🔧 Update ref pointers

[migbro]

Description

A recent export of refs to a proper bucket changed the File IDs. This points them to the right files. Also discovered a pipefail bug in one of the tools during testing, added those tests

Fixes # Related to BIXU-3655

Type of change

Please delete options that are not relevant.

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

How Has This Been Tested?

Deleted existing refs from repo, running new app copied updated refs, task completed successfully

• Ref Update
• Pipefail catch fail
• Pipefail OK

Test Configuration:

• Environment:
• Test files:

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published in downstream modules
• I have checked my code and corrected any misspellings
• I have committed any related changes to the PR

[wongjessica93]

Did you mean to add that single quote at the end of .vcf.gz?

[migbro]

Yes! It's a hack in which I can start the cwl basecommand/arg block with a ' after bash -c , and then throw it on in the end to essentially run the whole thing into an inline bash script. Other than actually making it bash script or having a single arg be a shell quote, the pipefail won't quite persist, and the resy is just an sh command. It's a whole shell/sub shell scope thing. Does that make sense?