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[Documentation] Update MIDAS database documentation in TheiaProk #667

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merged 1 commit into from
Nov 5, 2024

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fraser-combe
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@fraser-combe fraser-combe commented Nov 4, 2024

🗑️ This dev branch should be deleted after merging to main.

🧠 Summary

This PR updates the TheiaProk documentation to specify the use of the MIDAS v1.2 reference database as the default for bacterial species detection in metagenomic data. Minor adjustments for clarity were also made and indicate the user can also upload a custom database with link to midas github page to create new custom db

🔬 Final Developer Checklist

  • The workflow/task has been tested and results, including file contents, are as anticipated
  • The CI/CD has been adjusted and tests are passing (Theiagen developers)
  • Code changes follow the style guide
  • Documentation and/or workflow diagrams have been updated if applicable (Theiagen developers only)

🎯 Reviewer Checklist

  • All changed results have been confirmed
  • You have tested the PR appropriately (see the testing guide for more information)
  • All code adheres to the style guide
  • MD5 sums have been updated
  • The PR author has addressed all comments
  • The documentation has been updated

@fraser-combe fraser-combe requested a review from a team as a code owner November 4, 2024 02:25
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@fraser-combe, what other MIDAS DBs are out there that we could throw into a requestor-pays bucket & provide details to users? See how we do this for kraken, for reference of what I'm envisioning. https://theiagen.github.io/public_health_bioinformatics/latest/workflows/standalone/kraken2/?h=kraken#databases

EDIT: I completely forgot about a slack conversation that we had regarding this. There is only one DB, and it's been added to the documentation.

@AndrewLangvt AndrewLangvt merged commit 6566344 into main Nov 5, 2024
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@AndrewLangvt AndrewLangvt deleted the fc-midas-doc-update-dev branch November 5, 2024 17:00
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2 participants