DolphinNext: A graphical user interface for creating, deploying and executing Nextflow pipelines

摘要

Background The emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) are transforming biological research. The processing of high throughput datasets typically involves many different computational programs, each of which performs a specific step in a pipeline. Given the wide range of applications and organizational infrastructures, there is a great need for a highly parallel, flexible, portable, and reproducible data processing frameworks. Several platforms currently exist for the design and execution of complex pipelines. Unfortunately, current platforms lack the necessary combination of parallelism, portability, flexibility and/or reproducibility. To address these shortcomings, workflow frameworks that provide a platform to develop and portable pipelines have recently arisen. We complement these new platforms by providing a graphical user interface to create, maintain, and execute complex pipelines. To simplify development, maintenance, and execution of complex data processing pipelines we created DolphinNext. DolphinNext facilitates building and deployment of complex pipelines using a modular approach implemented in a graphical interface that relies on the powerful NextFlow workflow framework by providing 1. A drag and drop user interface that visualizes pipelines and allows users to create pipelines without familiarity in underlying programming languages. 2. Modules to execute and monitor pipelines in distributed computing environments such as high-performance clusters and/or cloud 3. Reproducible pipelines with version tracking and stand-alone versions that can be run independently. 4. Modular process design with process revisioning support to increase reusability and pipeline development efficiency. 5. Pipeline sharing with GitHub and automated testing 6. Extensive reports with R-markdown and shiny support for interactive data visualization and analysis.