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feat(susie_finemapper): allow for extraction of the log file from manifest #859

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merged 4 commits into from
Oct 18, 2024

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@project-defiant project-defiant commented Oct 17, 2024

✨ Context

After successful run of ukb_ppp_eur finemapping we spotted, that the finemapping logs were saved along with the finemapping outputs - see thread.

This is not ideal and requires moving the logs after the finemapping is finished, which due to the number of files, takes significant amount of time ~30 minutes of GCSToGCSOperator.

To address this issue we want to save the logs into a separate directory.

🛠 What does this PR implement

  • infer log path from the manifest directly, when the log_path column is available in the manifest.

🙈 Missing

🚦 Before submitting

  • Do these changes cover one single feature (one change at a time)?
  • Did you read the contributor guideline?
  • Did you make sure to update the documentation with your changes?
  • Did you make sure there is no commented out code in this PR?
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  • Did you make sure the branch is up-to-date with the dev branch?
  • Did you write any new necessary tests?
  • Did you make sure the changes pass local tests (make test)?
  • Did you make sure the changes pass pre-commit rules (e.g poetry run pre-commit run --all-files)?

@project-defiant project-defiant merged commit d650a29 into dev Oct 18, 2024
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2 participants