1 změnil soubory, kde provedl 3 přidání a 2 odebrání
+ 3
- 2
tasks/Haplotyper.wdl
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| File? regions | File? regions | ||||
| Int? interval_padding | Int? interval_padding | ||||
| String INTERVAL = if regions then "--interval ${regions} --interval_padding ${interval_padding}" else "" | |||||
| String | |||||
| command <<< | command <<< | ||||
| set -o pipefail | set -o pipefail | ||||
| set -e | set -e | ||||
| export SENTIEON_LICENSE=192.168.0.55:8990 | export SENTIEON_LICENSE=192.168.0.55:8990 | ||||
| nt=$(nproc) | |||||
| nt=$(nproc) | |||||
| if ${regions} then INTERVAL="--interval ${regions} --interval_padding ${interval_padding}" else INTERVAL="" | |||||
| ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt \ | ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt \ | ||||
| -i ${recaled_bam} ${INTERVAL} \ | -i ${recaled_bam} ${INTERVAL} \ | ||||
| --algo Haplotyper -d ${dbsnp_dir}/${dbsnp} ${sample}_hc.vcf | --algo Haplotyper -d ${dbsnp_dir}/${dbsnp} ${sample}_hc.vcf |
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