Add a pipeline test that invokes pheval.template

monarch-initiative / pheval

A framework for empirical evaluation of phenotype matching and prioritisation

https://monarch-initiative.github.io/pheval/

Apache License 2.0

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Add a pipeline test that invokes pheval.template #338

Closed souzadevinicius closed 2 weeks ago

souzadevinicius commented 3 months ago

Fixes #337

I apologize if this review seems a bit extensive, but it's necessary because the Makefile pipeline in this project was outdated compared to the one in the Monarch PhEval repository. Basically in this PR, I made changes to the QC workflow file removing --no-root flag, to install PhEval into the poetry environment. The test itself is located in tests/test_pipeline_workflow.yaml, it executes "make all" and ensures that pheval run is called and checks the presence of result files.

matentzn commented 2 weeks ago

@yaseminbridges we ran this locally and it seems to work good! Can you look this over when you get a minute?