GvsUnified WDL to wrap the 6 core GVS WDLs [VS-382] #7789
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,159 @@ | ||
| version 1.0 | ||
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| import "GvsAssignIds.wdl" as AssignIds | ||
| import "GvsImportGenomes.wdl" as ImportGenomes | ||
| import "GvsCreateAltAllele.wdl" as CreateAltAllele | ||
| import "GvsCreateFilterSet.wdl" as CreateFilterSet | ||
| import "GvsPrepareRangesCallset.wdl" as PrepareRangesCallset | ||
| import "GvsExtractCallset.wdl" as ExtractCallset | ||
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| workflow GvsUnified { | ||
| input { | ||
| # Begin GvsAssignIds | ||
| String dataset_name | ||
| String project_id | ||
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| Array[String] external_sample_names | ||
| Boolean samples_are_controls = false | ||
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| File? gatk_override | ||
| String? service_account_json_path | ||
| # End GvsAssignIds | ||
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| # Begin GvsImportGenomes | ||
| Array[File] input_vcfs | ||
| Array[File] input_vcf_indexes | ||
| File interval_list = "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.noCentromeres.noTelomeres.interval_list" | ||
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| Int? load_data_preemptible_override | ||
| Int? load_data_maxretries_override | ||
| # End GvsImportGenomes | ||
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| # Begin GvsCreateFilterSet | ||
| String filter_set_name | ||
| Array[String] indel_recalibration_annotation_values = ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"] | ||
| Int create_filter_set_scatter_count | ||
| Array[String] snp_recalibration_annotation_values = ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"] | ||
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| Int? INDEL_VQSR_max_gaussians_override = 4 | ||
| Int? INDEL_VQSR_mem_gb_override | ||
| Int? SNP_VQSR_max_gaussians_override = 6 | ||
| Int? SNP_VQSR_mem_gb_override | ||
| # End GvsCreateFilterSet | ||
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| # Begin GvsPrepareRangesCallset | ||
| String extract_table_prefix | ||
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| String query_project = project_id | ||
| String destination_project = project_id | ||
|
There was a problem hiding this comment. Why is destination_project needed? There was a problem hiding this comment. They are used with GvsExtractCohortFromSampleNames.wdl where the GVS dataset and the delivered/billed datasets might be different. |
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| String destination_dataset = dataset_name | ||
| String fq_temp_table_dataset = "~{destination_project}.~{destination_dataset}" | ||
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| Array[String]? query_labels | ||
| File? sample_names_to_extract | ||
| # End GvsPrepareRangesCallset | ||
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| # Begin GvsExtractCallset | ||
| Int extract_scatter_count | ||
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| File interval_weights_bed = "gs://broad-public-datasets/gvs/weights/gvs_vet_weights_1kb.bed" | ||
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| String extract_output_file_base_name = filter_set_name | ||
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| Int? extract_maxretries_override | ||
| Int? extract_preemptible_override | ||
| String? extract_output_gcs_dir | ||
| Int? split_intervals_disk_size_override | ||
| Int? split_intervals_mem_override | ||
| # End GvsExtractCallset | ||
| } | ||
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| call AssignIds.GvsAssignIds as AssignIds { | ||
| input: | ||
| dataset_name = dataset_name, | ||
| project_id = project_id, | ||
| external_sample_names = external_sample_names, | ||
| samples_are_controls = samples_are_controls, | ||
| assign_ids_gatk_override = gatk_override, | ||
| service_account_json_path = service_account_json_path | ||
| } | ||
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| call ImportGenomes.GvsImportGenomes { | ||
| input: | ||
| go = AssignIds.done, | ||
| dataset_name = dataset_name, | ||
| project_id = project_id, | ||
| external_sample_names = external_sample_names, | ||
| input_vcfs = input_vcfs, | ||
| input_vcf_indexes = input_vcf_indexes, | ||
| interval_list = interval_list, | ||
| load_data_preemptible_override = load_data_preemptible_override, | ||
| load_data_maxretries_override = load_data_maxretries_override, | ||
| load_data_gatk_override = gatk_override, | ||
| service_account_json_path = service_account_json_path | ||
| } | ||
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| call CreateAltAllele.GvsCreateAltAllele { | ||
| input: | ||
| go = GvsImportGenomes.done, | ||
| dataset_name = dataset_name, | ||
| project_id = project_id, | ||
| service_account_json_path = service_account_json_path | ||
| } | ||
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| call CreateFilterSet.GvsCreateFilterSet { | ||
| input: | ||
| go = GvsCreateAltAllele.done, | ||
| dataset_name = dataset_name, | ||
| project_id = project_id, | ||
| filter_set_name = filter_set_name, | ||
| indel_recalibration_annotation_values = indel_recalibration_annotation_values, | ||
| scatter_count = create_filter_set_scatter_count, | ||
| snp_recalibration_annotation_values = snp_recalibration_annotation_values, | ||
| interval_list = interval_list, | ||
| gatk_override = gatk_override, | ||
| INDEL_VQSR_max_gaussians_override = INDEL_VQSR_max_gaussians_override, | ||
| INDEL_VQSR_mem_gb_override = INDEL_VQSR_mem_gb_override, | ||
| service_account_json_path = service_account_json_path, | ||
| SNP_VQSR_max_gaussians_override = SNP_VQSR_max_gaussians_override, | ||
| SNP_VQSR_mem_gb_override = SNP_VQSR_mem_gb_override | ||
| } | ||
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| call PrepareRangesCallset.GvsPrepareCallset { | ||
| input: | ||
| go = GvsCreateFilterSet.done, | ||
| project_id = project_id, | ||
| dataset_name = dataset_name, | ||
| control_samples = samples_are_controls, | ||
| extract_table_prefix = extract_table_prefix, | ||
| query_project = query_project, | ||
| destination_project = destination_project, | ||
| destination_dataset = destination_dataset, | ||
| fq_temp_table_dataset = fq_temp_table_dataset, | ||
| query_labels = query_labels, | ||
| sample_names_to_extract = sample_names_to_extract, | ||
| service_account_json_path = service_account_json_path | ||
| } | ||
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| call ExtractCallset.GvsExtractCallset { | ||
| input: | ||
| go = GvsPrepareCallset.done, | ||
| dataset_name = dataset_name, | ||
| project_id = project_id, | ||
| control_samples = samples_are_controls, | ||
| extract_table_prefix = extract_table_prefix, | ||
| filter_set_name = filter_set_name, | ||
| query_project = query_project, | ||
| scatter_count = extract_scatter_count, | ||
| interval_list = interval_list, | ||
| interval_weights_bed = interval_weights_bed, | ||
| gatk_override = gatk_override, | ||
| output_file_base_name = extract_output_file_base_name, | ||
| extract_maxretries_override = extract_maxretries_override, | ||
| extract_preemptible_override = extract_preemptible_override, | ||
| output_gcs_dir = extract_output_gcs_dir, | ||
| service_account_json_path = service_account_json_path, | ||
| split_intervals_disk_size_override = split_intervals_disk_size_override, | ||
| split_intervals_mem_override = split_intervals_mem_override | ||
| } | ||
| } | ||
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Duplicate with that on line 56.
And why is this even needed?
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Good catch! I'm surprised WDL allows completely duplicate declarations like that 😦
The
queryanddestinationversions of project and dataset are used inGvsPrepareCallsetandGvsExtractCallset, though I do not know circumstances under which they would be used.There was a problem hiding this comment.
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They are used with GvsExtractCohortFromSampleNames.wdl where the GVS dataset and the delivered/billed datasets might be different.