implement GVS ID assignment #7355
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| workflow GvsAssignIds { | ||
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| input { | ||
| Array[String] external_sample_names |
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Would this be more usable as a File that we then do a read_lines on? Or have both options?
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we currently get this from the data model. is there a reason someone would use a file instead?
| echo "project_id = ~{project_id}" > ~/.bigqueryrc | ||
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| # create the lock table | ||
| bq --project_id=~{project_id} mk ~{dataset_name}.metadata_lock |
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just checking, this script exits with an error of the metadata_lock table already exists?
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also -- maybe we should name this differently now that this isn't going into the "metadata" table? sample_info_lock or sample_id_assignment_lock?
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also also… I'm surprised that this doesn't have to specify the schema when the table is created?
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will explicitly check whether the table exists and exit with error if it does.
renaming to sample_id_assignment_lock
adding schema when creating
| call GetMaxTableId { | ||
| input: | ||
| sample_map = sample_map | ||
| if (defined(sample_map)) { |
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What do we need the legacy mode for?
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will leaving this in be helpful for anyone? I wasn't sure if people had tests that used a sample map file. Although, this won't update the sample_info table anymore, so maybe I should just remove it. If anyone else has an opinion, let me know.
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Assign Ids to samples.
Update the sample info table.
Update import wdl to remove the generation of the sample_info.tsv files