Configuring and running pipelines

Run the cellhub –help command to view the help documentation and find available pipelines to run cellhub.

The cellhub pipelines are written using cgat-core pipelining system. From more information please see the CGAT-core paper. Here we illustrate how the pipelines can be run using the cellranger pipeline as an example.

Following installation, to find the available pipelines run:

cellhub -h

Next generate a configuration yml file:

cellhub cellranger config -v5

To fully run the example cellhub pipeline run:

cellhub cellranger make full -v5

However, it may be best to begin by running the individual tasks of the pipeline to get a feel of what each task is doing. To list the pipline tasks and their current status, use the ‘show’ command:

cellhub cellranger show

Individual tasks can then be executed by name, e.g.

cellhub cellranger make cellrangerMulti -v5


If any upstream tasks are out of date they will automatically be run before the named task is executed.

Getting Started

To get started please see the IFNb example.

For an example configuration files for a multimodal immune profiling experiment please see the PBMC 10k example.