[TheiaMeta] krona bugfix for NCBI taxon IDs & reduce compute resources

Keeping as draft for now, I am working on reproducing the original bug reported in #518 ; Do not include in v2.1.0 release

This PR closes #518

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

:brain: Aim, Context and Functionality

A user alerted to us that krona plots produced by TheiaMeta workflow were not accurately displaying the NCBI taxonomy ID.

: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

Docker/software or software versions changed: N/A

Databases or database versions changed: N/A

Data processing/commands changed: added -t 5 to krona command so that 5th column of kraken2 report is used for NCBI taxon IDs

File processing changed: N/A

Compute resources changed: lowered cpus from 4 to 2

➡️ Inputs

⬅️ Outputs

: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
[ ] 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

theiagen / public_health_bioinformatics