Fix bug: workflow

workflow.wdl

@@ -55,55 +55,67 @@ workflow {{ project_name }} {
       cluster_config=cluster_config
     }
 
-    File deduped_bam=Dedup.deduped_bam
-    File deduped_bam_index=Dedup.deduped_bam_index
-  }
-
-  if (deduped_bam!= "") {
     call Realigner.Realigner as Realigner {
       input:
       SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
       SENTIEON_LICENSE=SENTIEON_LICENSE,
       fasta=fasta,
       ref_dir=ref_dir,
-      deduped_bam=deduped_bam,
-      deduped_bam_index=deduped_bam_index,
+      deduped_bam=Dedup.deduped_bam,
+      deduped_bam_index=Dedup.deduped_bam_index,
       db_mills=db_mills,
       dbmills_dir=dbmills_dir,
       docker=sentieon_docker,
       disk_size=disk_size,
       cluster_config=cluster_config
     }
+  }
 
-    call BQSR.BQSR as BQSR {
+  if (deduped_bam!= "") {
+    call Realigner.Realigner as Realigner {
       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,
+      deduped_bam=deduped_bam,
+      deduped_bam_index=deduped_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 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 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
   }
 }