Alter: Varscan2 input is deduped BAM

workflow.wdl

@@ -302,10 +302,10 @@ workflow {{ project_name }} {
     call somatic.somatic as somatic {
       input:
       sample=sample_id,
-      tumor_bam=tumor_BQSR.recaled_bam,
-      tumor_bam_index=tumor_BQSR.recaled_bam_index,
-      normal_bam=normal_BQSR.recaled_bam,
-      normal_bam_index=normal_BQSR.recaled_bam_index,
+      tumor_bam=tumor_Dedup.deduped_bam,
+      tumor_bam_index=tumor_Dedup.deduped_bam_index,
+      normal_bam=normal_Dedup.deduped_bam,
+      normal_bam_index=normal_Dedup.deduped_bam_index,
       ref_dir=ref_dir,
       fasta=fasta,    
       docker=varscan_docker,