Fix bug: workflow

workflow.wdl

@@ -27,7 +27,7 @@ workflow {{ project_name }} {
   String disk_size
   
   if (fastq_1!= "") {
-    call mapping.mapping as mapping {
+    call mapping.mapping as fastq_mapping {
       input: 
       group=sample_id,
       sample=sample_id,
@@ -43,26 +43,26 @@ workflow {{ project_name }} {
       cluster_config=cluster_config
     }
 
-    call Dedup.Dedup as Dedup {
+    call Dedup.Dedup as fastq_Dedup {
       input:
       SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
       SENTIEON_LICENSE=SENTIEON_LICENSE,
-      sorted_bam=mapping.sorted_bam,
-      sorted_bam_index=mapping.sorted_bam_index,
+      sorted_bam=fastq_mapping.sorted_bam,
+      sorted_bam_index=fastq_mapping.sorted_bam_index,
       sample=sample_id,
       docker=sentieon_docker,
       disk_size=disk_size,
       cluster_config=cluster_config
     }
 
-    call Realigner.Realigner as Realigner {
+    call Realigner.Realigner as fastq_Realigner {
       input:
       SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
       SENTIEON_LICENSE=SENTIEON_LICENSE,
       fasta=fasta,
       ref_dir=ref_dir,
-      deduped_bam=Dedup.deduped_bam,
-      deduped_bam_index=Dedup.deduped_bam_index,
+      deduped_bam=fastq_Dedup.deduped_bam,
+      deduped_bam_index=fastq_Dedup.deduped_bam_index,
       db_mills=db_mills,
       dbmills_dir=dbmills_dir,
       docker=sentieon_docker,
@@ -70,14 +70,14 @@ workflow {{ project_name }} {
       cluster_config=cluster_config
     }
 
-    call BQSR.BQSR as BQSR {
+    call BQSR.BQSR as fastq_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,
+      realigned_bam=fastq_Realigner.realigner_bam,
+      realigned_bam_index=fastq_Realigner.realigner_bam_index,
       db_mills=db_mills,
       dbmills_dir=dbmills_dir,
       dbsnp=dbsnp,
@@ -87,24 +87,23 @@ workflow {{ project_name }} {
       cluster_config=cluster_config
     }
 
-    call PoN.PoN as PoN {
+    call PoN.PoN as fastq_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,
+      normal_bam=fastq_BQSR.recaled_bam,
+      normal_bam_index=fastq_BQSR.recaled_bam_index,
       docker=sentieon_docker,
       disk_size=disk_size,
       cluster_config=cluster_config
     }
   }
-
   
   if (deduped_bam!= "") {
-    call Realigner.Realigner as Realigner {
+    call Realigner.Realigner as bam_Realigner {
       input:
       SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
       SENTIEON_LICENSE=SENTIEON_LICENSE,
@@ -119,14 +118,14 @@ workflow {{ project_name }} {
       cluster_config=cluster_config
     }
 
-    call BQSR.BQSR as BQSR {
+    call BQSR.BQSR as bam_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,
+      realigned_bam=bam_Realigner.realigner_bam,
+      realigned_bam_index=bam_Realigner.realigner_bam_index,
       db_mills=db_mills,
       dbmills_dir=dbmills_dir,
       dbsnp=dbsnp,
@@ -136,15 +135,15 @@ workflow {{ project_name }} {
       cluster_config=cluster_config
     }
 
-    call PoN.PoN as PoN {
+    call PoN.PoN as bam_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,
+      normal_bam=bam_BQSR.recaled_bam,
+      normal_bam_index=bam_BQSR.recaled_bam_index,
       docker=sentieon_docker,
       disk_size=disk_size,
       cluster_config=cluster_config