_chr8 {
-		input:
-		ref_dir=ref_dir,
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		fasta=fasta,
-		gvcf_dir=gvcf_dir,
-		project=project,
-		docker=docker,
-		cluster_config=cluster_config,
-		disk_size=disk_size
-	}
-	call GVCFtyper_chrX.GVCFtyper_chrX as GVCFtyper_chrX {
+	call GVCFtyper.GVCFtyper as GVCFtyper {
 		input:
 		ref_dir=ref_dir,
 		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 		fasta=fasta,
-		gvcf_dir=gvcf_dir,
+		gvcfs=gvcfs,
+		gvcf_idxs=gvcf_idxs,
+		chromo=chromo,
 		project=project,
 		docker=docker,
 		cluster_config=cluster_config,