test04

tasks/Realigner.wdl

@@ -1,41 +0,0 @@
-task Realigner {
-
-    File ref_dir
-    File dbmills_dir
-
-	String SENTIEON_INSTALL_DIR
-	String fasta
-
-	File Dedup_bam
-	File Dedup_bam_index
-	String sample = basename(Dedup_bam,".sorted.deduped.bam")
-	String db_mills
-	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/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${Dedup_bam} --algo Realigner -k ${dbmills_dir}/${db_mills} ${sample}.sorted.deduped.realigned.bam
-	
-	>>>
-
-	runtime {
-		docker:docker
-		cluster: cluster_config
-    	systemDisk: "cloud_ssd 40"
-    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File realigner_bam = "${sample}.sorted.deduped.realigned.bam"
-		File realigner_bam_index = "${sample}.sorted.deduped.realigned.bam.bai"
-
-	}
-}
-
-

tasks/deduped_Metrics.wdl

@@ -13,33 +13,15 @@ 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 /
-		# --algo QualityYield ${sample}_deduped_QualityYield.txt /
-		# --algo WgsMetricsAlgo ${sample}_deduped_WgsMetricsAlgo.txt
-		
-		# alignment stats
 		java -jar picard.jar CollectAlignmentSummaryMetrics /
 			-I ${Dedup_bam} /
 			-O ${sample}_deduped_aln_metrics.txt /
 			-R ${ref_dir}/${fasta} /
 			--VALIDATION_STRINGENCY LENIENT
-
-		# insert size stats
 		java -jar picard.jar CollectInsertSizeMetrics /
 			-I ${Dedup_bam} /
 			-O ${sample}_deduped_is_metrics.txt /
 			-H ${sample}_deduped_is_metrics.pdf
-
-		# quality yield stats
 		java -jar picard.jar CollectQualityYieldMetrics /
 			-I ${Dedup_bam} /
 			-O ${sample}_deduped_QualityYield.txt

workflow.wdl

@@ -5,7 +5,6 @@ import "./tasks/Dedup.wdl" as Dedup
 import "./tasks/qualimap.wdl" as qualimap
 import "./tasks/deduped_Metrics.wdl" as deduped_Metrics
 import "./tasks/sentieon.wdl" as sentieon
-import "./tasks/Realigner.wdl" as Realigner
 import "./tasks/BQSR.wdl" as BQSR
 import "./tasks/Haplotyper.wdl" as Haplotyper
 import "./tasks/benchmark.wdl" as benchmark