[Mercury] prevent silent failures

[sage-wright]

This PR closes #615

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

🧠 Summary

Causes the task to fail if the Mercury script fails.

⚡ Impacted Workflows/Tasks

• Mercury_Prep_N_Batch

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

Adds set -euo pipefail to the top of the script to catch all potential errors so that the workflow fails as expected, preventing silent failures. Should greatly help in troubleshooting.

⚙️ Algorithm

➡️ Inputs

None

⬅️ Outputs

None

🧪 Testing

Testing here with files that were already uploaded -- expecting error due to lack of deletion permissions.

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

[AndrewLangvt]

Code change is minor & correct syntax; looks good to merge. @kapsakcj would you be able to run the few tests you were hoping to run in the next day or two so we can get this merged, perhaps by Friday?

[kapsakcj]

Yes, I'll launch a test or 2 today and ping back here with the workflow links when they fail successfully.

[kapsakcj]

OK here's 2 tests I launched where the mercury task failed as expected, instead of the downstream genbank_trim_fastas step in the workflow:

1. https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/CDPH_Support_Sandbox/job_history/2112b397-8188-4bc6-986d-08d75fcc725f
   a. Expected failure due to user (me) improperly setting optional input variable single_end to false and thus Mercury did not find a column called read2_dehosted since this is ClearLabs/nanopore data and that column doesn't exist.

Second attempt on same dataset: Expected success ✅ instead of failure. I set single_end to true and re-ran the wf on the same set. Want to also ensure this wf runs successfully with these code changes! https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/CDPH_Support_Sandbox/job_history/afdd2366-bc12-4960-9667-616ee2c36efb

---

2. https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/CDPH_Support_Sandbox/job_history/791b9b12-e32e-44f0-8d15-930e7c1f2a13
   a. expected failure due to inability to delete objects off sra transfer bucket. This previously failed for the original user on the genbank_trim_fasta step instead of the expected mercury step. Running as Curtis' theiagen.cloud account to ensure theaccount does not have object admin privileges to delete objects off the bucket
   b. It failed as expected during mercury task due to GCP permission error