Fix bug: basename

tasks/BQSR.wdl

@@ -6,7 +6,6 @@ task BQSR {
   File dbmills_dir
   String db_mills
   
-  String sample=basename(realigned_bam, ".*")
   String SENTIEON_INSTALL_DIR
   String SENTIEON_LICENSE
   String fasta
@@ -17,6 +16,8 @@ task BQSR {
   String cluster_config
   String disk_size
 
+  String sample=basename(realigned_bam, ".*")
+
   command <<<
     set -o pipefail
     set -e

tasks/PoN.wdl

@@ -8,10 +8,11 @@ task PoN {
 
   File normal_bam
   File normal_bam_index
-  String sample=basename(normal_bam, ".*")
   String docker
   String cluster_config
   String disk_size
+
+  String sample=basename(normal_bam, ".*")
   
   command <<<
     set -o pipefail

tasks/Realigner.wdl

@@ -7,13 +7,14 @@ task Realigner {
 
   String SENTIEON_INSTALL_DIR
   String SENTIEON_LICENSE
-  String sample=basename(deduped_bam, ".*")
 
   File deduped_bam
   File deduped_bam_index
   String docker
   String cluster_config
   String disk_size
+
+  String sample=basename(deduped_bam, ".*")
   
   command <<<
     set -o pipefail