General: Update CI to test template pipelines with nf-test #3559
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hmm, might be overkill to also make sure the outputs are stable... just testing that nf-test is running should be good enough. |
I think it's good to check the outputs, it will help us avoid errors like we had some versions ago where we didn't have an output directory at all, but didn't notice because the pipeline was running and Nextflow didn't throw an error. |
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true. okay, then let's create one snapshot per feature and track it in git? |
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That would be great! What do you mean by "track it in git"? how would you do it? |
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generate them once locally and have them in the repo. |
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TODO:
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snapshots added! Could you have another look @mashehu ? |
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is __snapshots__ a standard directory name for snapshots?
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no, I did some research to see how people call these directories but didn't fine any standard. Would you rename it?
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I would call it snapshots or maybe .snapshots. the double underscore feels too pythony.
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
When testing a new template pipeline, test it by running it and with nf-test.
When creating a pipeline skipping features, test it only with nf-test
Close #3497
Global issue #2994
Note
The fresh created pipeline will fail nf-test CI since we don't have a snapshot file.
Should we consider running nf-test to generate the snapshot after creating the pipeline?
Can't be added through template because it will be different depending on the steps skipped.
Snapshots are tracked now!