LUYAO REN
3 anni fa
1 ha cambiato i file con 4 aggiunte e 4 eliminazioni
+ 4
- 4
tasks/benchmark.wdl
Vedi File
| @@ -35,13 +35,13 @@ task benchmark { | |||
| /opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${sample}.rtg.vcf.gz | |||
| 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 | |||
| /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 | |||
| /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 | |||
| /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 | |||
| echo "only for quartet samples" | |||
| fi | |||
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