test10

tasks/deduped_Metrics.wdl

@@ -13,20 +13,20 @@ task deduped_Metrics {
 	command <<<
 		set -o pipefail
 		set -e
-		java -jar picard.jar CollectAlignmentSummaryMetrics \
+		/usr/local/jdk-20.0.1/bin/java -jar /usr/local/picard.jar CollectAlignmentSummaryMetrics \
 			-I ${Dedup_bam} \
 			-O ${sample}_deduped_aln_metrics.txt \
 			-R ${ref_dir}/${fasta} \
 			--VALIDATION_STRINGENCY LENIENT
-		java -jar picard.jar CollectInsertSizeMetrics \
+		/usr/local/jdk-20.0.1/bin/java -jar /usr/local/picard.jar CollectInsertSizeMetrics \
 			-I ${Dedup_bam} \
 			-O ${sample}_deduped_is_metrics.txt \
 			-H ${sample}_deduped_is_metrics.pdf
-		java -jar picard.jar CollectQualityYieldMetrics \
+		/usr/local/jdk-20.0.1/bin/java -jar /usr/local/picard.jar CollectQualityYieldMetrics \
 			-I ${Dedup_bam} \
 			-O ${sample}_deduped_QualityYield.txt
 
-		java -jar picard.jar CollectWgsMetrics 
+		/usr/local/jdk-20.0.1/bin/java -jar /usr/local/picard.jar CollectWgsMetrics 
 			-I ${Dedup_bam} \
 			-O ${sample}_deduped_WgsMetricsAlgo.txt \
 			-R ${ref_dir}/${fasta} \