Test snakemake rules individually
During testing of the workflow, we need to reliably test each of the rules and their output independent of the other rules.
A proposed way to do this is:
- Create test folder for each of the rules within the test/test_rules_individually/test_(name of rule)
- put config file specific for this test, since the relative path is incompatible with the other test paths
- run snakemake once to produce the file that is required as input by the rule
- delete all other files BUT the required input
- run the snakemake TARGET rule (only this is executed)
- create md5sum
- remove output and then each time this runs check the md5sum of the output
This still relies on the general sample.tsv
One downside is that we need to have stored the input files of the rules, otherwise we cannot guarantee that these are not corrupted by some other rule.
Activity
changed milestone to %v0.1.0 release
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added Testing & CI/CD label
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Decided to drop this, at least for now, as the foreseen benefits are too little to justify the development efforts. Faulty rules would still be found in the integration test and functional tests for individual tools should happen elsewhere.
Reopen if we run into a real-world problem where individual rule-testing would have saved us.
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assigned to @burri0000 and unassigned @katsanto
Snakemake has an option to create unit tests: https://snakemake.readthedocs.io/en/stable/snakefiles/testing.html
The feature is only available from
snakemake v5.27.0onward, we specifiedsnakemake v5.19.2.The command
snakemake --generate-unit-testswould only create one unit test per rule.Either we decide to bump up the snakemake version to a more recent version and incorporate unit tests in this way. The advantage could be the automatic generation of tests, also for new rules. Alternatively, I can start to write an unit test from scratch, respectively from a temporary execution of the command above for a CI test.
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