AoU GVS Cohort Extract wdl #7242
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| version 1.0 | ||
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| import "GvsPrepareCallset.wdl" as GvsPrepareCallset | ||
| import "GvsExtractCallset.wdl" as GvsExtractCallset | ||
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| # Workflow used by AoU to extract variants for a given cohort of sample_names | ||
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| workflow GvsExtractCohortFromSampleNames { | ||
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| input { | ||
| File cohort_sample_names | ||
| String query_project | ||
| String gvs_project | ||
| String gvs_dataset | ||
| String fq_gvs_extraction_cohorts_dataset | ||
| String fq_gvs_extraction_destination_dataset | ||
| String fq_gvs_extraction_temp_tables_dataset | ||
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There was a problem hiding this comment. You can make these 2 optional since they are defaulted in the called workflow. There was a problem hiding this comment. good catch. removed. regarding the two optionals though, do you mean the arguments on lines 16 and 17? those are passed directly into Prepare There was a problem hiding this comment. yes. if you make |
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| String extraction_uuid | ||
| String? output_gcs_dir | ||
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| # Extract parameters | ||
| File wgs_intervals | ||
| Int scatter_count | ||
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| File reference | ||
| File reference_index | ||
| File reference_dict | ||
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| String output_file_base_name | ||
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| Boolean do_not_filter_override = false | ||
| String? filter_set_name | ||
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There was a problem hiding this comment. should not be optional. or if optional, should default to a valid filter set name |
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| String fq_filter_set_info_table = "~{gvs_project}.~{gvs_dataset}.filter_set_info" | ||
| String fq_filter_set_site_table = "~{gvs_project}.~{gvs_dataset}.filter_set_sites" | ||
| String fq_filter_set_tranches_table = "~{gvs_project}.~{gvs_dataset}.filter_set_tranches" | ||
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There was a problem hiding this comment. I don't think you need to set these values or pass them to the workflow since they are defaulted in the workflow. If you want to allow the caller to set them, you should make them optional and then you would pass them into the workflow. |
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| # if these are unset, default sensitivity levels will be used | ||
| Float? snps_truth_sensitivity_filter_level_override | ||
| Float? indels_truth_sensitivity_filter_level_override | ||
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| File? gatk_override | ||
| } | ||
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| call GvsPrepareCallset.GvsPrepareCallset { | ||
| input: | ||
| destination_cohort_table_prefix = extraction_uuid, | ||
| sample_names_to_extract = cohort_sample_names, | ||
| data_project = query_project, | ||
| default_dataset = gvs_dataset, # unused if fq_* args are given | ||
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There was a problem hiding this comment. even though it's unused here, it still needs to be passed into the task |
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| fq_petvet_dataset = "~{gvs_project}.~{gvs_dataset}", | ||
| fq_sample_mapping_table = "~{gvs_project}.~{gvs_dataset}.sample_info", | ||
| fq_temp_table_dataset = fq_gvs_extraction_temp_tables_dataset, | ||
| fq_destination_dataset = fq_gvs_extraction_destination_dataset | ||
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There was a problem hiding this comment. maybe make these parameters in the definition of the task optional, since they are assigned defaults and then you won't have to pass the hard coded values There was a problem hiding this comment. so these do have defaults in There was a problem hiding this comment. ah, well then maybe add a comment that you are explicitly overriding the default values |
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| } | ||
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| call GvsExtractCallset.GvsExtractCallset { | ||
| input: | ||
| data_project = gvs_project, # unused if fq_filter_set_* args are given or filtering is off | ||
| query_project = query_project, | ||
| default_dataset = gvs_dataset, # unused if fq_filter_set_* args are given or filtering is off | ||
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| wgs_intervals = wgs_intervals, | ||
| scatter_count = scatter_count, | ||
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| reference = reference, | ||
| reference_index = reference_index, | ||
| reference_dict = reference_dict, | ||
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| fq_cohort_extract_table_prefix = GvsPrepareCallset.fq_cohort_extract_table_prefix, | ||
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| do_not_filter_override = do_not_filter_override, | ||
| filter_set_name = filter_set_name, | ||
| fq_filter_set_info_table = fq_filter_set_info_table, | ||
| fq_filter_set_site_table = fq_filter_set_site_table, | ||
| fq_filter_set_tranches_table = fq_filter_set_tranches_table, | ||
| snps_truth_sensitivity_filter_level_override = snps_truth_sensitivity_filter_level_override, | ||
| indels_truth_sensitivity_filter_level_override = indels_truth_sensitivity_filter_level_override, | ||
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| output_file_base_name = output_file_base_name, | ||
| output_gcs_dir = output_gcs_dir, | ||
| gatk_override = gatk_override | ||
| } | ||
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| } | ||
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Filter set name should not be optional. This will be named something that indicates which release of the filtering model the extract should use.
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should it be set even if filtering is not going to be used? for example, if do_not_filter_override is true, the argument will never be used
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oh, i didn't catch that. It's fine to be optional.