Install the requirements as instructed in the README.
TODO
The general command from the directory of interest is:
snakemake --configfile <configfile> <snakemake args>
You need to specify a config file that is specific to the data you want to run the pipeline on. This is most useful for testing or reusing the modules for other workflows.
Make sure a test dataset pbmc68k.h5ad exists in data/.
This will be the default test object
If it doesn't exist, create it by running data/generate_data.py in the scanpy environment (see envs for environment config files).
Check out the test directories of each module for an example.
Here's an example for calling a module pipeline from the repository root:
bash workflow/integration/test/run_test.sh
...