This repository was derived from a template repository located at https:/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.
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-reciperepository contains the data processing pipeline. Thepooled-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:
- A
batchis the data pipeline welding unit, and a batch consists of one or moreplates. - A batch can also be referred to as a
dataset. - An
experimentis designed around a specific question and may contain single or multiple batches, depending on the experimental design. - A
projectis an encompassing term and may contain any number of experiments (and therefore any number of batches).