1 changed files with 5 additions and 5 deletions
+ 5
- 5
tasks/TNseq.wdl
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| INTERVAL="" | INTERVAL="" | ||||
| fi | fi | ||||
| if [ ${normal_bam} ]; then | |||||
| #if [ ${normal_bam} ]; then | |||||
| INPUT="-i ${tumor_bam} -i ${normal_bam}" | INPUT="-i ${tumor_bam} -i ${normal_bam}" | ||||
| SAMPLE="--tumor_sample ${tumor_name} --normal_sample ${normal_name}" | SAMPLE="--tumor_sample ${tumor_name} --normal_sample ${normal_name}" | ||||
| else | |||||
| INPUT="-i ${tumor_bam}" | |||||
| SAMPLE="--tumor_sample ${tumor_name}" | |||||
| fi | |||||
| #else | |||||
| # INPUT="-i ${tumor_bam}" | |||||
| # SAMPLE="--tumor_sample ${tumor_name}" | |||||
| #fi | |||||
| sentieon driver -t $nt -r ${ref_dir}/${ref_fasta} \ | sentieon driver -t $nt -r ${ref_dir}/${ref_fasta} \ | ||||
| $INPUT $INTERVAL \ | $INPUT $INTERVAL \ |
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