diff --git a/.dockstore.yml b/.dockstore.yml index d6b3e3909b0..ac75c9358f6 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -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 @@ -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 @@ -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 diff --git a/scripts/variantstore/wdl/GvsAssignIds.wdl b/scripts/variantstore/wdl/GvsAssignIds.wdl index 18527bd68ec..d2366f2db88 100644 --- a/scripts/variantstore/wdl/GvsAssignIds.wdl +++ b/scripts/variantstore/wdl/GvsAssignIds.wdl @@ -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" } output { Boolean done = true diff --git a/scripts/variantstore/wdl/GvsBenchmarkExtractTask.wdl b/scripts/variantstore/wdl/GvsBenchmarkExtractTask.wdl index 4fbc43790f2..199ae972cb8 100644 --- a/scripts/variantstore/wdl/GvsBenchmarkExtractTask.wdl +++ b/scripts/variantstore/wdl/GvsBenchmarkExtractTask.wdl @@ -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://gvs_quickstart_storage/jars/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" diff --git a/scripts/variantstore/wdl/GvsCallsetCost.wdl b/scripts/variantstore/wdl/GvsCallsetCost.wdl index 10ce04a809e..ee773353709 100644 --- a/scripts/variantstore/wdl/GvsCallsetCost.wdl +++ b/scripts/variantstore/wdl/GvsCallsetCost.wdl @@ -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 { diff --git a/scripts/variantstore/wdl/GvsCreateAltAllele.wdl b/scripts/variantstore/wdl/GvsCreateAltAllele.wdl index 3651398f1a1..d46c3c318e1 100644 --- a/scripts/variantstore/wdl/GvsCreateAltAllele.wdl +++ b/scripts/variantstore/wdl/GvsCreateAltAllele.wdl @@ -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 diff --git a/scripts/variantstore/wdl/GvsCreateFilterSet.wdl b/scripts/variantstore/wdl/GvsCreateFilterSet.wdl index 3067ff20d04..2d106098b40 100644 --- a/scripts/variantstore/wdl/GvsCreateFilterSet.wdl +++ b/scripts/variantstore/wdl/GvsCreateFilterSet.wdl @@ -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://gvs_quickstart_storage/jars/gatk-package-4.2.0.0-552-g0f9780a-SNAPSHOT-local.jar" Int? INDEL_VQSR_max_gaussians_override = 4 Int? INDEL_VQSR_mem_gb_override diff --git a/scripts/variantstore/wdl/GvsCreateVAT.wdl b/scripts/variantstore/wdl/GvsCreateVAT.wdl index 503225640ff..b7c1cd068a8 100644 --- a/scripts/variantstore/wdl/GvsCreateVAT.wdl +++ b/scripts/variantstore/wdl/GvsCreateVAT.wdl @@ -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" diff --git a/scripts/variantstore/wdl/GvsCreateVATAnnotations.wdl b/scripts/variantstore/wdl/GvsCreateVATAnnotations.wdl index ede47f11348..17265fab23e 100644 --- a/scripts/variantstore/wdl/GvsCreateVATAnnotations.wdl +++ b/scripts/variantstore/wdl/GvsCreateVATAnnotations.wdl @@ -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 @@ -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" diff --git a/scripts/variantstore/wdl/GvsCreateVATFromAnnotations.wdl b/scripts/variantstore/wdl/GvsCreateVATFromAnnotations.wdl index b11fa4c7dea..2f53906152d 100644 --- a/scripts/variantstore/wdl/GvsCreateVATFromAnnotations.wdl +++ b/scripts/variantstore/wdl/GvsCreateVATFromAnnotations.wdl @@ -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" @@ -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" diff --git a/scripts/variantstore/wdl/GvsExtractCallset.wdl b/scripts/variantstore/wdl/GvsExtractCallset.wdl index 78f8600955b..c4d88bdbe7e 100644 --- a/scripts/variantstore/wdl/GvsExtractCallset.wdl +++ b/scripts/variantstore/wdl/GvsExtractCallset.wdl @@ -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://gvs_quickstart_storage/jars/gatk-package-4.2.0.0-552-g0f9780a-SNAPSHOT-local.jar" String output_file_base_name = filter_set_name diff --git a/scripts/variantstore/wdl/GvsImportGenomes.wdl b/scripts/variantstore/wdl/GvsImportGenomes.wdl index 6e766d3f101..d30ad7163c2 100644 --- a/scripts/variantstore/wdl/GvsImportGenomes.wdl +++ b/scripts/variantstore/wdl/GvsImportGenomes.wdl @@ -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://gvs_quickstart_storage/jars/gatk-package-4.2.0.0-552-g0f9780a-SNAPSHOT-local.jar" String? service_account_json_path } @@ -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 diff --git a/scripts/variantstore/wdl/GvsJointVariantCalling.wdl b/scripts/variantstore/wdl/GvsJointVariantCalling.wdl index 24cec5a7ec0..fa1b2fae4cc 100644 --- a/scripts/variantstore/wdl/GvsJointVariantCalling.wdl +++ b/scripts/variantstore/wdl/GvsJointVariantCalling.wdl @@ -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://gvs_quickstart_storage/jars/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"] diff --git a/scripts/variantstore/wdl/GvsPrepareRangesCallset.wdl b/scripts/variantstore/wdl/GvsPrepareRangesCallset.wdl index 7b760db652c..207f50c824b 100644 --- a/scripts/variantstore/wdl/GvsPrepareRangesCallset.wdl +++ b/scripts/variantstore/wdl/GvsPrepareRangesCallset.wdl @@ -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 diff --git a/scripts/variantstore/wdl/GvsUtils.wdl b/scripts/variantstore/wdl/GvsUtils.wdl index 67ba464a8e3..07307bbe29d 100644 --- a/scripts/variantstore/wdl/GvsUtils.wdl +++ b/scripts/variantstore/wdl/GvsUtils.wdl @@ -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