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LUYAO REN vor 5 Jahren
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30278c1429
2 geänderte Dateien mit 16 neuen und 13 gelöschten Zeilen
  1. +14
    -13
      tasks/vcfeval.wdl
  2. +2
    -0
      workflow.wdl

+ 14
- 13
tasks/vcfeval.wdl Datei anzeigen

File giab_snv_idx File giab_snv_idx
File giab_indel File giab_indel
File giab_indel_idx File giab_indel_idx

File sdf File sdf
String kernel
String nu
String docker String docker
String cluster_config String cluster_config
String disk_size String disk_size
set -o pipefail set -o pipefail
set -e set -e
/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b ${giab_snv} -c ${snv_true_vcf} -o snv_true -t ${sdf}
/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b ${giab_snv} -c ${snv_true_vcf} -o ${kernel}_${nu}_snv_true -t ${sdf}


/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b ${giab_snv} -c ${snv_false_vcf} -o snv_false -t ${sdf}
/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b ${giab_snv} -c ${snv_false_vcf} -o ${kernel}_${nu}_snv_false -t ${sdf}


/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b ${giab_indel} -c ${indel_true_vcf} -o indel_true -t ${sdf}
/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b ${giab_indel} -c ${indel_true_vcf} -o ${kernel}_${nu}_indel_true -t ${sdf}


/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b ${giab_indel} -c ${indel_false_vcf} -o indel_false -t ${sdf}
/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b ${giab_indel} -c ${indel_false_vcf} -o ${kernel}_${nu}_indel_false -t ${sdf}


tar -zcvf snv_true.zip snv_true
tar -zcvf snv_false.zip snv_false
tar -zcvf indel_true.zip indel_true
tar -zcvf indel_false.zip indel_false
tar -zcvf ${kernel}_${nu}_snv_true.zip ${kernel}_${nu}_snv_true
tar -zcvf ${kernel}_${nu}_snv_false.zip ${kernel}_${nu}_snv_false
tar -zcvf ${kernel}_${nu}_indel_true.zip ${kernel}_${nu}_indel_true
tar -zcvf ${kernel}_${nu}_indel_false.zip ${kernel}_${nu}_indel_false


>>> >>>


dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
} }
output { output {
File snv_true_zip="snv_true.zip"
File snv_false_zip="snv_false.zip"
File indel_true_zip="indel_true.zip"
File indel_false_zip="indel_false.zip"
File snv_true_zip="${kernel}_${nu}_snv_true.zip"
File snv_false_zip="${kernel}_${nu}_snv_false.zip"
File indel_true_zip="${kernel}_${nu}_indel_true.zip"
File indel_false_zip="${kernel}_${nu}_indel_false.zip"
} }
} }

+ 2
- 0
workflow.wdl Datei anzeigen

giab_indel=giab_indel, giab_indel=giab_indel,
giab_indel_idx=giab_indel_idx, giab_indel_idx=giab_indel_idx,
sdf=sdf, sdf=sdf,
kernel=kernel,
nu=nu,
cluster_config=cluster_config, cluster_config=cluster_config,
disk_size=disk_size disk_size=disk_size
} }

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