first commit

workflow.wdl

@@ -25,8 +25,8 @@ workflow {{ project_name }} {
 		sample=sample_id,
 		fasta=fasta,
 		ref_dir=ref_dir,
-		normal_recaled_bam=BQSR.recaled_bam,
-		normal_recaled_bam_index=BQSR.recaled_bam_index,
+		normal_recaled_bam=normal_recaled_bam,
+		normal_recaled_bam_index=normal_recaled_bam_index,
 		cosmic_vcf=cosmic_vcf,
 		cosmic_dir=cosmic_dir,
 		dbsnp=dbsnp,