WDL workflows and scripts for running a CellProfiler pipeline on Google Cloud hardware. Includes workflows for all steps of a full Cell Painting pipeline.
Works well in Terra, and will also work on any Cromwell server that can run WDLs. Currently specific to a Google Cloud backend. (We are open to supporting more backends, specifically cloud storage locations, in the future, including AWS and Azure.)
You can see these workflows in action and try them yourself in Terra workspace cellpainting!
cytominer-database
ingest step to create a SQLite database containing all the extracted features.pycytominer
to create CSV files.CellProfiler (distributed or single VM)
.cppipe
pipeline
on a dataset.These workflows are all publicly available, and hosted in Dockstore. From there, you can import and run the workflows in Terra or any other place you like to run WDL workflows.
You can clone the Terra workspace cellpainting, which is conveniently preconfigured to run on three plates of sample data, if you just want to give it a try.