[kSNP3] fix behaviour when phandango colouring is set to false

This PR closes #420 This PR closes #465 This PR closes #497

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

:brain: Aim, Context and Functionality

This PR makes some changes to kSNP3 and other phylogenetic inference workflows that rely on the reorder_matrix task (augur, core_gene_snp, mashtree_fasta, snippy_tree and snippy_streamline).

Now the matrix produced will no longer have cell A1 populated, making it compatible with (hopefully) most downstream applications such as phangando and MicrobeTrace.
Phandango coloring is no longer set to true by default. When set to true it will affect two outputs:
- The summarize data optional module if activated
- The snp matrix produced after reordering

:hammer_and_wrench: Impacted Workflows/Tasks & Changes Being Made

This will affect the behavior of the workflow(s) even if users don’t change any workflow inputs relative to the last version : Yes, Phandango coloring is no longer on by default

Running this workflow on different occasions could result in different results, e.g. due to use of a live database, "latest" docker image, or stochastic data processing : No

:clipboard: Workflow/Task Step Changes

🔄 Data Processing

Docker/software or software versions changed: None

Databases or database versions changed: None

Data processing/commands changed: Phandango coloring is now set to false by default

File processing changed: None

Compute resources changed: None

➡️ Inputs

Various input samples for all workflows tested, representing a large diversity of scenarios.

⬅️ Outputs

:test_tube: Testing

Test Dataset

Commandline Testing with MiniWDL or Cromwell (optional)

kSNP3 was tested locally with both true and false settings for phandango_coloring

Terra Testing

Suggested Scenarios for Reviewer to Test

I believe I tested all the scenarios but a second pair of eyes would be great!

Theiagen Version Release Testing (optional)

:microscope: Final Developer Checklist

[x] The workflow/task has been tested locally and results, including file contents, are as anticipated
[x] The workflow/task has been tested on Terra and results, including file contents, are as anticipated
[x] The CI/CD has been adjusted and tests are passing (to be completed by Theiagen developer)
[x] Code changes follow the style guide

🎯 Reviewer Checklist

[ ] All impacted workflows/tasks have been tested on Terra with a different dataset than used for development
[x] All reviewer-suggested scenarios have been tested and any additional
[x] All changed results have been confirmed to be accurate
[ ] All workflows/tasks impacted by change/s have been tested using a standard validation dataset to ensure no unintended change of functionality
[x] All code adheres to the style guide
[ ] MD5 sums have been updated
[x] The PR author has addressed all comments

🗂️ Associated Documentation (to be completed by Theiagen developer)

[ ] Relevant documentation on the Public Health Resources "PHB Main" has been updated
[ ] Workflow diagrams have been updated to reflect changes

theiagen / public_health_bioinformatics