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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,150 @@ | ||
| version 1.0 | ||
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| workflow GvsPrepareCallset { | ||
| input { | ||
| String data_project | ||
| String default_dataset | ||
| String destination_cohort_table_prefix | ||
| File? sample_names_to_extract | ||
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| # inputs with defaults | ||
| String query_project = data_project | ||
| Array[String]? query_labels | ||
| String destination_project = data_project | ||
| String destination_dataset = default_dataset | ||
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| String fq_petvet_dataset = "~{data_project}.~{default_dataset}" | ||
| String fq_sample_mapping_table = "~{data_project}.~{default_dataset}.sample_info" | ||
| String fq_temp_table_dataset = "~{destination_project}.temp_tables" | ||
| String fq_destination_dataset = "~{destination_project}.~{destination_dataset}" | ||
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| Int temp_table_ttl_in_hours = 72 | ||
| Boolean skip_vet_new_insert = false | ||
| String? service_account_json_path | ||
| String? docker | ||
| } | ||
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| String docker_final = select_first([docker, "us.gcr.io/broad-dsde-methods/variantstore:kc_ranges_prepare_2022_01_18"]) | ||
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| call PrepareRangesCallsetTask { | ||
| input: | ||
| destination_cohort_table_prefix = destination_cohort_table_prefix, | ||
| sample_names_to_extract = sample_names_to_extract, | ||
| query_project = query_project, | ||
| query_labels = query_labels, | ||
| fq_petvet_dataset = fq_petvet_dataset, | ||
| fq_sample_mapping_table = fq_sample_mapping_table, | ||
| fq_temp_table_dataset = fq_temp_table_dataset, | ||
| fq_destination_dataset = fq_destination_dataset, | ||
| temp_table_ttl_in_hours = temp_table_ttl_in_hours, | ||
| service_account_json_path = service_account_json_path, | ||
| docker = docker_final | ||
| } | ||
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| output { | ||
| String fq_cohort_extract_table_prefix = PrepareRangesCallsetTask.fq_cohort_extract_table_prefix | ||
| } | ||
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| } | ||
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| task PrepareRangesCallsetTask { | ||
| # indicates that this task should NOT be call cached | ||
| meta { | ||
| volatile: true | ||
| } | ||
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| input { | ||
| String destination_cohort_table_prefix | ||
| File? sample_names_to_extract | ||
| String query_project | ||
| Array[String]? query_labels | ||
|
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||
| String fq_petvet_dataset | ||
| String fq_sample_mapping_table | ||
| String fq_temp_table_dataset | ||
| String fq_destination_dataset | ||
| Int temp_table_ttl_in_hours | ||
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| String? service_account_json_path | ||
| String docker | ||
| } | ||
| # Note the coercion of optional query_labels using select_first([expr, default]) | ||
| Array[String] query_label_args = if defined(query_labels) then prefix("--query_labels ", select_first([query_labels])) else [] | ||
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| String has_service_account_file = if (defined(service_account_json_path)) then 'true' else 'false' | ||
| String use_sample_names_file = if (defined(sample_names_to_extract)) then 'true' else 'false' | ||
| String sample_list_param = if (defined(sample_names_to_extract)) then '--sample_names_to_extract sample_names_file' else '--fq_cohort_sample_names ' + fq_sample_mapping_table | ||
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| parameter_meta { | ||
| sample_names_to_extract: { | ||
| localization_optional: true | ||
| } | ||
| } | ||
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| command <<< | ||
| set -e | ||
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| echo ~{sample_list_param} | ||
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| if [ ~{has_service_account_file} = 'true' ]; then | ||
| gsutil cp ~{service_account_json_path} local.service_account.json | ||
| SERVICE_ACCOUNT_STANZA="--sa_key_path local.service_account.json " | ||
| fi | ||
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| if [ ~{use_sample_names_file} = 'true' ]; then | ||
| gsutil cp ~{sample_names_to_extract} sample_names_file | ||
| fi | ||
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| python3 /app/create_ranges_cohort_extract_data_table.py \ | ||
| --fq_ranges_dataset ~{fq_petvet_dataset} \ | ||
| --fq_temp_table_dataset ~{fq_temp_table_dataset} \ | ||
| --fq_destination_dataset ~{fq_destination_dataset} \ | ||
| --destination_cohort_table_prefix ~{destination_cohort_table_prefix} \ | ||
| ~{sample_list_param} \ | ||
| --query_project ~{query_project} \ | ||
| ~{sep=" " query_label_args} \ | ||
| --fq_sample_mapping_table ~{fq_sample_mapping_table} \ | ||
| --ttl ~{temp_table_ttl_in_hours} \ | ||
| $SERVICE_ACCOUNT_STANZA | ||
| >>> | ||
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| output { | ||
| String fq_cohort_extract_table_prefix = "~{fq_destination_dataset}.~{destination_cohort_table_prefix}" # implementation detail of create_cohort_extract_data_table.py | ||
| } | ||
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| runtime { | ||
| docker: docker | ||
| memory: "3 GB" | ||
| disks: "local-disk 100 HDD" | ||
| bootDiskSizeGb: 15 | ||
| preemptible: 0 | ||
| cpu: 1 | ||
| } | ||
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| } | ||
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| task LocalizeFile { | ||
| input { | ||
| String file | ||
| String service_account_json_path | ||
| } | ||
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| command { | ||
| set -euo pipefail | ||
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| gsutil cp ~{service_account_json_path} local.service_account.json | ||
| gcloud auth activate-service-account --key-file=local.service_account.json | ||
| gsutil cp '~{file}' . | ||
| } | ||
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| output { | ||
| File localized_file = basename(file) | ||
| } | ||
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| runtime { | ||
| docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:305.0.0" | ||
| memory: "3.75 GiB" | ||
| cpu: "1" | ||
| disks: "local-disk 50 HDD" | ||
| } | ||
| } |
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