Adding Unit Test for the Coverage Rules

[gordonkoehn]

I'd like to store some data secretly so that I can add unit tests with real data to a GitHub CI pipeline.

Therefore, let's try to do this on Github with Secrets.

[gordonkoehn]

Currently working on this with the amplicon coverage data.

[gordonkoehn]

Check with Matteo weather the Files he have me of the alignment for July are already on ENA.

If so check with Ivan weather to put them for test data there.

[gordonkoehn]

on Hold as Ivan will check my Unit test anyways

[gordonkoehn]

Checked with Matteo and David if the Data is online already:

• Matteo said check with David
• David showed me where to check the dates, if the original reads are online it's no problem.

I am not 100 % sure how to check the dates. So back to waiting.

[gordonkoehn]

Alright, Ivan told us where to find the data to write some proper unit tests for the smallgnom package.

• [x] See in "Snake-deploy" tests on the rubicon branch in the artefacts, there is free to us HIV and Sars Data

[gordonkoehn]

Roadmap

• [x] get the test data
• [x] get expected results
• [ ] move test data and expected results to unit test and commit to repo
• [x] decide unit-test as done for the mock snakemake test
• [x] debug

[gordonkoehn]

Also test snakemake unittests with early snakemake versions

[gordonkoehn]

So the issue is not that the python script is just not found - as the path is card coded

[gordonkoehn]

Still cleanup the other scripts not needed.