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Pooled Cell Painting: Data Pipeline Welding Template :hammer_and_wrench:

This repository was derived from a template repository located at https://github.com/broadinstitute/pooled-cell-painting-profiling-template. The purpose of the repository is to weld together a versioned data processing pipeline with versioned processed output data for a single Pooled Cell Painting experiment.

<p align="center"> <img src="https://raw.githubusercontent.com/broadinstitute/pooled-cp-profiling-template/a57cb7f9e36b89ff56acf094f18ca06b1a53b719/media/pipeline_weld.png" width="500"> </p>

Figure 1: Data Pipeline Welding is a procedure that links together version controlled data with a version controlled processing pipeline. The procedure results in a new repository for each dataset within a Pooled Cell Painting project. The pooled-cell-painting-profiling-recipe repository contains the data processing pipeline. The pooled-cell-painting-profiling-template (this repo) contains recipe configuration files that must be edited for each dataset. A user's recipe fork is added to the dataset-specific repo as a Github submodule. The weld is finalized when the user prepares the recipe, outputting version controlled morphology profiles that are used for downstream biological discovery.

Notes about terminology: