Innovation In Science - The story behind Nextflow

  • Maria Chatzou
  • 9 June 2015

Innovation can be viewed as the application of solutions that meet new requirements or existing market needs. Academia has traditionally been the driving force of innovation. Scientific ideas have shaped the world, but only a few of them were brought to market by the inventing scientists themselves, resulting in both time and financial loses.

Lately there have been several attempts to boost scientific innovation and translation, with most notable in Europe being the Horizon 2020 funding program. The problem with these types of funding is that they are not designed for PhDs and Postdocs, but rather aim to promote the collaboration of senior scientists in different institutions. This neglects two very important facts, first and foremost that most of the Nobel prizes were given for discoveries made when scientists were in their 20’s / 30’s (not in their 50’s / 60’s). Secondly, innovation really happens when a few individuals (not institutions) face a problem in their everyday life/work, and one day they just decide to do something about it (end-user innovation). Without realizing, these people address a need that many others have. They don’t do it for the money or the glory; they do it because it bothers them! Many examples of companies that started exactly this way include Apple, Google, and Virgin Airlines.

The story of Nextflow

Similarly, Nextflow started as an attempt to solve the every-day computational problems we were facing with “big biomedical data” analyses. We wished that our huge and almost cryptic BASH-based pipelines could handle parallelization automatically. In our effort to make that happen we stumbled upon the Dataflow programming model and Nextflow was created. We were getting furious every time our two-week long pipelines were crashing and we had to re-execute them from the beginning. We, therefore, developed a caching system, which allows Nextflow to resume any pipeline from the last executed step. While we were really enjoying developing a new DSL and creating our own operators, at the same time we were not willing to give up our favorite Perl/Python scripts and one-liners, and thus Nextflow became a polyglot.

Another problem we were facing was that our pipelines were invoking a lot of third-party software, making distribution and execution on different platforms a nightmare. Once again while searching for a solution to this problem, we were able to identify a breakthrough technology Docker, which is now revolutionising cloud computation. Nextflow has been one of the first framework, that fully supports Docker containers and allows pipeline execution in an isolated and easy to distribute manner. Of course, sharing our pipelines with our friends rapidly became a necessity and so we had to make Nextflow smart enough to support Github and Bitbucket integration.

I don’t know if Nextflow will make as much difference in the world as the Dataflow programming model and Docker container technology are making, but it has already made a big difference in our lives and that is all we ever wanted…


Summarising, it is a pity that PhDs and Postdocs are the neglected engine of Innovation. They are not empowered to innovate, by identifying and addressing their needs, and to potentially set up commercial solutions to their problems. This fact becomes even sadder when you think that only 3% of Postdocs have a chance to become PIs in the UK. Instead more and more money is being invested into the senior scientists who only require their PhD students and Postdocs to put another step into a well-defined ladder. In todays world it seems that ideas, such as Nextflow, will only get funded for their scientific value, not as innovative concepts trying to address a need.

innovation science pipelines nextflow