From 83df2835e5fea510796e18b0a12fa5c5756a75f1 Mon Sep 17 00:00:00 2001 From: gbggrant Date: Mon, 25 Nov 2024 13:25:00 -0500 Subject: [PATCH 1/2] Remove parameter_meta block with localization_optional --- scripts/variantstore/wdl/GvsExtractCallset.wdl | 9 --------- 1 file changed, 9 deletions(-) diff --git a/scripts/variantstore/wdl/GvsExtractCallset.wdl b/scripts/variantstore/wdl/GvsExtractCallset.wdl index a62bccb4cd5..622338d422a 100644 --- a/scripts/variantstore/wdl/GvsExtractCallset.wdl +++ b/scripts/variantstore/wdl/GvsExtractCallset.wdl @@ -516,15 +516,6 @@ task CreateManifestAndOptionallyCopyOutputs { String? output_gcs_dir String cloud_sdk_docker } - parameter_meta { - # Not `volatile: true` since there shouldn't be a need to re-run this if there has already been a successful execution. - output_vcfs: { - localization_optional: true - } - output_vcf_indices: { - localization_optional: true - } - } command <<< # Prepend date, time and pwd to xtrace log entries. From 3fe77990c398b71eedc1deed41625c0bf4805225 Mon Sep 17 00:00:00 2001 From: gbggrant Date: Mon, 25 Nov 2024 13:27:35 -0500 Subject: [PATCH 2/2] Add disk dynamic sizing. Fix input errors in GvsExtractCohortFromSampleNames.wdl --- scripts/variantstore/wdl/GvsExtractCallset.wdl | 4 +++- scripts/variantstore/wdl/GvsExtractCohortFromSampleNames.wdl | 2 -- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/scripts/variantstore/wdl/GvsExtractCallset.wdl b/scripts/variantstore/wdl/GvsExtractCallset.wdl index 622338d422a..2b433a9ad37 100644 --- a/scripts/variantstore/wdl/GvsExtractCallset.wdl +++ b/scripts/variantstore/wdl/GvsExtractCallset.wdl @@ -517,6 +517,8 @@ task CreateManifestAndOptionallyCopyOutputs { String cloud_sdk_docker } + Int disk_size_gb = ceil(2*size(output_vcfs, "GiB") + 2*size(output_vcf_indices, "GiB")) + 200 + command <<< # Prepend date, time and pwd to xtrace log entries. PS4='\D{+%F %T} \w $ ' @@ -575,7 +577,7 @@ task CreateManifestAndOptionallyCopyOutputs { runtime { docker: cloud_sdk_docker memory: "3 GB" - disks: "local-disk 500 HDD" + disks: "local-disk ${disk_size_gb} HDD" preemptible: 3 cpu: 1 } diff --git a/scripts/variantstore/wdl/GvsExtractCohortFromSampleNames.wdl b/scripts/variantstore/wdl/GvsExtractCohortFromSampleNames.wdl index dfab3823ef4..b28925e6755 100644 --- a/scripts/variantstore/wdl/GvsExtractCohortFromSampleNames.wdl +++ b/scripts/variantstore/wdl/GvsExtractCohortFromSampleNames.wdl @@ -126,7 +126,6 @@ workflow GvsExtractCohortFromSampleNames { destination_dataset = destination_dataset_name, fq_temp_table_dataset = fq_gvs_extraction_temp_tables_dataset, write_cost_to_db = write_cost_to_db, - cloud_sdk_docker = effective_cloud_sdk_docker, enable_extract_table_ttl = true, interval_list = effective_interval_list, control_samples = control_samples, @@ -165,7 +164,6 @@ workflow GvsExtractCohortFromSampleNames { control_samples = control_samples, cloud_sdk_docker = effective_cloud_sdk_docker, - gatk_docker = effective_gatk_docker, gatk_override = gatk_override, gatk_docker = effective_gatk_docker, git_hash = effective_git_hash,