In CGAT we have developed a set of ruffus based pipelines in comparative genomics and NGS analysis. The pipelines are generally available and should be fairly portable. Some documentation of the pipelines is here.
We are working on improving the existing documentation and portability of the code to release a set of production pipelines soon so please stay tuned.
Meanwhile, in this repository you may find a set of working pipelines that are under continuous development and changing rapidly. However, they might give some ideas or building blocks when developing your own pipelines.
For questions, please open a new issue on GitHub.