[TheiaProk] expose hicap outputs in theiaprok_fasta and theiaprok_ont

This PR closes #285

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

:brain: Aim, Context and Functionality

In the TheiaProk_ONT and TheiaProk_FASTA workflow, the hicap task is launched for Haemophilus influenzae samples but the outputs are not currently included in the workflow outputs. This PR fixes this.

:hammer_and_wrench: Impacted Workflows/Tasks & Changes Being Made

TheiaProk_FASTA
- New outputs added to the main workflow and export_taxon table
TheiaProk_ONT
- New outputs added to the main workflow and export_taxon table

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

Docker/software or software versions changed: N/A

Databases or database versions changed: N/A

Data processing/commands changed: N/A

File processing changed: N/A

Compute resources changed: N/A

➡️ Inputs

No outputs have been modified.

⬅️ Outputs

New outputs:

String? hicap_serotype
String? hicap_genes
File? hicap_results_tsv
String? hicap_version
String? hicap_docker

:test_tube: Testing

Test Dataset

Commandline Testing with MiniWDL or Cromwell (optional)

Terra Testing

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

[ ] 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

theiagen / public_health_bioinformatics