VS-280 Create a VAT intermediary #7657
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rsasch
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| | workspace_namespace | name of the current workspace namespace | ## is this still needed? | ||
| | workspace_name | name of the current workspace | ## is this still needed? |
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I don't see either of these inputs in GvsAssignIds, so feel free to remove them.
rsasch
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| The first two of these inputs are two files — one of the file/vcf/shards you want to use for the VAT, and their corresponding index files. These are labelled as `inputFileofFileNames` and `inputFileofIndexFileNames` and need to be copied into a GCP bucket that this pipeline will have access to (eg. this bucket: `gs://aou-genomics-curation-prod-processing/vat/`) for easy access during the workflow. | ||
| The third input is the ancestry file from the ancestry pipeline which will be used to calculate AC, AN and AF for all subpopulations. It needs to be copied into a GCP bucket that this pipeline will have access to. This input has been labelled as the `ancestry_file`. | ||
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| Most of the other files are specific to where the VAT will live, like the project_id and dataset_name and the table_suffix which will name the VAT itself as vat_`table_suffix` as well as a GCP bucket location, the output_path, for the intermediary files and the VAT export in tsv form. |
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I thought the export for the VAT was CSV not TSV?
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| These numbers are cumulative. Also the names of these json files are retained from the original shard names so as to not cause collisions. If you run the same shards through the VAT twice, the second runs should overwrite the first and the total number of jsons should not change. | ||
| Once the shards have make it into the /genes/ and /vt/ directories, the majority of the expense and transformations needed for that shard are complete. | ||
| They are ready to be loaded into BQ. You will notice that past this step, all there is to do is create the BQ tables, load the BQ tables, run a join query and then the remaining steps are all validations or an export into tsv. |
rsasch
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This was referenced Mar 17, 2023
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Add an extensive and instructional ReadMe
Move the expensive step and the saving data step into a subworkflow to that they can complete their mission together in harmony even when a fellow shard has failed.