LUYAO REN
3 lat temu
1 zmienionych plików z 4 dodań i 4 usunięć
+ 4
- 4
tasks/benchmark.wdl
Wyświetl plik
| /opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${sample}.rtg.vcf.gz | /opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${sample}.rtg.vcf.gz | ||||
| if [[ ${sample} =~ "LCL5" ]];then | if [[ ${sample} =~ "LCL5" ]];then | ||||
| /opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL5.high.confidence.calls.vcf ${sample}.rtg.vcf.gz -f /cromwell_root/tmp/reference_datasets_v202103/high.confidence.exon.gencode.v36.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta} | |||||
| /opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL5.high.confidence.calls.vcf ${sample}.rtg.vcf.gz -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta} | |||||
| elif [[ ${sample} =~ "LCL6" ]]; then | elif [[ ${sample} =~ "LCL6" ]]; then | ||||
| /opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL6.high.confidence.calls.vcf ${sample}.rtg.vcf.gz -f /cromwell_root/tmp/reference_datasets_v202103/high.confidence.exon.gencode.v36.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta} | |||||
| /opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL6.high.confidence.calls.vcf ${sample}.rtg.vcf.gz -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta} | |||||
| elif [[ ${sample} =~ "LCL7" ]]; then | elif [[ ${sample} =~ "LCL7" ]]; then | ||||
| /opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL7.high.confidence.calls.vcf ${sample}.rtg.vcf.gz -f /cromwell_root/tmp/reference_datasets_v202103/high.confidence.exon.gencode.v36.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta} | |||||
| /opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL7.high.confidence.calls.vcf ${sample}.rtg.vcf.gz -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta} | |||||
| elif [[ ${sample} =~ "LCL8" ]]; then | elif [[ ${sample} =~ "LCL8" ]]; then | ||||
| /opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL8.high.confidence.calls.vcf ${sample}.rtg.vcf.gz -f /cromwell_root/tmp/reference_datasets_v202103/high.confidence.exon.gencode.v36.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta} | |||||
| /opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL8.high.confidence.calls.vcf ${sample}.rtg.vcf.gz -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta} | |||||
| else | else | ||||
| echo "only for quartet samples" | echo "only for quartet samples" | ||||
| fi | fi |
Ładowanie…