Update 'workflow.wdl'

workflow.wdl

@@ -513,10 +513,10 @@ workflow {{ project_name }} {
         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
         SENTIEON_LICENSE=SENTIEON_LICENSE,
         sample=sample_id,
-        normal_recaled_bam=normal_BQSR_fb.recaled_bam,
-        normal_recaled_bam_index=normal_BQSR_fb.recaled_bam_index,
-        tumor_recaled_bam=tumor_BQSR_fb.recaled_bam,
-        tumor_recaled_bam_index=tumor_BQSR_fb.recaled_bam_index,
+        normal_recaled_bam=normal_replaceRG.deduped_bam,
+        normal_recaled_bam_index=normal_replaceRG.deduped_bam_index,
+        tumor_recaled_bam=tumor_replaceRG.deduped_bam,
+        tumor_recaled_bam_index=tumor_replaceRG.deduped_bam_index,
         normal_name=sample_id + ".N",
         tumor_name=sample_id + ".T",
         fasta=fasta,
@@ -570,10 +570,10 @@ workflow {{ project_name }} {
         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
         SENTIEON_LICENSE=SENTIEON_LICENSE,
         sample=sample_id,
-        normal_recaled_bam=normal_BQSR_fb.recaled_bam,
-        normal_recaled_bam_index=normal_BQSR_fb.recaled_bam_index,
-        tumor_recaled_bam=tumor_BQSR_fb.recaled_bam,
-        tumor_recaled_bam_index=tumor_BQSR_fb.recaled_bam_index,
+        normal_recaled_bam=normal_replaceRG.deduped_bam,
+        normal_recaled_bam_index=normal_replaceRG.deduped_bam_index,
+        tumor_recaled_bam=tumor_replaceRG.deduped_bam,
+        tumor_recaled_bam_index=tumor_replaceRG.deduped_bam_index,
         normal_name=sample_id + ".N",
         tumor_name=sample_id + ".T",
         fasta=fasta,
@@ -625,10 +625,10 @@ workflow {{ project_name }} {
       call somatic.somatic as somatic_fb {
         input:
         sample=sample_id,
-        normal_bam=normal_BQSR_fb.recaled_bam,
-        normal_bam_index=normal_BQSR_fb.recaled_bam_index,
-        tumor_bam=tumor_BQSR_fb.recaled_bam,
-        tumor_bam_index=tumor_BQSR_fb.recaled_bam_index,
+        normal_recaled_bam=normal_replaceRG.deduped_bam,
+        normal_recaled_bam_index=normal_replaceRG.deduped_bam_index,
+        tumor_recaled_bam=tumor_replaceRG.deduped_bam,
+        tumor_recaled_bam_index=tumor_replaceRG.deduped_bam_index,
         ref_dir=ref_dir,
         fasta=fasta,    
         docker=varscan_docker,