enhancement - input data/output_path

[reJELIN]

Hello,

I'm succesfully running your first step of your pipeline. Waiting for results.

Perhaps you could add in the configuration yaml file a variable that is taking the path of the h5ad file and a variable to the path of an output folder where you would like your result to be save. Because it's not very user friendly to save your result directly in your snakefile pipeline folder, it mean i cannot run mutliple instance of your pipeline in the same time.

[reJELIN]

Also I note that if you're not giving any continuous_covariates it will by default add: library_size, is it normal behavior ? In my case I only have one factor_covariates. Would it impact my run ?