From 688b59c6d69008bedd8762ed613e8e9834334e4c Mon Sep 17 00:00:00 2001 From: gbggrant Date: Fri, 15 Apr 2022 14:38:28 -0400 Subject: [PATCH] Update to latest version of ah_var_store gatk override jar --- scripts/variantstore/wdl/GvsCreateFilterSet.wdl | 2 +- scripts/variantstore/wdl/GvsImportGenomes.wdl | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/variantstore/wdl/GvsCreateFilterSet.wdl b/scripts/variantstore/wdl/GvsCreateFilterSet.wdl index 76c88591e58..1192dc99c31 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/ah_var_store_20220406/gatk-package-4.2.0.0-480-gb62026a-SNAPSHOT-local.jar" + File gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/ah_var_store_20220415/gatk-package-4.2.0.0-492-g1387d47-SNAPSHOT-local.jar" Int? INDEL_VQSR_max_gaussians_override = 4 Int? INDEL_VQSR_mem_gb_override diff --git a/scripts/variantstore/wdl/GvsImportGenomes.wdl b/scripts/variantstore/wdl/GvsImportGenomes.wdl index fefabf2659c..584f6ad7433 100644 --- a/scripts/variantstore/wdl/GvsImportGenomes.wdl +++ b/scripts/variantstore/wdl/GvsImportGenomes.wdl @@ -14,7 +14,7 @@ workflow GvsImportGenomes { File interval_list = "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.noCentromeres.noTelomeres.interval_list" Int? load_data_preemptible_override Int? load_data_maxretries_override - File? load_data_gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/ah_var_store_20220406/gatk-package-4.2.0.0-480-gb62026a-SNAPSHOT-local.jar" + File? load_data_gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/ah_var_store_20220415/gatk-package-4.2.0.0-492-g1387d47-SNAPSHOT-local.jar" String? service_account_json_path }