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Gg revert localization optional on extract copy #9056

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merged 3 commits into from
Nov 26, 2024
Merged

Gg revert localization optional on extract copy #9056

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83df283
Remove parameter_meta block with localization_optional
gbggrant Nov 25, 2024
3fe7799
Add disk dynamic sizing.
gbggrant Nov 25, 2024
4b5584d
Merge remote-tracking branch 'origin/rwb_echo_release' into gg_Revert…
gbggrant Nov 26, 2024
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13 changes: 3 additions & 10 deletions scripts/variantstore/wdl/GvsExtractCallset.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -516,15 +516,8 @@ task CreateManifestAndOptionallyCopyOutputs {
String? output_gcs_dir
String cloud_sdk_docker
}
parameter_meta {
# Not `volatile: true` since there shouldn't be a need to re-run this if there has already been a successful execution.
output_vcfs: {
localization_optional: true
}
output_vcf_indices: {
localization_optional: true
}
}

Int disk_size_gb = ceil(2*size(output_vcfs, "GiB") + 2*size(output_vcf_indices, "GiB")) + 200

command <<<
# Prepend date, time and pwd to xtrace log entries.
Expand Down Expand Up @@ -584,7 +577,7 @@ task CreateManifestAndOptionallyCopyOutputs {
runtime {
docker: cloud_sdk_docker
memory: "3 GB"
disks: "local-disk 500 HDD"
disks: "local-disk ${disk_size_gb} HDD"
preemptible: 3
cpu: 1
}
Expand Down
2 changes: 0 additions & 2 deletions scripts/variantstore/wdl/GvsExtractCohortFromSampleNames.wdl
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Expand Up @@ -126,7 +126,6 @@ workflow GvsExtractCohortFromSampleNames {
destination_dataset = destination_dataset_name,
fq_temp_table_dataset = fq_gvs_extraction_temp_tables_dataset,
write_cost_to_db = write_cost_to_db,
cloud_sdk_docker = effective_cloud_sdk_docker,
enable_extract_table_ttl = true,
interval_list = effective_interval_list,
control_samples = control_samples,
Expand Down Expand Up @@ -165,7 +164,6 @@ workflow GvsExtractCohortFromSampleNames {
control_samples = control_samples,

cloud_sdk_docker = effective_cloud_sdk_docker,
gatk_docker = effective_gatk_docker,
gatk_override = gatk_override,
gatk_docker = effective_gatk_docker,
git_hash = effective_git_hash,
Expand Down
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