indexBam fix output

tasks/indexBam.wdl

@@ -1,8 +1,6 @@
 task indexBam {
 	File sorted_bam
 	String sample
-	String base = basename(sorted_bam,'.bam')
-	String bam_index = base + ".bam.bai"
 	String SAMdocker
 	String cluster_config
 	String disk_size
@@ -10,7 +8,7 @@ task indexBam {
 	command <<<
 		set -o pipefail
 		set -e	
-		/opt/conda/bin/samtools index ${sorted_bam}
+		/opt/conda/bin/samtools index ${sorted_bam} ${sample}.bam.bai
 	>>>
 
 	runtime {
@@ -20,6 +18,6 @@ task indexBam {
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File sorted_bam_index = bam_index
+		File sorted_bam_index = "${sample}.bam.bai"
 	}
 }