saks-nf: A json solution for Nextflow pipeline construction

Abstract

To address the increasing complexity of data in scientific research, researchers have developed many workflow manager tools. Nextflow is one of the most widely used tools, enabling scalability and reproducibility of scientific workflows across various computational platforms through the implementation of domain-specific language (DSL) with a dataflow paradigm. We developed saks-nf, a JavaScript Object Notation (JSON) solution for constructing Nextflow pipelines. Our solution flattens the learning curve for Nextflow. Users can build and maintain a pipeline without prior programming experience by editing a JSON specification on any text editor. The saks-nf solution can be used to construct a multi-step pipeline with parallel and scatter-gather capacity in a computing platform of choice, such as a local machine, a high-performance cluster, or cloud computing. This solution allows users to focus on analysis, thereby increasing productivity.