[TheiaProk] Update default versions for TB-Profiler and tbp-parser

[sage-wright]

This PR closes #427

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

🧠 Summary

This PR implements several changes that were requested by users, and sets the default variant caller in TBProfiler to GATK. These changes lived on various different development branches that are very out of sync with the latest updates. This branch collects those changes.

Other changes include:

• TBProfiler task has been tidied
• TBProfiler version has been bumped to v6.4.0
• TBProfiler default variant caller is now GATK.
• tNGS options and other optional inputs to tbp-parser are now available to be modified by the user in merlin_magic
  • TBProfiler_tNGS is still the recommended method for analyzing tNGS data. However, some of the customization options may be of interest to WGS users
• a silent-ish syntax error has been corrected in tbp-parser
  • I was passing a WDL variable incorrectly to an awk script

⚡ Impacted Workflows/Tasks

• TBProfiler_tNGS
• TheiaProk_Illumina_PE
• TheiaProk_Illumina_SE

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

• TBProfiler outputs will be different due to using the WHO v2 mutation catalogue.
• tbp-parser results will also be changed since it relies on TBProfiler results.

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

🛠️ Changes

⚙️ Algorithm

TBProfiler -> v6.4.0
tbp-parser -> v2.0.0

➡️ Inputs

Boolean tbprofiler_additional_parameters -> Boolean call_tbp_parser
All tbp-parser optional inputs are now available for modification.

⬅️ Outputs

Int? tbprofiler_median_coverage -> Float? tbprofiler_median_depth

🧪 Testing

TheiaProk_Illumina_PE here

Suggested Scenarios for Reviewer to Test

🔬 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