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galaxyproject / training-material

A collection of Galaxy-related training material
https://training.galaxyproject.org
MIT License
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Workflow testing cofest discussion #2002

Closed cat-bro closed 3 years ago

cat-bro commented 3 years ago

I'm interested in checking that tests in the */workflows directories are working and writing some new ones for untested workflows. If I am writing a test for one I'll write it down here as an effort not to double-up with other cofest contributors. There are a lot to choose from that do not have tests.

Some tests already exist in https://github.com/usegalaxy-eu/workflow-testing but may be out of date.

This tutorial is a good for understanding the format of the tests: https://galaxyproject.github.io/training-material/topics/contributing/tutorials/create-new-tutorial-technical/tutorial.html#testing-the-workflow-recommended.

An example of a workflow test in this repo: https://github.com/galaxyproject/training-material/blob/master/topics/statistics/tutorials/machinelearning/workflows/machine_learning-test.yml

cat-bro commented 3 years ago

I'm currently checking/updating tests for topics/variant-analysis/tutorials/microbial-variants/workflows/microbial_variant_calling.ga and topics/variant-analysis/tutorials/mapping-by-sequencing/workflows/workflow-arabidopsis.ga

[UPDATE]: topics/variant-analysis/tutorials/microbial-variants/workflows/microbial_variant_calling.ga already has a test that passes topics/variant-analysis/tutorials/microbial-variants/workflows/microbial_variant_calling.ga won't load on Galaxy Europe or Galaxy Australia due to the version of snpeff it uses.

Checking tests for assembly tutorials excluding assembly-with-preprocessing

bgruening commented 3 years ago

@cat-bro sorry I missed that completely! But I think this is a great idea and fits nicely the push of workfow related work that @jmchilton and @mvdbeek have been doing recently.