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VS_492 - Beta User Jar release #7934

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merged 5 commits into from
Jul 11, 2022
Merged

VS_492 - Beta User Jar release #7934

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af2c874
updated a jar
gbggrant Jul 8, 2022
911ca31
Updated the override jars.
gbggrant Jul 8, 2022
ea0d3ff
Updated to latest docker
gbggrant Jul 8, 2022
6a75d3c
Add to .dockstore.yml
gbggrant Jul 8, 2022
dec034e
Put override jar in gs://gvs_quickstart_storage/jars
gbggrant Jul 11, 2022
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3 changes: 3 additions & 0 deletions .dockstore.yml
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Expand Up @@ -190,6 +190,7 @@ workflows:
- master
- ah_var_store
- rsa_metadata_from_python
- gg_VS-492_BetaUserJarRelease
- name: GvsJointVariantCalling
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsJointVariantCalling.wdl
Expand All @@ -199,6 +200,7 @@ workflows:
- ah_var_store
- rc-vs-483-beta-user-wdl
- vs_486_rightsize_import_batches
- gg_VS-492_BetaUserJarRelease
- name: GvsCalculatePrecisionAndSensitivity
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsCalculatePrecisionAndSensitivity.wdl
Expand All @@ -214,6 +216,7 @@ workflows:
- master
- ah_var_store
- rsa_metadata_from_python
- gg_VS-492_BetaUserJarRelease
- name: GvsIngestTieout
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsIngestTieout.wdl
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsAssignIds.wdl
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Expand Up @@ -214,7 +214,7 @@ task CreateCostObservabilityTable {
fi
>>>
runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:rsa_metadata_from_python_20220628"
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_08"
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are we sure our users will have access to this image? and/or is it public?

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poked around the methods GCR / GCS bucket and it and all images within it appears to be public

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us.gcr.io/broad-dsde-methods/variantstore is publicly accessible.

}
output {
Boolean done = true
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsBenchmarkExtractTask.wdl
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Expand Up @@ -47,7 +47,7 @@ workflow GvsBenchmarkExtractTask {

String output_file_base_name
String? output_gcs_dir
File? gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/kc_vqsr_magic_20220324/gatk-package-4.2.0.0-478-gd0e381c-SNAPSHOT-local.jar"
File? gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/ah_var_store_20220708/gatk-package-4.2.0.0-552-g0f9780a-SNAPSHOT-local.jar"
Int local_disk_for_extract = 150

String fq_samples_to_extract_table = "~{data_project}.~{default_dataset}.~{extract_table_prefix}__SAMPLES"
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsCallsetCost.wdl
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Expand Up @@ -63,7 +63,7 @@ task WorkflowComputeCosts {
>>>

runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:rsa_metadata_from_python_20220628"
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_08"
}

output {
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsCreateAltAllele.wdl
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Expand Up @@ -204,7 +204,7 @@ task PopulateAltAlleleTable {
$SERVICE_ACCOUNT_STANZA
>>>
runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:rsa_metadata_from_python_20220628"
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_08"
memory: "3 GB"
disks: "local-disk 10 HDD"
cpu: 1
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsCreateFilterSet.wdl
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Expand Up @@ -15,7 +15,7 @@ workflow GvsCreateFilterSet {
Array[String] snp_recalibration_annotation_values = ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"]

File interval_list = "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.noCentromeres.noTelomeres.interval_list"
File gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/gg_VS-479_gatk_cost_to_metadata_20220705/gatk-package-4.2.0.0-558-gf0b438a-SNAPSHOT-local.jar"
File gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/ah_var_store_20220708/gatk-package-4.2.0.0-552-g0f9780a-SNAPSHOT-local.jar"

Int? INDEL_VQSR_max_gaussians_override = 4
Int? INDEL_VQSR_mem_gb_override
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsCreateVAT.wdl
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Expand Up @@ -155,7 +155,7 @@ task MakeSubpopulationFiles {
# ------------------------------------------------
# Runtime settings:
runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:rsa_metadata_from_python_20220628"
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_08"
memory: "1 GB"
preemptible: 3
cpu: "1"
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4 changes: 2 additions & 2 deletions scripts/variantstore/wdl/GvsCreateVATAnnotations.wdl
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Expand Up @@ -186,7 +186,7 @@ task ExtractAnAcAfFromVCF {
# ------------------------------------------------
# Runtime settings:
runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:rsa_metadata_from_python_20220628"
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_08"
maxRetries: 3
memory: "16 GB"
preemptible: 3
Expand Down Expand Up @@ -317,7 +317,7 @@ task PrepAnnotationJson {
# ------------------------------------------------
# Runtime settings:
runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:rsa_metadata_from_python_20220628"
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_08"
memory: "8 GB"
preemptible: 5
cpu: "1"
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4 changes: 2 additions & 2 deletions scripts/variantstore/wdl/GvsCreateVATFromAnnotations.wdl
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Expand Up @@ -92,7 +92,7 @@ task GetAnnotations {
# ------------------------------------------------
# Runtime settings:
runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:rsa_metadata_from_python_20220628"
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_08"
memory: "1 GB"
preemptible: 3
cpu: "1"
Expand Down Expand Up @@ -151,7 +151,7 @@ task PrepAnnotationJson {
# ------------------------------------------------
# Runtime settings:
runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:rsa_metadata_from_python_20220628"
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_08"
memory: "8 GB"
preemptible: 5
cpu: "1"
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsExtractCallset.wdl
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Expand Up @@ -22,7 +22,7 @@ workflow GvsExtractCallset {

File interval_list = "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.noCentromeres.noTelomeres.interval_list"
File interval_weights_bed = "gs://broad-public-datasets/gvs/weights/gvs_vet_weights_1kb.bed"
File gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/gg_VS-479_gatk_cost_to_metadata_20220705/gatk-package-4.2.0.0-558-gf0b438a-SNAPSHOT-local.jar"
File gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/ah_var_store_20220708/gatk-package-4.2.0.0-552-g0f9780a-SNAPSHOT-local.jar"

String output_file_base_name = filter_set_name

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4 changes: 2 additions & 2 deletions scripts/variantstore/wdl/GvsImportGenomes.wdl
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Expand Up @@ -19,7 +19,7 @@ workflow GvsImportGenomes {
Int? load_data_batch_size
Int? load_data_preemptible_override
Int? load_data_maxretries_override
File? load_data_gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/gg_VS-443_VETIngestValidation_20220531/gatk-package-4.2.0.0-531-gf8f4ede-SNAPSHOT-local.jar"
File? load_data_gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/ah_var_store_20220708/gatk-package-4.2.0.0-552-g0f9780a-SNAPSHOT-local.jar"
String? service_account_json_path
}

Expand Down Expand Up @@ -426,7 +426,7 @@ task CurateInputLists {
--output_files True
>>>
runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:rsa_metadata_from_python_20220628"
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_08"
memory: "3 GB"
disks: "local-disk 100 HDD"
bootDiskSizeGb: 15
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsJointVariantCalling.wdl
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Expand Up @@ -35,7 +35,7 @@ workflow GvsJointVariantCalling {
Int SNP_VQSR_max_gaussians_override = 6
Int SNP_VQSR_mem_gb_override = ""
}
File gatk_override = "gs://gvs_quickstart_storage/jars/gatk-package-4.2.0.0-531-gf8f4ede-SNAPSHOT-local.jar"
File gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/ah_var_store_20220708/gatk-package-4.2.0.0-552-g0f9780a-SNAPSHOT-local.jar"
File interval_list = "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.noCentromeres.noTelomeres.interval_list"
Array[String] indel_recalibration_annotation_values = ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"]
Array[String] snp_recalibration_annotation_values = ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"]
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsPrepareRangesCallset.wdl
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Expand Up @@ -116,7 +116,7 @@ task PrepareRangesCallsetTask {
}

runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:rsa_metadata_from_python_20220628"
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_08"
memory: "3 GB"
disks: "local-disk 100 HDD"
bootDiskSizeGb: 15
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsUtils.wdl
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Expand Up @@ -367,7 +367,7 @@ task ScaleXYBedValues {
}

runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:rsa_metadata_from_python_20220628"
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_08"
maxRetries: 3
memory: "7 GB"
preemptible: 3
Expand Down