Zhenguo Zhang's Blog
Sharing makes life better
[Bioinfo] Nextflow framework

Recently, I was introduced to an amazing pipeline-writing framework – nextflow. It has the following features:

  1. it abstracts a pipeline, which can be written in any language and run on many computing platforms such as Linux Slurm, PBS, AWS, etc.

  2. it is composed of many processes, the executing order of which is determined by the dependencies of the input and output channels of each process.

  3. the nextflow language is extension of the Groovy programming language, which is a programming language for Java virtual machine. The language syntax is most similar to Python.

  4. it allows parallel processing and caching (thus resuming from middle processes).

The key component here is connecting different processes using channels, so that the input and output of a process can be well coordinated between processes.

This seems a promising pipeline-writing program, but it needs some time to learn the programming language.


Last modified on 2019-09-19

Comments powered by Disqus