sentieon quality yeild

tasks/deduped_Metrics.wdl

@@ -1,7 +1,6 @@
 task deduped_Metrics {
 
     File ref_dir
-    
 	String SENTIEON_INSTALL_DIR
 	String sample
 	String fasta
@@ -17,9 +16,7 @@ task deduped_Metrics {
 		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 QualityYield ${sample}_deduped_QualityYield
-
-		ls > file
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${Dedup_bam} --algo QualityYield ${sample}_deduped_QualityYield --algo WgsMetricsAlgo ${sample}_deduped_WgsMetricsAlgo --algo CoverageMetrics ${sample}_deduped_CoverageMetrics
 	>>>
 
 	runtime {
@@ -31,6 +28,7 @@ task deduped_Metrics {
 
 	output {
 		File deduped_QualityYield = "${sample}_deduped_QualityYield"
-		File files = "file"
+		File deduped_WgsMetricsAlgo = "${sample}_deduped_WgsMetricsAlgo"
+		File deduped_CoverageMetrics = "${sample}_deduped_CoverageMetrics"
 	}
 }