test09

tasks/Dedup.wdl

 
 		/usr/local/jdk-20.0.1/bin/java -jar /usr/local/picard.jar  MarkDuplicates \
 					-I ${sorted_bam}  \
-					-O ${sample}.sorted.deduped.bam 
+					-O ${sample}.sorted.deduped.bam \
 					-M ${sample}_dedup_metrics.txt \
 					--REMOVE_DUPLICATES
 					

tasks/deduped_Metrics.wdl

 	command <<<
 		set -o pipefail
 		set -e
-		java -jar picard.jar CollectAlignmentSummaryMetrics /
-			-I ${Dedup_bam} /
-			-O ${sample}_deduped_aln_metrics.txt /
-			-R ${ref_dir}/${fasta} /
+		java -jar picard.jar CollectAlignmentSummaryMetrics \
+			-I ${Dedup_bam} \
+			-O ${sample}_deduped_aln_metrics.txt \
+			-R ${ref_dir}/${fasta} \
 			--VALIDATION_STRINGENCY LENIENT
-		java -jar picard.jar CollectInsertSizeMetrics /
-			-I ${Dedup_bam} /
-			-O ${sample}_deduped_is_metrics.txt /
+		java -jar picard.jar CollectInsertSizeMetrics \
+			-I ${Dedup_bam} \
+			-O ${sample}_deduped_is_metrics.txt \
 			-H ${sample}_deduped_is_metrics.pdf
-		java -jar picard.jar CollectQualityYieldMetrics /
-			-I ${Dedup_bam} /
+		java -jar picard.jar CollectQualityYieldMetrics \
+			-I ${Dedup_bam} \
 			-O ${sample}_deduped_QualityYield.txt
 
 		java -jar picard.jar CollectWgsMetrics 
-			-I ${Dedup_bam} /
-			-O ${sample}_deduped_WgsMetricsAlgo.txt /
-			-R ${ref_dir}/${fasta} /
+			-I ${Dedup_bam} \
+			-O ${sample}_deduped_WgsMetricsAlgo.txt \
+			-R ${ref_dir}/${fasta} \
 			--VALIDATION_STRINGENCY LENIENT
 
 	>>>