bam and index location

tasks/Dedup.wdl

@@ -14,8 +14,8 @@ 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})
+		sentieon_bam=`basename ${sorted_bam}`
+		sentieon_bam_index=`basename ${sorted_bam_index}`
 		cp ${sorted_bam} .
 		cp ${sorted_bam_index} .
 		nt=$(nproc)

tasks/Metrics.wdl

@@ -19,8 +19,8 @@ task Metrics {
 		set -e
 		export SENTIEON_LICENSE=192.168.0.55:8990
 		nt=$(nproc)
-		sentieon_bam=basename(${sorted_bam})
-		sentieon_bam_index=basename(${sorted_bam_index})
+		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