Hi everyone,

To better organize my lab's NGS processing pipelines and ensure reproducibility, I devised some containerized (and thus reproducible) pipelines for running alignment, filtering, and feature counting. I maintain a set of Docker images for specific versions of each tool used, and leverage Cromwell to run the pipelines in a proper workflow-like manner. Personally, I find them extremely useful, and thought that some other people would as well:

You can find it on our lab's GitHub with some documentation to get you started. Open an issue if you can't figure anything out!