LUYAO REN
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tasks/benchmark.wdl
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| File ref_dir | File ref_dir | ||||
| File fasta | File fasta | ||||
| String sample = basename(vcf,".vcf.gz") | String sample = basename(vcf,".vcf.gz") | ||||
| String file_type = basename(vcf) | |||||
| String docker | String docker | ||||
| String cluster_config | String cluster_config | ||||
| String disk_size | String disk_size | ||||
| export HGREF=/cromwell_root/tmp/reference_data/GRCh38.d1.vd1.fa | export HGREF=/cromwell_root/tmp/reference_data/GRCh38.d1.vd1.fa | ||||
| if [[ ${sample} =~ "gz" ]];then | |||||
| if [[ ${file_type} =~ "gz" ]];then | |||||
| gunzip ${vcf} -c > unzip.vcf | gunzip ${vcf} -c > unzip.vcf | ||||
| else | else | ||||
| cp ${vcf} unzip.vcf | cp ${vcf} unzip.vcf |
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