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workflow_total_pipeline.wdl
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| @@ -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, | |||
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