diff --git a/scripts/variantstore/wdl/GvsUtils.wdl b/scripts/variantstore/wdl/GvsUtils.wdl index cfc9012ea72..52cb56c41a8 100644 --- a/scripts/variantstore/wdl/GvsUtils.wdl +++ b/scripts/variantstore/wdl/GvsUtils.wdl @@ -72,7 +72,7 @@ task GetToolVersions { # GVS generally uses the smallest `alpine` version of the Google Cloud SDK as it suffices for most tasks, but # there are a handlful of tasks that require the larger GNU libc-based `slim`. String cloud_sdk_slim_docker = "gcr.io/google.com/cloudsdktool/cloud-sdk:435.0.0-slim" - String variants_docker = "us.gcr.io/broad-dsde-methods/variantstore:2023-11-30-alpine-38a6c5ce9" + String variants_docker = "us.gcr.io/broad-dsde-methods/variantstore:2023-11-30-alpine-02a0c5bd7" String gatk_docker = "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_10_31_e7746ce7c38a8226bcac5b89284782de2a4cdda1" String variants_nirvana_docker = "us.gcr.io/broad-dsde-methods/variantstore:nirvana_2022_10_19" String real_time_genomics_docker = "docker.io/realtimegenomics/rtg-tools:latest" diff --git a/scripts/variantstore/wdl/extract/create_ranges_cohort_extract_data_table.py b/scripts/variantstore/wdl/extract/create_ranges_cohort_extract_data_table.py index 399eaea4738..fd5dd7c5efc 100644 --- a/scripts/variantstore/wdl/extract/create_ranges_cohort_extract_data_table.py +++ b/scripts/variantstore/wdl/extract/create_ranges_cohort_extract_data_table.py @@ -110,20 +110,19 @@ def get_all_sample_ids(fq_destination_table_samples, only_output_vet_tables, fq_ def create_extract_samples_table(control_samples, fq_destination_table_samples, fq_sample_name_table, fq_sample_mapping_table, honor_withdrawn, extract_table_ttl): - ttl = "" if extract_table_ttl: ttl = "OPTIONS( expiration_timestamp=TIMESTAMP_ADD(CURRENT_TIMESTAMP(), INTERVAL 14 DAY))" sql = f""" - - CREATE OR REPLACE TABLE `{fq_destination_table_samples}` AS ( + CREATE OR REPLACE TABLE `{fq_destination_table_samples}` + {ttl} + AS ( SELECT m.sample_id, m.sample_name, m.is_loaded, {"m.withdrawn," if honor_withdrawn else "NULL as withdrawn,"} m.is_control FROM `{fq_sample_name_table}` s JOIN `{fq_sample_mapping_table}` m ON (s.sample_name = m.sample_name) WHERE m.is_loaded IS TRUE AND m.is_control = {control_samples} {"AND m.withdrawn IS NULL" if honor_withdrawn else ""} ) - {ttl} """ print(sql) @@ -164,6 +163,7 @@ def create_final_extract_ref_table(fq_destination_table_ref_data, extract_table_ ttl = "" if extract_table_ttl: ttl = "OPTIONS( expiration_timestamp=TIMESTAMP_ADD(CURRENT_TIMESTAMP(), INTERVAL 14 DAY))" + sql = f""" CREATE OR REPLACE TABLE `{fq_destination_table_ref_data}` (