add short-read-mngs end-to-end test to CI (using viral databases)

chanzuckerberg / idseq-workflows

Portable WDL workflows for IDseq production pipelines

https://idseq.net/

MIT License

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add short-read-mngs end-to-end test to CI (using viral databases) #44

Closed mlin closed 4 years ago

mlin commented 4 years ago

This first cut tests that the workflow runs successfully but doesn't include output correctness checks.

mlin commented 4 years ago

@morsecodist @katrinakalantar @cdebourcy With the viral databases, we can now run the mngs workflow from beginning to end in GitHub Action, which is great.

Since it takes only 10-15 minutes, I'm actually thinking of replacing the task-level unit tests from earlier in the summer, since the latter have a lot more maintenance overhead for test fixtures etc. A little further work is needed so that we can still write test assertions on intermediate results in the workflow.