Fix bug: workflow

workflow.wdl

@@ -69,8 +69,40 @@ workflow {{ project_name }} {
       disk_size=disk_size,
       cluster_config=cluster_config
     }
+
+    call BQSR.BQSR as BQSR {
+      input:
+      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+      SENTIEON_LICENSE=SENTIEON_LICENSE,
+      fasta=fasta,
+      ref_dir=ref_dir,
+      realigned_bam=Realigner.realigner_bam,
+      realigned_bam_index=Realigner.realigner_bam_index,
+      db_mills=db_mills,
+      dbmills_dir=dbmills_dir,
+      dbsnp=dbsnp,
+      dbsnp_dir=dbsnp_dir,
+      docker=sentieon_docker,
+      disk_size=disk_size,
+      cluster_config=cluster_config
+    }
+
+    call PoN.PoN as PoN {
+      input:
+      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+      SENTIEON_LICENSE=SENTIEON_LICENSE,
+      fasta=fasta,
+      ref_dir=ref_dir,
+      regions=regions,
+      normal_bam=BQSR.recaled_bam,
+      normal_bam_index=BQSR.recaled_bam_index,
+      docker=sentieon_docker,
+      disk_size=disk_size,
+      cluster_config=cluster_config
+    }
   }
 
+  
   if (deduped_bam!= "") {
     call Realigner.Realigner as Realigner {
       input:
@@ -86,36 +118,36 @@ workflow {{ project_name }} {
       disk_size=disk_size,
       cluster_config=cluster_config
     }
-  }
-  
-  call BQSR.BQSR as BQSR {
-    input:
-    SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-    SENTIEON_LICENSE=SENTIEON_LICENSE,
-    fasta=fasta,
-    ref_dir=ref_dir,
-    realigned_bam=Realigner.realigner_bam,
-    realigned_bam_index=Realigner.realigner_bam_index,
-    db_mills=db_mills,
-    dbmills_dir=dbmills_dir,
-    dbsnp=dbsnp,
-    dbsnp_dir=dbsnp_dir,
-    docker=sentieon_docker,
-    disk_size=disk_size,
-    cluster_config=cluster_config
-  }
 
-  call PoN.PoN as PoN {
-    input:
-    SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-    SENTIEON_LICENSE=SENTIEON_LICENSE,
-    fasta=fasta,
-    ref_dir=ref_dir,
-    regions=regions,
-    normal_bam=BQSR.recaled_bam,
-    normal_bam_index=BQSR.recaled_bam_index,
-    docker=sentieon_docker,
-    disk_size=disk_size,
-    cluster_config=cluster_config
+    call BQSR.BQSR as BQSR {
+      input:
+      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+      SENTIEON_LICENSE=SENTIEON_LICENSE,
+      fasta=fasta,
+      ref_dir=ref_dir,
+      realigned_bam=Realigner.realigner_bam,
+      realigned_bam_index=Realigner.realigner_bam_index,
+      db_mills=db_mills,
+      dbmills_dir=dbmills_dir,
+      dbsnp=dbsnp,
+      dbsnp_dir=dbsnp_dir,
+      docker=sentieon_docker,
+      disk_size=disk_size,
+      cluster_config=cluster_config
+    }
+
+    call PoN.PoN as PoN {
+      input:
+      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+      SENTIEON_LICENSE=SENTIEON_LICENSE,
+      fasta=fasta,
+      ref_dir=ref_dir,
+      regions=regions,
+      normal_bam=BQSR.recaled_bam,
+      normal_bam_index=BQSR.recaled_bam_index,
+      docker=sentieon_docker,
+      disk_size=disk_size,
+      cluster_config=cluster_config
+    }
   }
 }