sentieon and mapping and bam

inputs

@@ -1,24 +1,24 @@
 {
-  "{{ project_name }}.SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
-  "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
-  "{{ project_name }}.PIdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/picard:2.20.2",
-  "{{ project_name }}.platform": "ILLUMINA",
-  "{{ project_name }}.dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
-  "{{ project_name }}.disk_size": "500",
-  "{{ project_name }}.SAdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/star:2.7.0",
-  "{{ project_name }}.fastq_1": "{{ read1 }}",
-  "{{ project_name }}.machine": "{{ machine }}",
-  "{{ project_name }}.STdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
-  "{{ project_name }}.library": "{{ library }}",
-  "{{ project_name }}.fastq_2": "{{ read2 }}",
-  "{{ project_name }}.dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
-  "{{ project_name }}.cluster_config": "OnDemand bcs.ps.g.8xlarge img-ubuntu-vpc",
-  "{{ project_name }}.SAref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/STAR_GRCh38_2.7.0d/",
-  "{{ project_name }}.SAMdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",
-  "{{ project_name }}.STref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/",
-  "{{ project_name }}.db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
-  "{{ project_name }}.sample": "{{ sample }}",
-  "{{ project_name }}.dbsnp": "dbsnp_146.hg38.vcf",
-  "{{ project_name }}.id": "{{ id }}",
-  "{{ project_name }}.GATKdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/gatk:v2019.01"
-}
+  "{{ projecr_name }} .indexBam.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",
+  "{{ projecr_name }} .Haplotyper.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
+  "{{ projecr_name }} .SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
+  "{{ projecr_name }} .fasta": "GRCh38.d1.vd1.fa",
+  "{{ projecr_name }} .Dedup.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
+  "{{ projecr_name }} .dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
+  "{{ projecr_name }} .deduped_Metrics.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
+  "{{ projecr_name }} .disk_size": "500",
+  "{{ projecr_name }} .fastq_1": "{{ fastq_1 }}",
+  "{{ projecr_name }} .Metrics.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
+  "{{ projecr_name }} .STARref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/STAR_GRCh38_2.7.0d/",
+  "{{ projecr_name }} .fastq_2": "{{ fastq_2 }}",
+  "{{ projecr_name }} .dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
+  "{{ projecr_name }} .SplitReads.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
+  "{{ projecr_name }} .cluster_config": "OnDemand bcs.ps.g.8xlarge img-ubuntu-vpc",
+  "{{ projecr_name }} .Hardfiltration.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
+  "{{ projecr_name }} .BQSR.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
+  "{{ projecr_name }} .mapping.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/star:2.7.0",
+  "{{ projecr_name }} .db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
+  "{{ projecr_name }} .sample": "{{ sample }}",
+  "{{ projecr_name }} .dbsnp": "dbsnp_146.hg38.vcf",
+  "{{ projecr_name }} .ref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/"
+}

tasks/BQSR.wdl

@@ -9,8 +9,8 @@ task BQSR {
 	String db_mills
 	File Split_bam
 	File Split_bam_index
-	File STref_dir
-	String STdocker
+	File ref_dir
+	String docker
 	String cluster_config
 	String disk_size
 
@@ -21,17 +21,17 @@ task BQSR {
 		export SENTIEON_LICENSE=192.168.0.55:8990
 		nt=$(nproc)
 
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${STref_dir}/${fasta} -t $nt -i ${Split_bam} --algo QualCal -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} ${sample}_recal_data.table
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver --traverse_param 1000000/10000 -r ${ref_dir}/${fasta} -t $nt -i ${Split_bam} --algo QualCal -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} ${sample}_recal_data.table
 
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${STref_dir}/${fasta} -t $nt -i ${Split_bam} -q ${sample}_recal_data.table --algo QualCal -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} ${sample}_recal_data.table.post --algo ReadWriter ${sample}.sorted.deduped.recaled.bam
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver --traverse_param 1000000/10000 -r ${ref_dir}/${fasta} -t $nt -i ${Split_bam} -q ${sample}_recal_data.table --algo QualCal -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} ${sample}_recal_data.table.post --algo ReadWriter ${sample}.sorted.deduped.recaled.bam
 
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --algo QualCal --plot --before ${sample}_recal_data.table --after ${sample}_recal_data.table.post ${sample}_recal_data.csv
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver --traverse_param 1000000/10000 -t $nt --algo QualCal --plot --before ${sample}_recal_data.table --after ${sample}_recal_data.table.post ${sample}_recal_data.csv
 
 		${SENTIEON_INSTALL_DIR}/bin/sentieon plot QualCal -o ${sample}_bqsrreport.pdf ${sample}_recal_data.csv
 
 	>>>
 	runtime {
-	dockerTag:STdocker
+	dockerTag:docker
     cluster: cluster_config
     systemDisk: "cloud_ssd 40"
     dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"	

tasks/Dedup.wdl

@@ -5,7 +5,7 @@ task Dedup {
 
 	File sorted_bam
 	File sorted_bam_index
-	String STdocker
+	String docker
 	String cluster_config
 	String disk_size
 
@@ -19,11 +19,11 @@ task Dedup {
 		cp ${sorted_bam} .
 		cp ${sorted_bam_index} .
 		nt=$(nproc)
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -i $sentieon_bam --algo LocusCollector --fun score_info ${sample}_score.txt
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -i $sentieon_bam --algo Dedup --rmdup --score_info ${sample}_score.txt --metrics ${sample}_dedup_metrics.txt ${sample}.sorted.deduped.bam	
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver --traverse_param 1000000/10000 -t $nt -i $sentieon_bam --algo LocusCollector --fun score_info ${sample}_score.txt
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver --traverse_param 1000000/10000 -t $nt -i $sentieon_bam --algo Dedup --rmdup --score_info ${sample}_score.txt --metrics ${sample}_dedup_metrics.txt ${sample}.sorted.deduped.bam	
 	>>>
 	runtime {
-		docker:STdocker
+		docker:docker
     	cluster: cluster_config
     	systemDisk: "cloud_ssd 40"
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"

tasks/Haplotyper.wdl

@@ -5,9 +5,9 @@ task Haplotyper {
 	File recaled_bam_index
 	File dbsnp_dir
 	String dbsnp
-	File STref_dir
+	File ref_dir
 	String sample
-	String STdocker
+	String docker
 	String cluster_config
 	String disk_size
 
@@ -16,11 +16,11 @@ command <<<
 		set -e
 		export SENTIEON_LICENSE=192.168.0.55:8990
 		nt=$(nproc)	
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${STref_dir}/${fasta} -t $nt -i ${recaled_bam} --algo Haplotyper -d ${dbsnp_dir}/${dbsnp} --trim_soft_clip --call_conf 20 --emit_conf 20 ${sample}_hc.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver --traverse_param 1000000/10000 -r ${ref_dir}/${fasta} -t $nt -i ${recaled_bam} --algo Haplotyper -d ${dbsnp_dir}/${dbsnp} --trim_soft_clip --call_conf 20 --emit_conf 20 ${sample}_hc.vcf
 	>>>
 	
 	runtime {
-		dockerTag:STdocker
+		dockerTag:docker
     	cluster: cluster_config
     	systemDisk: "cloud_ssd 40"
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"

tasks/Hardfiltration.wdl

@@ -2,10 +2,10 @@ task Hardfiltration {
 	
 	File vcf_file
 	File vcf_index
-	File STref_dir
+	File ref_dir
 	String fasta
 	String sample
-	String GATKdocker
+	String docker
 	String disk_size
 	String cluster_config
 	
@@ -13,14 +13,14 @@ task Hardfiltration {
 	command <<<
 		set -o pipefail
 		set -e
-		java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx32G -jar /gatk/gatk-package-4.1.0.0-local.jar VariantFiltration -V ${vcf_file} -O ${sample}_hc_filtered.vcf -R ${STref_dir}/${fasta} --cluster-window-size 35 --cluster-size 3 --filter-name FS --filter-expression "FS > 30.0" --filter-name QD --filter-expression "QD < 2.0" --filter-name LowDepth --filter-expression "DP < 5"
+		java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx32G -jar /gatk/gatk-package-4.1.0.0-local.jar VariantFiltration -V ${vcf_file} -O ${sample}_hc_filtered.vcf -R ${ref_dir}/${fasta} --cluster-window-size 35 --cluster-size 3 --filter-name FS --filter-expression "FS > 30.0" --filter-name QD --filter-expression "QD < 2.0" --filter-name LowDepth --filter-expression "DP < 5"
 		cat ${sample}_hc_filtered.vcf |grep "#" > ${sample}_hc_filtered.vcf.header.tmp
 		cat ${sample}_hc_filtered.vcf |grep PASS > ${sample}_hc_filtered.vcf.tmp
 		cat ${sample}_hc_filtered.vcf.header.tmp ${sample}_hc_filtered.vcf.tmp > ${sample}_hc_PASS.vcf
 		>>>
 
 		runtime {
-		docker:GATKdocker
+		docker:docker
     	cluster:cluster_config
     	systemDisk: "cloud_ssd 40"
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"

tasks/Metrics.wdl

@@ -1,10 +1,9 @@
 task Metrics {
 
-
-    File STref_dir
+    File ref_dir
 	String SENTIEON_INSTALL_DIR
 	String sample
-	String STdocker
+	String docker
 	String cluster_config
 
 	String fasta
@@ -23,7 +22,7 @@ task Metrics {
 		sentieon_bam_index=`basename ${sorted_bam_index}`
 		cp ${sorted_bam} .
 		cp ${sorted_bam_index} .
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${STref_dir}/${fasta} -t $nt -i $sentieon_bam \
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver --traverse_param 1000000/10000 -r ${ref_dir}/${fasta} -t $nt -i $sentieon_bam \
 		--algo GCBias --summary ${sample}_gc_summary.txt ${sample}_gc_metrics.txt \
 		--algo MeanQualityByCycle ${sample}_mq_metrics.txt \
 		--algo QualDistribution ${sample}_qd_metrics.txt \
@@ -34,7 +33,7 @@ task Metrics {
 	>>>
 	
 	runtime {
-		docker:STdocker
+		docker:docker
     	cluster: cluster_config
     	systemDisk: "cloud_ssd 40"
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"

tasks/SamToBamSentieon.wdl

@@ -0,0 +1,30 @@
+task SamToBamSentieon {
+	File aligned_sam
+
+	String SENTIEON_INSTALL_DIR
+	String sample
+	String STdocker
+	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/sentieon util sort -t $nt --sam2bam -i ${aligned_sam} -o ${sample}.bam
+
+	>>>
+
+	runtime {
+		docker:STdocker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File sorted_bam = "${sample}.bam"
+	}
+}

tasks/SplitReads.wdl

@@ -3,12 +3,12 @@ task SplitReads {
 	String SENTIEON_INSTALL_DIR
 	String sample
 
-	File STref_dir
+	File ref_dir
     File fasta
 	File Dedup_bam
 	File Dedup_bam_index
 
-	String STdocker
+	String docker
 	String cluster_config
 	String disk_size
 
@@ -18,10 +18,10 @@ task SplitReads {
 		set -e
 		export SENTIEON_LICENSE=192.168.0.55:8990
 		nt=$(nproc)
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${STref_dir}/${fasta} -i ${Dedup_bam} --algo RNASplitReadsAtJunction --reassign_mapq 255:60 ${sample}.split.bam
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver --traverse_param 1000000/10000 -t $nt -r ${ref_dir}/${fasta} -i ${Dedup_bam} --algo RNASplitReadsAtJunction --reassign_mapq 255:60 ${sample}.split.bam
 	>>>
 	runtime {
-		docker:STdocker
+		docker:docker
     	cluster: cluster_config
     	systemDisk: "cloud_ssd 40"
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"

tasks/deduped_Metrics.wdl

@@ -1,13 +1,13 @@
 task deduped_Metrics {
 
-    File STref_dir
+    File ref_dir
     
 	String SENTIEON_INSTALL_DIR
 	String sample
 	String fasta
 	File Dedup_bam
 	File Dedup_bam_index
-	String STdocker
+	String docker
 	String cluster_config
 	String disk_size
 
@@ -17,7 +17,7 @@ task deduped_Metrics {
 		set -e
 		export SENTIEON_LICENSE=192.168.0.55:8990
 		nt=$(nproc)
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${STref_dir}/${fasta} -t $nt -i ${Dedup_bam} \
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver --traverse_param 1000000/10000 -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 \
@@ -27,7 +27,7 @@ task deduped_Metrics {
 	>>>
 
 	runtime {
-		docker:STdocker
+		docker:docker
     	cluster: cluster_config
     	systemDisk: "cloud_ssd 40"
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" 

tasks/indexBam.wdl

@@ -1,23 +1,23 @@
 task indexBam {
 	File sorted_bam
 	String sample
-	String SAMdocker
+	String docker
 	String cluster_config
 	String disk_size
 
 	command <<<
 		set -o pipefail
 		set -e	
-		/opt/conda/bin/samtools index ${sorted_bam} ${sample}.bam.bai
+		/opt/conda/bin/samtools index ${sorted_bam} ${sample}_Aligned.sortedByCoord.out.bai
 	>>>
 
 	runtime {
-		docker:SAMdocker
+		docker:docker
     	cluster: cluster_config
     	systemDisk: "cloud_ssd 40"
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File sorted_bam_index = "${sample}.bam.bai"
+		File sorted_bam_index = "${sample}_Aligned.sortedByCoord.out.bai"
 	}
 }

tasks/mapping.wdl

@@ -1,13 +1,13 @@
 task mapping {
 
-    File SAref_dir
-    File STref_dir
+    File STARref_dir
+    File ref_dir
     File fasta
 	File fastq_1
 	File fastq_2
 
 	String sample
-	String SAdocker
+	String docker
 	String cluster_config
 	String disk_size
 
@@ -15,21 +15,25 @@ task mapping {
 		set -o pipefail
 		set -e	
 
-		STAR --genomeDir ${SAref_dir} --readFilesIn ${fastq_1} ${fastq_2} --readFilesCommand zcat --runThreadN 20 --outFileNamePrefix OnePass_ 
+		STAR --genomeDir ${STARref_dir} --readFilesIn ${fastq_1} ${fastq_2} --readFilesCommand zcat --runThreadN 20 --outFileNamePrefix OnePass_ 
 
-		STAR --runMode genomeGenerate --genomeDir "./" --genomeFastaFiles ${STref_dir}/${fasta} --sjdbFileChrStartEnd OnePass_SJ.out.tab --sjdbOverhang 75 --runThreadN 12
+		STAR --runMode genomeGenerate --genomeDir "./" --genomeFastaFiles ${ref_dir}/${fasta} --sjdbFileChrStartEnd OnePass_SJ.out.tab --sjdbOverhang 75 --runThreadN 12
 
 
-		STAR --genomeDir "./" --readFilesIn ${fastq_1} ${fastq_2} --readFilesCommand zcat --runThreadN 20 --outFileNamePrefix ${sample}_
+		STAR --genomeDir "./" --readFilesIn ${fastq_1} ${fastq_2} --readFilesCommand zcat --runThreadN 20 --outFileNamePrefix ${sample}_ --outSAMtype BAM SortedByCoordinate --outSAMattrRGline "ID:${sample}" "SM:${sample}" "PL:ILLUMINAL"
 	>>>
 
 	runtime {
-		docker:SAdocker
+		docker:docker
     	cluster: cluster_config
     	systemDisk: "cloud_ssd 40"
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File aligned_sam = "${sample}_Aligned.out.sam"
+		File sorted_bam = "${sample}_Aligned.sortedByCoord.out.bam"
+		File SJ_out_tab = "${sample}_SJ.out.tab"
+		File log_progress_out = "${sample}_Log.progress.out"
+		File log_final_out = "${sample}_Log.final.out"
+		File log_out = "${sample}_Log.out"
 	}
 }

workflow.wdl

@@ -1,5 +1,4 @@
 import "./tasks/mapping.wdl" as mapping
-import "./tasks/SamToBam.wdl" as SamToBam
 import "./tasks/indexBam.wdl" as indexBam
 import "./tasks/Metrics.wdl" as Metrics
 import "./tasks/Dedup.wdl" as Dedup
@@ -13,52 +12,28 @@ workflow {{ project_name }} {
 
 	File fastq_1
 	File fastq_2
-	File SAref_dir
-	File STref_dir
 	File dbsnp_dir
 	File dbsnp
 	File dbmills_dir
 	File db_mills
+	File STARref_dir
+    File ref_dir
 
 	String SENTIEON_INSTALL_DIR
 	String sample
-	String STdocker
-	String SAMdocker
-	String SAdocker
-	String PIdocker
-	String GATKdocker
 	String fasta
 	String disk_size
 	String cluster_config
 
-	String id
-	String library
-	String platform
-	String machine
-
 
 	call mapping.mapping as mapping {
 		input: 
-		SAref_dir=SAref_dir,
-		STref_dir=STref_dir,
 		sample=sample,
+		STARref_dir=STARref_dir,
+		ref_dir=ref_dir,
 		fasta=fasta,
 		fastq_1=fastq_1,
 		fastq_2=fastq_2,
-		SAdocker=SAdocker,
-		disk_size=disk_size,
-		cluster_config=cluster_config
-	}
-
-	call SamToBam.SamToBam as SamToBam {
-		input:
-		aligned_sam=mapping.aligned_sam,
-		sample=sample,
-		id=id,
-		library=library,
-		platform=platform,
-		machine=machine, 
-		PIdocker=PIdocker,
 		disk_size=disk_size,
 		cluster_config=cluster_config
 	}
@@ -66,21 +41,19 @@ workflow {{ project_name }} {
 	call indexBam.indexBam as indexBam {
 		input: 
 		sample=sample,
-		sorted_bam=SamToBam.sorted_bam,
-		SAMdocker=SAMdocker,
+		sorted_bam=mapping.sorted_bam,
 		disk_size=disk_size,
 		cluster_config=cluster_config
 	}
 
 	call Metrics.Metrics as Metrics {
 		input:
+		ref_dir=ref_dir,
 		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 		fasta=fasta,
-		STref_dir=STref_dir,
-		sorted_bam=SamToBam.sorted_bam,
+		sorted_bam=mapping.sorted_bam,
 		sorted_bam_index=indexBam.sorted_bam_index,		
 		sample=sample,
-		STdocker=STdocker,
 		disk_size=disk_size,
 		cluster_config=cluster_config
 	}
@@ -88,36 +61,33 @@ workflow {{ project_name }} {
 	call Dedup.Dedup as Dedup {
 		input:
 		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		sorted_bam=SamToBam.sorted_bam,
+		sorted_bam=mapping.sorted_bam,
 		sorted_bam_index=indexBam.sorted_bam_index,		
 		sample=sample,
-		STdocker=STdocker,
 		disk_size=disk_size,
 		cluster_config=cluster_config
 	}
 
 	call deduped_Metrics.deduped_Metrics as deduped_Metrics {
 		input:
+		ref_dir=ref_dir,
 		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 		fasta=fasta,
-		STref_dir=STref_dir,
 		Dedup_bam=Dedup.Dedup_bam,
 		Dedup_bam_index=Dedup.Dedup_bam_index,
 		sample=sample,
-		STdocker=STdocker,
 		disk_size=disk_size,
 		cluster_config=cluster_config
 	}
 
 	call SplitReads.SplitReads as SplitReads {
 		input:
+		ref_dir=ref_dir,
 		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 		fasta=fasta,
-		STref_dir=STref_dir,
 		Dedup_bam=Dedup.Dedup_bam,
 		Dedup_bam_index=Dedup.Dedup_bam_index,
 		sample=sample,
-		STdocker=STdocker,
 		disk_size=disk_size,
 		cluster_config=cluster_config
 	}
@@ -125,16 +95,15 @@ workflow {{ project_name }} {
 	call BQSR.BQSR as BQSR {
 		input:
 		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		ref_dir=ref_dir,
 		fasta=fasta,
 		dbsnp_dir=dbsnp_dir,
 		dbsnp=dbsnp,
 		dbmills_dir=dbmills_dir,
 		db_mills=db_mills,
-		STref_dir=STref_dir,
 		Split_bam=SplitReads.Split_bam,
 		Split_bam_index=SplitReads.Split_bam_index,
 		sample=sample,
-		STdocker=STdocker,
 		disk_size=disk_size,
 		cluster_config=cluster_config
 	}
@@ -143,28 +112,26 @@ workflow {{ project_name }} {
 		input:
 		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 		fasta=fasta,
-		STref_dir=STref_dir,
 		recaled_bam=BQSR.recaled_bam,
 		recaled_bam_index=BQSR.recaled_bam_index,
 		dbsnp_dir=dbsnp_dir,
 		dbsnp=dbsnp,
+		ref_dir=ref_dir,
 		sample=sample,
-		STdocker=STdocker,
 		disk_size=disk_size,
 		cluster_config=cluster_config
 	}
 
 	call Hardfiltration.Hardfiltration as Hardfiltration {
 		input:
+		ref_dir=ref_dir,
 		fasta=fasta,
-		STref_dir=STref_dir,
 		vcf_file=Haplotyper.vcf,
 		vcf_index=Haplotyper.vcf_idx,
 		sample=sample,
-		GATKdocker=GATKdocker,
 		disk_size=disk_size,
 		cluster_config=cluster_config
 	}
 
-	}
+}