The consensus rule is in the rulesfeature_select.smk not preprocessing.smk. Unless you want the feature_select and consensus rule in one .smk file.
I guess my question is - Is feature_select and consensus a preprocessing step?
This question led to both a discussion in that pull request and the opening of this issue, in which we can track how to create intuitively named .smk file names. It is not clear to me how they should be organized, and what they should be named. I do think that all CytoPipe/pycytominer steps are processing (and not preprocessing) - although I could be wrong!
This issue can be closed once we define a .smk framework and add intuitive names :)
@axiomcura asked an interesting question in #12
This question led to both a discussion in that pull request and the opening of this issue, in which we can track how to create intuitively named .smk file names. It is not clear to me how they should be organized, and what they should be named. I do think that all CytoPipe/pycytominer steps are
processing(and notpreprocessing) - although I could be wrong!This issue can be closed once we define a .smk framework and add intuitive names :)