Alter: replaceRG output

tasks/replaceRG.wdl

@@ -21,8 +21,8 @@ task replaceRG {
     dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
   }
   output {
-    File bam = "${bam_name}.bam"
-    File bam_index = "${bam_name}.bam.bai"
+    File deduped_bam = "${bam_name}.bam"
+    File deduped_bam_index = "${bam_name}.bam.bai"
   }
 }
 

workflow.wdl

@@ -472,8 +472,8 @@ workflow {{ project_name }} {
         SENTIEON_LICENSE=SENTIEON_LICENSE,
         fasta=fasta,
         ref_dir=ref_dir,
-        deduped_bam=tumor_replaceRG.bam,
-        deduped_bam_index=tumor_replaceRG.bam_index,
+        deduped_bam=tumor_replaceRG.deduped_bam,
+        deduped_bam_index=tumor_replaceRG.deduped_bam_index,
         db_mills=db_mills,
         dbmills_dir=dbmills_dir,
         dbsnp=dbsnp,
@@ -496,15 +496,15 @@ workflow {{ project_name }} {
         disk_size=disk_size,
         cluster_config=cluster_config
       }
-      
+
       call BQSR.BQSR as normal_BQSR_fb {
         input:
         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
         SENTIEON_LICENSE=SENTIEON_LICENSE,
         fasta=fasta,
         ref_dir=ref_dir,
-        deduped_bam=normal_replaceRG.bam,
-        deduped_bam_index=normal_replaceRG.bam_index,
+        deduped_bam=normal_replaceRG.deduped_bam,
+        deduped_bam_index=normal_replaceRG.deduped_bam_index,
         db_mills=db_mills,
         dbmills_dir=dbmills_dir,
         dbsnp=dbsnp,