Deploying a variant analysis pipeline with Nextflow

There are two main players in the pipeline framework space in bioinformatics: snakemake and Nextflow. They provide pipeline functionality whilst having different design approaches. Snakemake is based on Python, but its language and philosophy come from the make tool used to compile complex programs with dependencies. Nextflow is Java-based (more precisely, it’s implemented in Groovy – a language that works on top of the Java Virtual Machine) and has its own Domain Specific Language (DSL) for implementing pipelines. The main purpose of this recipe (and the previous recipe) is to give you a flavor of Nextflow so that you can compare it with snakemake and choose the one that better suits your needs.

TIP

There are many perspectives on how to evaluate a pipeline system. Here, we present a perspective based on the language used to specify the pipeline. However, there are others that you should consider when choosing...