Using PEP with workflows systems

PEP is designed to be used with any workflow system. It is a common way of organizing sample metadata that spans individual workflows and even workflow systems. In practice, we have worked with several workflow systems to try to make it particularly easy to adopt PEP with your existing system.


Snakemake has a built-in directive for reading PEPs. For an example of how to read a PEP into a Snakemake flow, see:


Using our pipeline submission engine looper, it is possible to run CWL pipelines on each sample in a PEP. This example repository shows how to do it:


Pypiper is our python-based pipeline manager. It is also PEP-compatible: