1 changed files with 3 additions and 2 deletions
+ 3
- 2
tasks/Haplotyper.wdl
View File
| @@ -15,13 +15,14 @@ task Haplotyper { | |||
| File? regions | |||
| Int? interval_padding | |||
| String INTERVAL = if regions then "--interval ${regions} --interval_padding ${interval_padding}" else "" | |||
| String | |||
| command <<< | |||
| set -o pipefail | |||
| set -e | |||
| export SENTIEON_LICENSE=192.168.0.55:8990 | |||
| nt=$(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 \ | |||
| -i ${recaled_bam} ${INTERVAL} \ | |||
| --algo Haplotyper -d ${dbsnp_dir}/${dbsnp} ${sample}_hc.vcf | |||
Loading…