更新 'workflow_total_pipeline.wdl'

workflow_total_pipeline.wdl

@@ -168,10 +168,10 @@ call TNseq.sentieon_TNseq as sentieon_TNseq{
 call TNscope.sentieon_TNscope as sentieon_TNscope{
 	input:
 		sample_id = sample_id,
-		tumor_bam = Sentieon_BQSR_tumor.recaled_bam,
-		tumor_bam_bai = Sentieon_BQSR_tumor.recaled_bam_index,
-		normal_bam = Sentieon_BQSR_normal.recaled_bam,
-		normal_bam_bai = Sentieon_BQSR_normal.recaled_bam_index,
+		tumor_bam = SentieonFastqToBam_tumor.deduped_bam,
+		tumor_bam_bai = SentieonFastqToBam_tumor.deduped_bam_bai,
+		normal_bam = SentieonFastqToBam_normal.deduped_bam,
+		normal_bam_bai = SentieonFastqToBam_normal.deduped_bam_bai,
 		tumor_name = sample_id+'_T',
 		normal_name = sample_id+'_N',
 		tumor_recall_data = Sentieon_BQSR_tumor.recal_table,