1 changed files with 5 additions and 5 deletions
+ 5
- 5
tasks/TNseq.wdl
View File
| nt=$(nproc) | nt=$(nproc) | ||||
| 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 \ | $INPUT \ |
Loading…