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ctmrbio / stag-mwc

StaG Metagenomic Workflow Collaboration
https://stag-mwc.readthedocs.org
MIT License
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Add rule to automatically download test data #195

Closed boulund closed 1 year ago

boulund commented 1 year ago

Maybe it would be nice to offer a rule in the Snakefile that users can call to download example input data to use for testing?

e.g. 

snakemake download_test_data

There is a small test data set available in https://github.com/boulund/stag-mwc_test_data that I often use to run tests. It's not a perfect test data set, but at least it works. Do you have any ideas on how to improve the test data situation @AroArz ?

AroArz commented 1 year ago

check https://github.com/ctmrbio/stag-mwc/tree/test_data! I made a very simple implementation what I thought your idea was, executed as snakemake --snakefile rules/sample_data/sample_data.smk.

Created a new directory .input with a sample sheet of the test data to specify the input although we might be able to work around that. The code to download the test data is not very sophisticated but it seems to work.

If we are happy with this type of system I feel the need to select other variable names as sample_data and .input might be confusing.

boulund commented 1 year ago

I think this is more easily resolved by the solution presented in #197, we should try it out on someone new to StaG