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WayScience / CytoSnake

Orchestrating high-dimensional cell morphology data processing pipelines
https://cytosnake.readthedocs.io
Creative Commons Attribution 4.0 International
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adding `get_input()` helper function #60

Closed axiomcura closed 1 year ago

axiomcura commented 1 year ago

About PR

This PR introduces a new helper function known as get_input() within the common.smk file.

In addition, this required to add a parameter into the workflow config known as input_data, where users explicitly state which dataset they want to use as input in a module.

Motivation

Currently, there is an issue where modules can accept multiple different types of inputs. For example, the annoate module can accept single cell morphology or aggregated datasets. The issue with this is that input paths are predefined within the common.smk module, despite the files exiting or not.

Looking at the documentation within the cp_process_singlecells, there is no aggregate file being produced, but the path is still defined within the annoate module; therefore, this will raise an error.

axiomcura commented 1 year ago

@d33bs I have attended all your comments and suggestions. I will be merging now. I will be implementing this in a separate PR just in case the changes become too much.

Also feel free to respond to continue the discussion here if necessary!