[Cauris_Cladetyper] Various improvements and removal of old TheiaCauris references

[sage-wright]

This PR closes #601 and closes #419

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

🧠 Summary

This PR update the old Cauris_Cladetyper workflow to have improved outputs, better documentation, and removal of any references to theiacauris, which was a workflow that ended up being called TheiaEuk.

⚡ Impacted Workflows/Tasks

• Cauris_Cladetyper
• TheiaEuk_Illumina_PE
• task_cauris_cladetyper.wdl

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

⚙️ Algorithm

No

➡️ Inputs

None

⬅️ Outputs

Several outputs have been renamed.

In Cauris_Cladetyper_PHB:

• theiacauris_pe_wf_version -> cauris_cladetyper_wf_version
• theiacauris_pe_wf_analysis_date -> cauris_cladetyper_wf_analysis_date
• theiacauris_pe_clade_assignment -> cladetyper_clade
• theiacauris_pe_docker -> cladetyper_docker_image
• String? cladetyper_gambit_version
• String? cladetyper_annotated_reference

TheiaEuk_Illumina_PE no longer has the cladetyper_analysis_date output variable as that seemed silly. The following outputs were renamed:

• clade_type -> cladetyper_clade
• cladetyper_version -> cladetyper_gambit_version
• cladetype_annotated_ref -> cladetyper_annotated_reference

This now matches the outputs from Cauris_Cladetyper_PHB so that if both workflows are run on the same samples, columns that are named slightly differently but mean the same thing will no longer appear.

Internally:

Within the task_cauris_cladetyper.wdl task:

• clade_spec_ref -> annotated_reference
• version -> gambit_version

Subsequent references to these outputs in merlin_magic have been updated accordingly.

🧪 Testing

Cauris_Cladetyper
TheiaEuk_Illumina_PE

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
  • 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

[Michal-Babins]

Test Cauris_Cladetyper_PHB, and TheiaEuk_Illumina_PE validated.

[Michal-Babins]

PR addresses theiacauris references and moves them over to correctly reflect cladetyper prefex when referring to outputs. No changes to inputs, only documentation and outputs as well as how outputs are passed across theiaEuk. All test passed on terra and outputs lined up with what was expected. Outputs will change expectations in future runs that cladetyper_xxx will be the emebeded output pattern.