|
|
|
|
|
|
|
|
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" |
|
|
} |
|
|
} |
|
|
} |
|
|
} |