Flowjomojo

Flow-based workflow generation from the comfort of your browser to help you keep your flow, Jo.

Flowjomojo is a ReactFlow-based web-app that generates ready-made Nextflow/WDL pipelines from drag-and-drop modules. It helps easing the process of writing bioinformatics pipelines, provide configuration settings and visualization of workflows.

Quick Start

1. Searching available modules

Modules can be searched using the main search bar.

2. Select / Drag and Drop modules to canvas

Then we can select / unselect modules to be used. Selected modules will appear under modules library section. They can then be dragged and dropped to the main canvas.

3. Build connection

By default, the Top Handle of a Module Node is the target, and the Bottom Handle is the source. Connect source to target to create a connection between modules.

4. Module editor

Module's attributes can be changed in the Modules & Dependencies section.

Adding modules to Flowjomojo

commands location

Currently we are storing our discovered commands from cmdsaw in public/cmdsaw/samtools_1.22.1 as commands.json files. For testing purpose, it's better to add modules as elements to this file. In the future, there will be designated locations to retrieve these commands in the future.

commands JSON format

Our current (subject to changes) commands.json ahere to the following structure:

{
    "modules" : {
        "id": string,
        "name": string,
        "label": string,
        "description": string,
        "inputs": [ 
            {
                "name": string,
                "suffix": string,
                "edam": string,
                "optional": boolean
            }
        ],
        "outputs": [
            {
                "name": string,
                "suffix": string,
                "edam": string,
                "optional": boolean
            }
        ],
        "commands": string
    }
}

Features

Drag-and-drop module nodes: Easily construct pipelines by dragging modules from the sidebar into the flow editor.

Node editing: Edit module names, inputs, and parameters directly in the sidebar.

Visual connections: Connect modules with intuitive lines to define data flow.

Export pipelines: Generate Nextflow or WDL scripts from your designed workflow.

Responsive interface: Works entirely in the browser without backend setup.

Under development for the St. Jude Biohackathon 2025