A popper pipeline using the toil genomics workflow engine
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README.md

Reproducibility: Combination of PopperCI and Toil

This repo shows how to leverage PopperCI and Toil to automate the process of running Cactus program reproducibly and conduct a parameter sweep thereof.

PopperCI--the integration of the Popper Convention and existing continuous integration (CI) systems/services--enables researchers to automate end-to-end execution and validation of computer science experiments.

Toil is an open-source, portable, and pure-Python workflow software package that supports contemporary workflow definition languages and can be used to securely, reproducibly run scientific workflows efficiently on a grand scale in cloud or high-performance computing environments.

Cactus is a reference-free, whole-genome multiple-sequence alignment program and uses Toil to coordinate its jobs.

This repo demonstrates a couple of examples of leveraging PopperCI to fully automate and further simplify the process of running Toil workflows reproducibly.