Nextflow: a DSL for parallel and scalable computational pipelines.

I return on pipeline creation tools because I was warned about Nextflow project, a DSL for parallel and scalable computational pipeline creation. As already discussed in a recent post, we can sort pipeline solutions according to how they deal with your code. Some of them are able to connect functions, some of them require dedicated modules, and others are able to connect different files by integrating the standard I/O.

If we think it up, the most of the people working in bioinformatics will end up mixing different things. Usually, a scripting language is used for data mining, and R comes over for statistical analysis, but other languages or tools may be needed. Thus, any solution that is able to integrate different languages, it is warmly suggested in the most of the cases.

The pretty amazing thing about Nextflow, is that the authors took their time to implement a real Domain Specific Language, namely a programming language dedicated to solve specific tasks. To better explain, languages as R, SQL o Mathematica are defined as DSL too. Of course, this bodes well in the extensibility and power of this language.

Nextflow is provided as a simple- installation package, and Java 7+ is the only required dependency. Syntax is simple as well as scalability, since you can develop on your laptop, run in the grid, and scale-out to the cloud with no modifications to your code needed. More intriguingly, the whole thing is designed to work with message passing to better deal with a parallel computing approach.

The project is developed at the CRG- Comparative Genomics group in Barcelona (the guys who created and maintain the T-COFFEE suite), and is headed by Paolo di Tommaso.


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