How do I write tests for a snakemake pipeline? I've been playing with snakemake, which is really powerful, however, I'd like to create a 'unit test' for the whole pipeline. e.g. a way to call the pipeline that tests that all the rules work together, all the steps complete, etc.
I assumed I could find some guides about how to do this, but I don't find any clear information about how to tests pipelines.
Any advice or suggestions would be welcome.
You can run CI on a snakemake workflow when provoding a minimal example dataset. Maybe an example from the snakemake-workflows repo will be helpful: https://github.com/snakemake-workflows/dna-seq-varlociraptor