bam and index location

tasks/Dedup.wdl

@@ -14,9 +14,13 @@ task Dedup {
 		set -o pipefail
 		set -e
 		export SENTIEON_LICENSE=192.168.0.55:8990
+		sentieon_bam=basename(${sorted_bam})
+		sentieon_bam_index=basename(${sorted_bam_index})
+		cp ${sorted_bam} .
+		cp ${sorted_bam_index} .
 		nt=$(nproc)
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -i ${sorted_bam} --algo LocusCollector --fun score_info ${sample}_score.txt
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -i ${sorted_bam} --algo Dedup --rmdup --score_info ${sample}_score.txt --metrics ${sample}_dedup_metrics.txt ${sample}.sorted.deduped.bam	
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -i ${sentieon_bam} --algo LocusCollector --fun score_info ${sample}_score.txt
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -i ${sentieon_bam} --algo Dedup --rmdup --score_info ${sample}_score.txt --metrics ${sample}_dedup_metrics.txt ${sample}.sorted.deduped.bam	
 	>>>
 	runtime {
 		docker:STdocker

tasks/Metrics.wdl

@@ -19,7 +19,11 @@ task 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 ${sorted_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 ${sample}_coverage_metrics
+		sentieon_bam=basename(${sorted_bam})
+		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 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
 	>>>