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Validate test data in CI job #36

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Validate test data in CI job #36

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amstilp
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@amstilp amstilp commented May 21, 2024

Add a CI job to run the validation workflows using cromwell with test data. I have no idea if this will work.

amstilp added 7 commits May 21, 2024 16:14
I have no idea if this syntax will work.
I had forgotten the .github directory.
The set_up_cromwell_action wanted a token, so try just setting up
java and checking out the cromwell repo without using the specific
action. This allows us some more flexibility hopefully.
Instead of cloning the cromwell repository, download the jar from
the release.
Also add a file that can be used for input to this workflow.
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amstilp commented May 22, 2024

This is failing due to the Bioconductor AnVIL package's implementation of gsutil_cp, which assumes that at least one of the paths is a Google bucket path: https://github.com/Bioconductor/AnVIL/blob/2cc3787e507cf40d689385c7a29ae26e284927b7/R/gsutil.R#L264

Runninggsutil cp file1 file2 works even if neither file1 nor file2 are a Google bucket path; it just copies the file like a regular cp command.

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amstilp commented May 28, 2024

We decided this was not worth it; closing.

@amstilp amstilp closed this May 28, 2024
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