[TheiaMeta] Remove subworkflow for assembly with metaspades and pilon; remove exposed krakendb input from QC subworkflow

[cimendes]

This PR closes #364 and closes #337.

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

:brain: Aim, Context and Functionality

This PR removes the metaspades assembly subworkflow in favour of incorporating it within the theiameta workflow. This reduces the number of dependencies needed and makes the inputs a little bit more neat.

Additionally, PR #279 added kraken as part of the QC trim sub-workflow. This created conflicts and confusion within TheiaMeta that already incorporates kraken on both raw and clean-reads. The inputs have been hidden to facilitate usage of TheiaMeta.

: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 : No

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

Nothing has been changed.

Docker/software or software versions changed: None

Databases or database versions changed: None

Data processing/commands changed: None

File processing changed: None

Compute resources changed: None

➡️ Inputs

Nothing has been changed.

⬅️ Outputs

Nothing has been changed.

:test_tube: Testing

Test Dataset

Commandline Testing with MiniWDL or Cromwell (optional)

Not performed!

Terra Testing

Inputs show up as expected!

- TheiaMeta Illumina PE Functional Test

Suggested Scenarios for Reviewer to Test

Theiagen Version Release Testing (optional)

:microscope: Final Developer Checklist

• [ ] 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)

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

[kevinlibuit]

With these changes, is there a need to maintain the wf_metaspades_assembly.wdl subworkflow?

[cimendes]

With these changes, is there a need to maintain the wf_metaspades_assembly.wdl subworkflow?

None at all! Will remove :)

[kevinlibuit]

Ready for merge :)

[kevinlibuit]

Now for docs!