VS-1159 - Enhance GVSWithdrawSamples #8599
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| LEFT JOIN `~{dataset_name}.sample_info` sample_info ON sample_info.sample_name = callset.sample_name | ||
| WHERE sample_info.sample_name IS NULL' > new_samples.txt | ||
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| echo "The following samples in the uploaded list have NOT been loaded into ~{dataset_name}" |
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I worry this message might get missed...could this condition be checked first and generate an error if there are samples that need to be loaded?
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I wondered about this too, but the AC are to let it pass if there are samples that have not been loaded.
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But I kind of feel that it should fail if there are samples in the file that haven't been uploaded.
Co-authored-by: Miguel Covarrubias <[email protected]>
Co-authored-by: Miguel Covarrubias <[email protected]>
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My only request is that you update the docs (https://github.com/broadinstitute/gatk/blob/ah_var_store/scripts/variantstore/docs/aou/AOU_DELIVERABLES.md) to include what to do with the outputs (e.g. ingest the missing samples, make sure the number of samples that are withdrawn is as expected).
…outputs of GvsWithdrawSamples.
…es yet to be ingested in the list.
This PR updates GvsWithdrawSamples to:
A) Example Run with 0 samples withdrawn and 0 new samples (samples in the withdrawn file that aren't in sample_info)
B) Example Run with 1 sample withdrawn and 0 new samples (samples in the withdrawn file that aren't in sample_info)
C) Example Run with 1 sample withdrawn and 1 new sample (sample in the withdrawn file that wasn't in sample_info). This run was run with the override flag allowing it to pass
D) Example Run with 1 sample withdrawn and 1 new sample (sample in the withdrawn file that wasn't in sample_info). This run failed (as intended)