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tasks/picard.wdl
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| set -o pipefail | set -o pipefail | ||||
| set -e | set -e | ||||
| nt=$(nproc) | nt=$(nproc) | ||||
| java -jar /usr/bin/picard/picard.jar LiftoverVcf I = ${vcf} O = ${sample}_picard.vcf CHAIN = ${chain_dir}/${chain} R = ${ref_dir}/${fasta} | |||||
| java -jar /usr/bin/picard/picard.jar LiftoverVcf I = ${vcf} O = ${sample}_picard.vcf REJECT=rejected_variants.vcf CHAIN = ${chain_dir}/${chain} R = ${ref_dir}/${fasta} | |||||
| >>> | >>> | ||||
| runtime { | runtime { | ||||
| output { | output { | ||||
| File picard_vcf = "${sample}_picard.vcf" | File picard_vcf = "${sample}_picard.vcf" | ||||
| File rejected_variants = "rejected_variants.vcf" | |||||
| } | } | ||||
| } | } |
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