Haonan917
2 years ago
1 changed files with 4 additions and 4 deletions
+ 4
- 4
tasks/deduped_Metrics.wdl
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| command <<< | command <<< | ||||
| set -o pipefail | set -o pipefail | ||||
| set -e | set -e | ||||
| java -jar picard.jar CollectAlignmentSummaryMetrics \ | |||||
| /usr/local/jdk-20.0.1/bin/java -jar /usr/local/picard.jar CollectAlignmentSummaryMetrics \ | |||||
| -I ${Dedup_bam} \ | -I ${Dedup_bam} \ | ||||
| -O ${sample}_deduped_aln_metrics.txt \ | -O ${sample}_deduped_aln_metrics.txt \ | ||||
| -R ${ref_dir}/${fasta} \ | -R ${ref_dir}/${fasta} \ | ||||
| --VALIDATION_STRINGENCY LENIENT | --VALIDATION_STRINGENCY LENIENT | ||||
| java -jar picard.jar CollectInsertSizeMetrics \ | |||||
| /usr/local/jdk-20.0.1/bin/java -jar /usr/local/picard.jar CollectInsertSizeMetrics \ | |||||
| -I ${Dedup_bam} \ | -I ${Dedup_bam} \ | ||||
| -O ${sample}_deduped_is_metrics.txt \ | -O ${sample}_deduped_is_metrics.txt \ | ||||
| -H ${sample}_deduped_is_metrics.pdf | -H ${sample}_deduped_is_metrics.pdf | ||||
| java -jar picard.jar CollectQualityYieldMetrics \ | |||||
| /usr/local/jdk-20.0.1/bin/java -jar /usr/local/picard.jar CollectQualityYieldMetrics \ | |||||
| -I ${Dedup_bam} \ | -I ${Dedup_bam} \ | ||||
| -O ${sample}_deduped_QualityYield.txt | -O ${sample}_deduped_QualityYield.txt | ||||
| java -jar picard.jar CollectWgsMetrics | |||||
| /usr/local/jdk-20.0.1/bin/java -jar /usr/local/picard.jar CollectWgsMetrics | |||||
| -I ${Dedup_bam} \ | -I ${Dedup_bam} \ | ||||
| -O ${sample}_deduped_WgsMetricsAlgo.txt \ | -O ${sample}_deduped_WgsMetricsAlgo.txt \ | ||||
| -R ${ref_dir}/${fasta} \ | -R ${ref_dir}/${fasta} \ |
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