[TheiaProk] Add additional input enabling characterization

[sage-wright]

This PR closes #545.

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

🧠 Aim, Context and Functionality

User requested ability to skip characterization and just perform assembly & assembly QC. This change adds the perform_characterization boolean which defaults to true. Users can set it to false to skip all genomic characterization

🛠️ 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/No

All TheiaProk workflows

📋 Workflow/Task Step Changes

• all organism specific tasks are thrown into the if (perform_characterization) { boolean switch.

🔄 Data Processing

Docker/software or software versions changed:

Databases or database versions changed:

Data processing/commands changed:

File processing changed:

Compute resources changed:

➡️ Inputs

• Boolean perform_characterization = true has been add to all TheiaProk workflows

⬅️ Outputs

• None. If perform_characterization = false then only read QC, assembly, and assembly QC will be performed

🧪 Testing

Test Dataset

PE success

Commandline Testing with MiniWDL or Cromwell (optional)

Terra Testing

Suggested Scenarios for Reviewer to Test

Theiagen Version Release Testing (optional)

🔬 Final Developer Checklist

• The workflow/task has been tested locally and results, including file contents, are as anticipated
• The workflow/task has been tested on Terra and results, including file contents, are as anticipated
• The CI/CD has been adjusted and tests are passing (to be completed by Theiagen developer)
• 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
• All reviewer-suggested scenarios have been tested and any additional
• 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
• All code adheres to the style guide
• MD5 sums have been updated
• 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

[kapsakcj]

Nice work, I reviewed the code and everything looks good (just hard to see diff because of indentation). I have no requested changes.

I made a new data table named PR547_test_sample for testing these changes. I launched a couple of samples per input data type (ILMN PE, SE, ONT, FASTA) with characterization on and off.

workflows launched:

• FASTA with characterization: https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/a4b89bfe-1516-41c6-bfb6-3eb88c0b6145
  • outputs look good, everything ran as expected ✅
• FASTA without characterization: https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/18ddcaf0-17fc-437a-bdb4-db99b69f47fd
  • outputs look good, only busco and quast ran as expected ✅
• ILMN PE with characterization: https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/be3446d0-d769-4d9a-97df-7f935027aed7
  • outputs look good, everything ran as expected ✅
• ILMN PE without characterization: https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/1ef9c32b-c3cb-4bd1-9b3c-31c20d74c842
  • outputs look good, only things that ran after assembly were busco, quast, cgpipline raw & clean ✅
• ILMN SE with characterization: https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/1ebf0587-32ec-4550-88c1-7cdaa8ac036e
  • outputs look good, everything ran as expected ✅
• ILMN SE without characterization: https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/a27ff891-f2c8-49eb-911d-817f43b1e0ce
  • outputs look good, only things that ran after assembly were busco, quast, cgpipline raw & clean ✅
• ONT with characterization: https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/4c778ffd-9e93-4e1b-afa5-2749d9a601dd
  • outputs look good, everything ran as expected ✅
• ONT without characterization: https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/f3de3b20-a57c-4cc2-9bfb-daaf5f01da5e
  • outputs look good, only things that ran after assembly were busco, quast, nanoplot raw & clean ✅

[kapsakcj]

Looks like documentation needs to be updated as I don't see the new optional input in the TheiaProk inputs table - could you please do that when you are able? I'll merge the PR once that is completed.

Not sure if we want to update the workflow diagram or not, might be useful to help highlight this new feature to users.