[Kraken2] Update Krona to be compatible with viral data

[sage-wright]

This PR closes #278 and closes #518

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

🧠 Summary

Krona for a while now has been incompatible with viral data due to a weird quirk where viral data was appearing in the krona plots as "Other root" which wasn't really what we wanted. This PR preprocesses the Kraken2 reports with KrakenTools to make the viral data appear appropriately in the HTML plots.

⚡ Impacted Workflows/Tasks

• Kraken2s that use Krona (PE and SE)
• TheiaMeta

This PR may lead to different results in pre-existing outputs: Yes

• viral data will now appear properly

This PR uses an element that could cause duplicate runs to have different results: No

🛠️ Changes

⚙️ Algorithm

• the krona task now uses the following docker image: us-docker.pkg.dev/general-theiagen/staphb/krona:2.8.1
• krona task now runs kreport2krona before making the krona visualization
• no variables have been changed.

➡️ Inputs

None

⬅️ Outputs

None

🧪 Testing

• Kraken_PE
• Kraken_SE=
• TheiaMeta_Illumina_PE

Suggested Scenarios for Reviewer to Test

• viral and bacterial stuff to confirm nothing is broken unintentionally

🔬 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
  • You have updated the latest version for any affected worklows in the respective workflow documentation page and for every entry in the three workflows_overview tables.

🎯 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

[sage-wright]

@cimendes i will want your eyes on this because i'm not sure how good this approach is and if it is what we want

[cimendes]

@sage-wright any reason why this step is no longer needed? This was used to update the NCBI's taxonomy file.

[cimendes]

Now that I looked a little better, krImportText doesn't require a taxonomy file (source: https://github.com/marbl/Krona/wiki/Installing) so good call!

[cimendes]

For reference purposes: https://github.com/marbl/Krona/wiki/Importing-text-and-XML-data

[cimendes]

Overall I think this is a valid approach to getting those Krona reports. It relies on two dependencies instead of just one but I think it's a fair trade-off to get the viral components of a community represented in the final plots.
The affected workflows are as follows:

• Kraken2 Standalone:
  • ONT
  • PE
  • SE
• TheiaMeta PE

Let me know once it's ready for review and I'll start testing!

[sage-wright]

This doesn't affect Kraken ONT -- we're not running krona in that workflow