Fix bug: tumor sample SM tag is not present in the bam file

tasks/BQSR.wdl

@@ -6,7 +6,7 @@ task BQSR {
   File dbmills_dir
   String db_mills
   
-  String sample
+  String sample=basename(normal_bam, ".*")
   String SENTIEON_INSTALL_DIR
   String SENTIEON_LICENSE
   String fasta

tasks/PoN.wdl

@@ -8,7 +8,7 @@ task PoN {
 
   File normal_bam
   File normal_bam_index
-  String sample
+  String sample=basename(normal_bam, ".*")
   String docker
   String cluster_config
   String disk_size

tasks/Realigner.wdl

@@ -1,16 +1,16 @@
 task Realigner {
 
   File ref_dir
+  String fasta
   File dbmills_dir
+  String db_mills
 
   String SENTIEON_INSTALL_DIR
   String SENTIEON_LICENSE
-  String sample
-  String fasta
+  String sample=basename(normal_bam, ".*")
 
   File deduped_bam
   File deduped_bam_index
-  String db_mills
   String docker
   String cluster_config
   String disk_size

workflow.wdl

@@ -32,7 +32,6 @@ workflow {{ project_name }} {
     deduped_bam_index=deduped_bam_index,
     db_mills=db_mills,
     dbmills_dir=dbmills_dir,
-    sample=sample_id,
     docker=sentieon_docker,
     disk_size=disk_size,
     cluster_config=cluster_config
@@ -50,7 +49,6 @@ workflow {{ project_name }} {
     dbmills_dir=dbmills_dir,
     dbsnp=dbsnp,
     dbsnp_dir=dbsnp_dir,
-    sample=sample_id,
     docker=sentieon_docker,
     disk_size=disk_size,
     cluster_config=cluster_config
@@ -65,7 +63,6 @@ workflow {{ project_name }} {
     regions=regions,
     normal_bam=BQSR.recaled_bam,
     normal_bam_index=BQSR.recaled_bam_index,
-    sample=sample_id,
     docker=sentieon_docker,
     disk_size=disk_size,
     cluster_config=cluster_config