Update: deduped_Matrics

tasks/deduped_Metrics.wdl

@@ -1,37 +1,45 @@
 task deduped_Metrics {
+    
+    File ref_dir
+    String SENTIEON_INSTALL_DIR
+    String SENTIEON_LICENSE
+    String sample
+    String fasta
+    File Dedup_bam
+    File Dedup_bam_index
+    String docker
+    String cluster_config
+    String disk_size
 
-	File ref_dir
-	String SENTIEON_INSTALL_DIR
-	String SENTIEON_LICENSE
-	String sample
-	String fasta
-	File Dedup_bam
-	File Dedup_bam_index
-	String docker
-	String cluster_config
-	String disk_size
 
+    command <<<
+        set -o pipefail
+        set -e
+        export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+        nt=$(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
+    >>>
 
-	command <<<
-		set -o pipefail
-		set -e
-		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
-		nt=$(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
-	>>>
+    runtime {
+        docker: docker
+        cluster: cluster_config
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" 
+    }
 
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" 
-	}
-
-	output {
-		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 = "${sample}_deduped_coverage_metrics.sample_interval_statistics"
-		File deduped_coverage_metrics_sample_cumulative_coverage_proportions = "${sample}_deduped_coverage_metrics.sample_cumulative_coverage_proportions"
-		File deduped_coverage_metrics_sample_cumulative_coverage_counts = "${sample}_deduped_coverage_metrics.sample_cumulative_coverage_counts"
-	}
+    output {
+        File deduped_coverage_metrics_sample_summary = "${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"
+        File deduped_coverage_metrics_sample_cumulative_coverage_proportions = "${sample}_deduped_coverage_metrics.sample_cumulative_coverage_proportions"
+        File deduped_coverage_metrics_sample_cumulative_coverage_counts = "${sample}_deduped_coverage_metrics.sample_cumulative_coverage_counts"
+        File deduped_mean_quality = "${sample}_deduped_mq_metrics.txt"
+        File deduped_qd_metrics = "${sample}_deduped_qd_metrics.txt"
+        File deduped_gc_summary = "${sample}_deduped_gc_summary.txt"
+        File deduped_gc_metrics = "${sample}_deduped_gc_metrics.txt"
+        File dedeuped_aln_metrics = "${sample}_deduped_aln_metrics.txt"
+        File deduped_is_metrics = "${sample}_deduped_is_metrics.txt"
+        File deduped_QualityYield = "${sample}_deduped_QualityYield.txt"
+        File deduped_wgsmetrics = "${sample}_deduped_WgsMetricsAlgo.txt"
+    }
 }