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gordonkoehn / UsefulGnom

Useful Genomic Tools
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Integrating Snakemake Unittests & CI / CD #8

Closed gordonkoehn closed 3 weeks ago

gordonkoehn commented 1 month ago

In this PR, I am attempting to integrate some Snakemake auto-generate unit tests for Auguste's Coverage scripts.

And Some Snakemake CIs.

In implements a brief example of a test that was partially generated by snakemake.

Whilst not fully integrating the auto generated unit test, I've learned and aligned my project structure a lot to snakemake.

With some more changes, I might get the auto-generated test working.

Already with these changes there is plenty to adjust in the other parts.

Hence, I'll merge this PR, even though it was initially intended to be a playground.

gordonkoehn commented 4 weeks ago

Got a Snakemake CI working !!! Hurray .;)

gordonkoehn commented 3 weeks ago

Tests work locally also in a temp directory and the snakemake precommits work. We have much more orderly snakemake structure up tot he standards. But now the github workflows it failing as it does not find the configs of snakemake:

Workflow defines configfile config/config.yaml but it is not present or accessible (full checked path: /github/workspace/.test/config/config.yaml).