Prevent Silent Errors

[sage-wright]

This PR closes #642

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

🧠 Summary

In tasks where python scripts are called, we are telling the WDL to actually stop when the exit code is 1.

⚡ Impacted Workflows/Tasks

This PR may lead to different results in pre-existing outputs: No

This PR uses an element that could cause duplicate runs to have different results: No

🛠️ Changes

⚙️ Algorithm

Truly, all I am doing is adding a pipefail warning

➡️ Inputs

⬅️ Outputs

🧪 Testing

Suggested Scenarios for Reviewer to Test

🔬 Final Developer Checklist

• The workflow/task has been tested and results, including file contents, are as anticipated
• The CI/CD has been adjusted and tests are passing (Theiagen developers)
• Code changes follow the style guide
• Documentation and/or workflow diagrams have been updated if applicable (Theiagen developers only)

🎯 Reviewer Checklist

• All changed results have been confirmed
• You have tested the PR appropriately (see the testing guide for more information)
• All code adheres to the style guide
• MD5 sums have been updated
• The PR author has addressed all comments
• The documentation has been updated

[kapsakcj]

FYI I found a bug in the export_taxon_tables task that causes a silent error:

Traceback (most recent call last):
File "<stdin>", line 365, in <module>
TypeError: bad operand type for unary ~: 'str'

It's due to a stray ~ in the code here:

public_health_bioinformatics/tasks/utilities/data_export/task_broad_terra_tools.wdl

Line 781 in 34a64fb

"srst2_vibrio_version": "~{srst2_vibrio_version}",~

I'm fixing it over on PR #662 but you may want to add to this PR if you're testing the task/workflow via TheiaProk wfs

[AndrewLangvt]

Thanks for adding these @sage-wright. We should make this standard practice for all WDL task development, going forward.