Output whole genome SNP matrix for Snippy_Streamline and Snippy_Tree workflows even when core_genome used

[jrotieno]

This PR closes #339.

🗑️ This dev branch should NOT be deleted after merging to main.

:brain: Aim, Context and Functionality

Knowing pairwise wgSNP distances is critical for assessing epi relationships, even when a core-genome tree is used. Currently, users have to run Snippy_Streamline_PHB or Snippy_Tree_PHB twice to get both a core tree and whole-genome SNP matrix, which is a bit cumbersome. This PR provides wgSNP matrix regardless of whether core or whole genome tree is made (in addition to cgSNP matrix if core_genome is used)

: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

New outputs produced for the Snippy_Streamline_PHB and Snippy_Tree_PHB workflows to produce wgSNP matrix regardless of whether core or whole genome tree is made (in addition to cgSNP matrix if core_genome is used)

The following workflows were impacted by adding the additional optional input midpoint_root_tree, but does not change the workflows in any way, unless the user changes the previous behaviour of the workflow by having the tree not mid-point rooted in the SNP matrix re-ordering task: Augur_PHB kSNP3_PHB Core_Gene_SNP_PHB MashTree_FASTA_PHB

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: N/A

Databases or database versions changed: N/A

Data processing/commands changed: Yes

We have added an optional input midpoint_root_tree that determines whether the tree used in the SNP matrix re-ordering task should be re-rooted or not. The default option is true, i.e. the tree will be mid-point rooted.

File processing changed: Yes Additional outputs as described above

Compute resources changed: N/A

➡️ Inputs

Added optional input midpoint_root_tree

⬅️ Outputs

The old output snippy_snp_matrix has been replaced with two new outputs snippy_wg_snp_matrix snippy_cg_snp_matrix

:test_tube: Testing

Test Dataset

Commandline Testing with MiniWDL or Cromwell (optional)

WDL Code passed check tests

Terra Testing

Snippy_Streamline_PHB with core_genome option set to true: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Doughty_Sandbox/job_history/a7295ae7-9980-4d82-97af-c550afbfcaef

Snippy_Streamline_PHB with core_genome option set to false: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Doughty_Sandbox/job_history/810ce538-aad6-41e5-a8c8-ee4b46d7de1c

Checks for changes in the kSNP3_PHB workflow: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Doughty_Sandbox/job_history/72d5ce6a-48d3-4d0a-84c3-857c56cb5454

Checks for changes in the MashTree_FASTA_PHB workflow: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Doughty_Sandbox/job_history/725b5847-7840-4617-8dd4-b8cb0c810d0d

Suggested Scenarios for Reviewer to Test

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

• [x] 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
• [x] 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
• [x] MD5 sums have been updated
• [x] The PR author has addressed all comments

🗂️ Associated Documentation (to be completed by Theiagen developer)

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

[sage-wright]

Testing the following scenarios; trees are compared to validation trees:

• kSNP3 with midpoint root = true on senterica_simulated dataset
  • resulting tree is as expected ✔️
• MashTree_FASTA with midpoint root = false on ecoli dataset
  • resulting tree is as expected ✔️
• Augur with default midpoint root (which is true) on sars-cov-2 dataset
  • resulting tree is as expected ✔️
• Snippy_Streamline with gubbins=true and core_genome=true on cjejuni dataset
  • resulting tree is as expected ✔️
  • outputs are as expected ✔️
• Snippy_Streamline with core_genome=false and gubbins=false on lmonocytogenes dataset
  • resulting tree is as expected ✔️
  • outputs are is as expected ✔️
• Core_Gene_SNP with pan=false and midpoint=false on senterica_tuna_scrape dataset
  • resulting tree is as expected ✔️