Helping biologists and clinicians learn how to write or reuse reproducible analysis pipelines

The Nextflow Workbench is a set of languages developed with the Jetbrains MPS Language Workbench that make it easier to write data analysis workflows with Nextflow.

The Nextflow Workbench has several features that complement Nextflow:

  • It enables the reuse and composition of Nextflow processes across workflows.
  • It provides a custom typesystem that detects incompatible type assignments and reports them directly in the editor.
  • It provides seamless language composition as an effective extension and customization mechanism.
  • It provides a WYSIWYG editor to write analysis workflows meant to be deployed in docker containers (this feature was introduced in feature 1.2).
  • It provides a WYSIWYG editor to create docker images (since 1.2) and to declare which set of popular bioinformatics tools and genome indices should be pre-installed in each image (since 1.3).
  • Its workflows are portable and execute unchanged from your laptop to the cloud (since 1.5). The workbench makes it easy to provision a cluster in the cloud to scale your analyses up across many nodes.

See these blog post announcements for an introduction to these features [1.0, 1.1, 1.2_docker, 1.2_bioinfo, 1.3 frozen images1.5 cloud].



The Nextflow Workbench is distributed as a plugin on the Jetbrains MPS plugin repository. Detailed installation instructions are provided.

Starting from release 1.5, the NextflowWorkbench supports 3 different types of workflow executions in order to cover a wider range of user needs and expertise.Installation Flow Each of them requires some additional configuration steps and offers a different level of scalability. Check out the Workflow Execution section to see how to configure your system to support your selected choice.

Recommended OS

We recommend running the workbench on MacOS (our development platform), or a flavor of Linux. Windows is not supported at this time since Nextflow is not really tested on this platform. While Windows users are able to use most features of the IDE, workflow execution from the IDE may not be possible, even with remote submission enabled.

Documentation Booklet

We are maintaing a documentation booklet that describes how to use the Nextflow Workbench. You can obtain the documentation in Tablet or PDF format:

Getting Started Video

You may find watching the following video useful if you are not familiar with the MPS platform.

User Forum

Please use the user forum if you have questions or feedback about the Nextflow Workbench.

Source Code

The source code of the project is on GitHub at

git clone

Training Sessions

We are offering training sessions which offer an introduction to workflow development with the NextflowWorkbench. Registration is required. You can access the registration form here.


We are grateful to the authors of the middleware: Paolo Di Tommaso, Maria Chatzou, Pablo Prieto and Cedric Notredame.  The Nextflow Workbench was developed by Jason P. Kurs and others during Jason’s summer internship in our lab (summer 2015).


NextflowWorkbench: Reproducible and Reusable Workflows for Beginners and Experts. , ,