This page outlines the principles that will guide the ongoing development of Cpipe.
Development of Cpipe will be conducted in a manner that ensures the needs of clinical users are always prioritised. This doesn’t mean that Cpipe won’t work for other users - we fully expect and hope that many other kinds of users will find Cpipe useful. What are clinical considerations?
- Versioning a robust and clinically meaningful change log and versioning system
- Tested regression tests that ensure clinically relevant mutations are always detected
- Input a process that includes direct input from real clinical users at diagnostic laboratories
- Quality adherence to a high standard of software engineering principles
Best Practise Consensus
Subject to ensuring clinical needs are met, Cpipe will attempt to implement an approach reflecting current best practises available. This doesn’t mean Cpipe will live on the bleeding edge of technology. However it does mean that Cpipe will steadily adopt new best practises as they emerge over time, to ensure that analyses remain current.
Regardless of what best practises or technologies are adopted into the pipeline, Cpipe will keep end users in control by ensuring the pipeline is fully customisable for their needs in a highly transparent, modular and clinically maintainable way.
Cpipe is open for collaboration. Development is conducted openly on Github, forks and pull requests are welcome. A road map will be publicly maintained so that end users know the direction Cpipe is heading in. Users wanting to become deeply involved are welcome to join our development meetings to contribute directly to the discussion, or to participate via our Google Group.
Cpipe will remain freely available and usable to all (including non-academic users). Further, to the greatest extent possible, Cpipe will employ tools in the pipeline that are also freely available. We recognise that there is tension here: often the best-in-class tools are not necessarily the ones that everyone can use for free. Where we cannot meet these constraints we will offer, where possible, alternatives so that a clinically viable pipeline that is still available, even if the default uses tools that may require commercial or clinical users to pay.