diff --git a/.dockstore.yml b/.dockstore.yml index cea493d9738..dabc17715ea 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -166,6 +166,7 @@ workflows: branches: - master - ah_var_store + - rsa_vs_1124 tags: - /.*/ - name: GvsImportGenomes @@ -235,6 +236,7 @@ workflows: branches: - master - ah_var_store + - rsa_vs_1124 tags: - /.*/ - name: GvsWithdrawSamples diff --git a/scripts/variantstore/wdl/GvsExtractCallset.wdl b/scripts/variantstore/wdl/GvsExtractCallset.wdl index 799fa5cbe57..526643c4c7c 100644 --- a/scripts/variantstore/wdl/GvsExtractCallset.wdl +++ b/scripts/variantstore/wdl/GvsExtractCallset.wdl @@ -18,6 +18,8 @@ workflow GvsExtractCallset { String query_project = project_id # This is optional now since the workflow will choose an appropriate value below if this is unspecified. Int? scatter_count + Int? memory_override + Int? disk_override Boolean zero_pad_output_vcf_filenames = true # set to "NONE" if all the reference data was loaded into GVS in GvsImportGenomes @@ -211,6 +213,8 @@ Int effective_split_intervals_disk_size_override = select_first([split_intervals max_last_modified_timestamp = GetBQTablesMaxLastModifiedTimestamp.max_last_modified_timestamp, extract_preemptible_override = extract_preemptible_override, extract_maxretries_override = extract_maxretries_override, + disk_override = disk_override, + memory_override = memory_override, emit_pls = emit_pls, emit_ads = emit_ads, write_cost_to_db = write_cost_to_db, @@ -304,6 +308,8 @@ task ExtractTask { File? gatk_override Int? extract_preemptible_override Int? extract_maxretries_override + Int? disk_override + Int? memory_override Int? local_sort_max_records_in_ram = 10000000 @@ -389,8 +395,8 @@ task ExtractTask { >>> runtime { docker: gatk_docker - memory: "12 GB" - disks: "local-disk 150 HDD" + memory: select_first([memory_override, 12]) + " GB" + disks: "local-disk " + select_first([disk_override, 150]) + " HDD" bootDiskSizeGb: 15 preemptible: select_first([extract_preemptible_override, "2"]) maxRetries: select_first([extract_maxretries_override, "3"]) diff --git a/scripts/variantstore/wdl/GvsExtractCohortFromSampleNames.wdl b/scripts/variantstore/wdl/GvsExtractCohortFromSampleNames.wdl index 206b6f0d6c0..3a6ea425ee1 100644 --- a/scripts/variantstore/wdl/GvsExtractCohortFromSampleNames.wdl +++ b/scripts/variantstore/wdl/GvsExtractCohortFromSampleNames.wdl @@ -26,7 +26,6 @@ workflow GvsExtractCohortFromSampleNames { String extraction_uuid String filter_set_name String output_file_base_name - Int? scatter_count String? output_gcs_dir # set to "NONE" if all the reference data was loaded into GVS in GvsImportGenomes @@ -34,6 +33,9 @@ workflow GvsExtractCohortFromSampleNames { Int? extract_preemptible_override Int? extract_maxretries_override + Int? extract_scatter_count_override + Int? extract_memory_override + Int? extract_disk_override Int? split_intervals_disk_size_override Int? split_intervals_mem_override @@ -56,17 +58,19 @@ workflow GvsExtractCohortFromSampleNames { call Utils.GetBQTableLastModifiedDatetime as SamplesTableDatetimeCheck { input: project_id = query_project, - fq_table = "~{gvs_project}.~{gvs_dataset}.sample_info" + fq_table = "~{gvs_project}.~{gvs_dataset}.sample_info", + cloud_sdk_docker = effective_cloud_sdk_docker } call Utils.GetNumSamplesLoaded { input: fq_sample_table = "~{gvs_project}.~{gvs_dataset}.sample_info", project_id = gvs_project, - sample_table_timestamp = SamplesTableDatetimeCheck.last_modified_timestamp + sample_table_timestamp = SamplesTableDatetimeCheck.last_modified_timestamp, + cloud_sdk_docker = effective_cloud_sdk_docker } - Int effective_scatter_count = if defined(scatter_count) then select_first([scatter_count]) + Int effective_scatter_count = if defined(extract_scatter_count_override) then select_first([extract_scatter_count_override]) else if GetNumSamplesLoaded.num_samples < 100 then 50 # Quickstart else if GetNumSamplesLoaded.num_samples < 1000 then 250 else if GetNumSamplesLoaded.num_samples < 5000 then 500 @@ -123,6 +127,8 @@ workflow GvsExtractCohortFromSampleNames { extract_maxretries_override = extract_maxretries_override, split_intervals_disk_size_override = split_intervals_disk_size_override, split_intervals_mem_override = split_intervals_mem_override, + memory_override = extract_memory_override, + disk_override = extract_disk_override, gatk_override = gatk_override, write_cost_to_db = write_cost_to_db