new cromwell

README.md

@@ -1,5 +1,3 @@
-## README
-
 **Author：** Huang Yechao
 
 **E-mail：**17210700095@fudan.edu.cn

inputs

@@ -7,7 +7,7 @@
   "{{ project_name }}.dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
   "{{ project_name }}.db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
   "{{ project_name }}.cluster_config": "{{ cluster if cluster != '' else 'OnDemand ecs.sn1ne.8xlarge img-ubuntu-vpc' }}",
-  "{{ project_name }}.docker": "localhost:5000/sentieon-genomics:v2018.08.01 oss://pgx-docker-images/dockers",
+  "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
   "{{ project_name }}.dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
   "{{ project_name }}.sample": "{{ sample_name }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}", 

tasks/BQSR.wdl

@@ -1,11 +1,12 @@
 task BQSR {
+	
+    File ref_dir
+    File dbsnp_dir
+    File dbmills_dir
 	String sample
 	String SENTIEON_INSTALL_DIR
 	String fasta
-
-	File dbsnp_dir
 	String dbsnp
-	File dbmills_dir
 	String db_mills
 	File realigned_bam
 	File realigned_bam_index
@@ -31,10 +32,10 @@ task BQSR {
 
 	>>>
 	runtime {
-	dockerTag:docker
-    cluster: cluster_config
-    systemDisk: "cloud_ssd 40"
-    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"	
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"	
 	}
 
 	output {

tasks/Dedup.wdl

@@ -19,7 +19,7 @@ task Dedup {
 		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -i ${sorted_bam} --algo Dedup --rmdup --score_info ${sample}_score.txt --metrics ${sample}_dedup_metrics.txt ${sample}.sorted.deduped.bam	
 	>>>
 	runtime {
-		dockerTag:docker
+		docker:docker
     	cluster: cluster_config
     	systemDisk: "cloud_ssd 40"
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"

tasks/Haplotyper.wdl

@@ -1,11 +1,14 @@
 task Haplotyper {
+	
+	
+    File ref_dir
+    File dbsnp_dir
+
 	String SENTIEON_INSTALL_DIR
 	String fasta
 	File recaled_bam
 	File recaled_bam_index
-	File dbsnp_dir
 	String dbsnp
-	File ref_dir
 	String sample
 	String docker
 	String cluster_config
@@ -20,15 +23,15 @@ command <<<
 	>>>
 	
 	runtime {
-		dockerTag:docker
+		docker:docker
     	cluster: cluster_config
     	systemDisk: "cloud_ssd 40"
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 
 	output {
-	File vcf = "${sample}_hc.vcf"
-	File vcf_idx = "${sample}_hc.vcf.idx"
+		File vcf = "${sample}_hc.vcf"
+		File vcf_idx = "${sample}_hc.vcf.idx"
 	}
 }
 

tasks/Metrics.wdl

@@ -1,11 +1,13 @@
-task Metrics{
+task Metrics {
+
+
+    File ref_dir
 	String SENTIEON_INSTALL_DIR
 	String sample
 	String docker
 	String cluster_config
 
 	String fasta
-	File ref_dir
 	File sorted_bam
 	File sorted_bam_index
 	String disk_size
@@ -23,7 +25,7 @@ task Metrics{
 	>>>
 	
 	runtime {
-		dockerTag:docker
+		docker:docker
     	cluster: cluster_config
     	systemDisk: "cloud_ssd 40"
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"

tasks/Realigner.wdl

@@ -1,13 +1,14 @@
 task Realigner {
 
+    File ref_dir
+    File dbmills_dir
+
 	String SENTIEON_INSTALL_DIR
 	String sample
 	String fasta
 
-	File ref_dir
 	File Dedup_bam
 	File Dedup_bam_index
-	File dbmills_dir
 	String db_mills
 	String docker	
 	String cluster_config
@@ -24,8 +25,8 @@ task Realigner {
 	>>>
 
 	runtime {
-		dockerTag:docker
-    	cluster: cluster_config
+		docker:docker
+		cluster: cluster_config
     	systemDisk: "cloud_ssd 40"
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}

tasks/TNscope.wdl

@@ -1,5 +1,9 @@
-task {
-	
+task TNscope {
+
+	File ref_dir
+    File dbsnp_dir
+    
+
 	String SENTIEON_INSTALL_DIR
 	String tumor_name
 	String normal_name
@@ -7,11 +11,8 @@ task {
 	String cluster_config
 
 	String fasta
-	File ref_dir
-
 	File corealigner_bam
 	File corealigner_bam_index
-	File dbsnp_dir
 	String dbsnp
 	String disk_size
 
@@ -34,7 +35,6 @@ task {
 	}
 
 	output {
-
 		File TNscope_vcf= "${sample}.TNscope.TN.vcf"
 		File TNscope_vcf_index = "${sample}.TNscope.TN.vcf.idx"
 	}

tasks/TNseq.wdl

@@ -1,5 +1,8 @@
-task {
+task TNseq {
 	
+    File ref_dir
+    File dbsnp_dir
+
 	String SENTIEON_INSTALL_DIR
 	String tumor_name
 	String normal_name
@@ -7,10 +10,8 @@ task {
 	String cluster_config
 
 	String fasta
-	File ref_dir
 	File corealigner_bam
 	File corealigner_bam_index
-	File dbsnp_dir
 	String dbsnp
 	String disk_size
 
@@ -33,7 +34,6 @@ task {
 	}
 
 	output {
-
 		File TNseq_vcf= "${sample}.TNseq.TN.vcf"
 		File TNseq_vcf_index = "${sample}.TNseq.TN.vcf.idx"
 	}

tasks/corealigner.wdl

@@ -1,15 +1,16 @@
-task {
+task corealigner {
+	
+    File ref_dir
+    File dbsnp_dir
+    File dbmills_dir
+
 	String sample
 	String SENTIEON_INSTALL_DIR
 	String docker
 	String cluster_config
 	String fasta
 
-
-	File ref_dir
-	File dbsnp_dir
 	String dbsnp
-	File dbmills_dir
 	String db_mills
 	File tumor_recaled_bam
 	File tumor_recaled_bam_index

tasks/deduped_Metrics.wdl

@@ -1,10 +1,10 @@
 task deduped_Metrics {
 
+    File ref_dir
+    
 	String SENTIEON_INSTALL_DIR
 	String sample
-
 	String fasta
-	File ref_dir
 	File Dedup_bam
 	File Dedup_bam_index
 	String docker
@@ -13,18 +13,18 @@ task deduped_Metrics {
 
 
 	command <<<
-	set -o pipefail
-	set -e
-	export SENTIEON_LICENSE=192.168.0.55:8990
-	nt=$(nproc)
-	${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${Dedup_bam} --algo CoverageMetrics --omit_base_output ${sample}_deduped_coverage_metrics --algo MeanQualityByCycle ${sample}_deduped_mq_metrics.txt --algo QualDistribution ${sample}_deduped_qd_metrics.txt --algo GCBias --summary ${sample}_deduped_gc_summary.txt ${sample}_deduped_gc_metrics.txt --algo AlignmentStat ${sample}_deduped_aln_metrics.txt --algo InsertSizeMetricAlgo ${sample}_deduped_is_metrics.txt
+		set -o pipefail
+		set -e
+		export SENTIEON_LICENSE=192.168.0.55:8990
+		nt=$(nproc)
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${Dedup_bam} --algo CoverageMetrics --omit_base_output ${sample}_deduped_coverage_metrics --algo MeanQualityByCycle ${sample}_deduped_mq_metrics.txt --algo QualDistribution ${sample}_deduped_qd_metrics.txt --algo GCBias --summary ${sample}_deduped_gc_summary.txt ${sample}_deduped_gc_metrics.txt --algo AlignmentStat ${sample}_deduped_aln_metrics.txt --algo InsertSizeMetricAlgo ${sample}_deduped_is_metrics.txt
 	>>>
 
 	runtime {
-		dockerTag:docker
+		docker:docker
     	cluster: cluster_config
     	systemDisk: "cloud_ssd 40"
-    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" 
 	}
 
 	output {

tasks/mapping.wdl

@@ -1,6 +1,8 @@
 task mapping {
+
+
+    File ref_dir
 	String fasta
-	File ref_dir
 	File fastq_1
 	File fastq_2
 
@@ -21,7 +23,7 @@ task mapping {
 	>>>
 
 	runtime {
-		dockerTag:docker
+		docker:docker
     	cluster: cluster_config
     	systemDisk: "cloud_ssd 40"
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"