metrics fix

tasks/Metrics.wdl

@@ -23,9 +23,14 @@ 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 --algo MeanQualityByCycle ${sample}_mq_metrics.txt --algo QualDistribution ${sample}_qd_metrics.txt --algo GCBias --summary ${sample}_gc_summary.txt ${sample}_gc_metrics.txt --algo AlignmentStat ${sample}_aln_metrics.txt --algo InsertSizeMetricAlgo ${sample}_is_metrics.txt --algo CoverageMetrics --omit_base_output ${sample}_coverage_metrics
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${STref_dir}/${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 \
+		--algo InsertSizeMetricAlgo ${sample}_is_metrics.txt \
+		--algo AlignmentStat ${sample}_aln_metrics.txt \
+		--algo CoverageMetrics --omit_base_output ${sample}_coverage_metrics
 
-		${SENTIEON_INSTALL_DIR}/bin/sentieon plot metrics -o ${sample}_metrics_report.pdf gc=${sample}_gc_metrics.txt qd=${sample}_qd_metrics.txt mq=${sample}_mq_metrics.txt isize=${sample}_is_metrics.txt
 	>>>
 	
 	runtime {
@@ -36,14 +41,10 @@ task Metrics {
 	}
 	output {
 		File qd_metrics = "${sample}_qd_metrics.txt"
-		File qd_metrics_pdf = "${sample}_qd_metrics.pdf"
 		File mq_metrics = "${sample}_mq_metrics.txt"
-		File mq_metrics_pdf = "${sample}_mq_metrics.pdf"
 		File is_metrics = "${sample}_is_metrics.txt"
-		File is_metrics_pdf = "${sample}_is_metrics.pdf"
 		File gc_summary = "${sample}_gc_summary.txt"
 		File gc_metrics = "${sample}_gc_metrics.txt"
-		File gc_metrics_pdf = "${sample}_gc_metrics.pdf"
 		File aln_metrics = "${sample}_aln_metrics.txt"
 		File coverage_metrics_sample_summary = "${sample}_coverage_metrics.sample_summary"
 		File coverage_metrics_sample_statistics = "${sample}_coverage_metrics.sample_statistics"

tasks/deduped_Metrics.wdl

@@ -17,7 +17,13 @@ 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} --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
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${STref_dir}/${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
 	>>>
 
 	runtime {
@@ -28,6 +34,12 @@ task deduped_Metrics {
 	}
 
 	output {
+		File deduped_qd_metrics = "${sample}_deduped_qd_metrics.txt"
+		File deduped_mq_metrics = "${sample}_deduped_mq_metrics.txt"
+		File deduped_is_metrics = "${sample}_deduped_is_metrics.txt"
+		File deduped_gc_summary = "${sample}_deduped_gc_summary.txt"
+		File deduped_gc_metrics = "${sample}_deduped_gc_metrics.txt"
+		File deduped_aln_metrics = "${sample}_deduped_aln_metrics.txt"
 		File deduped_coverage_metrics_sample_summary = "${sample}_deduped_coverage_metrics.sample_summary"
 		File deduped_coverage_metrics_sample_statistics = "${sample}_deduped_coverage_metrics.sample_statistics"
 		File deduped_coverage_metrics_sample_interval_statistics = "${sample}_deduped_coverage_metrics.sample_interval_statistics"