[Documentation - Freyja] Update and revamp documentation to focus on non-SC2 organisms

[cimendes]

This PR closes nothing but is long-overdue with all the Freyja updates that have been done in the past!

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

🧠 Summary

This PR focuses solely on documentation improvements! No code changes have been made!

Did you know that Freyja now allows for native non-SC2 organisms' support? Neither do our collaborators! This PR is a collaborative effort to make the documentation better and more concise, given the explosion of applicabilities of freyja in the latest releases.

⚡ Impacted Workflows/Tasks

• Only Freyja's documentation has been changed. No code changes whatsoever!

This PR may lead to different results in pre-existing outputs: No

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

🛠️ Changes

• Only Freyja's documentation has been changed. No code changes whatsoever!

⚙️ Algorithm

N/A

➡️ Inputs

N/A

⬅️ Outputs

N/A

🧪 Testing

mkdocs serve was pleased, and so am I!

Suggested Scenarios for Reviewer to Test

Eyeball test of the new documentation! Feedback is much appreciated!

🔬 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 "Last Known Changes" field for any affected workflows in the respective workflow documentation page and for every entry in the three workflows_overview tables to be the tag for the next upcoming release. If you do not know the tag, please put "vX.X.X"

🎯 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]

can you collapse the parallel ont/illumina segments? they're the same overall steps, but you can just list the tools in separate lines.

maybe also indicate that the freyja_update is only for sc2 or something?

[sage-wright]

i made a change to the diagram since you're busy. LMK if you approve the changes

[sage-wright]

⭐ thanks for the updates!!