pipeline-builder

Pipeline Builder

Pipeline Builder is a JavaScript library for visualizing and constructing bioinformatics workflows, using Workflow Description Language (WDL)

• Visualization of WDL scripts https://github.com/broadinstitute/wdl
• Visual editor for creation and customization of a bioinformatics workflow, composed from a set of tools
• Generation of a WDL (Workflow Definition Language) script for the workflow
• Integration API into on-premises and cloud workflow environments

Demo environment

Example of a Pipeline Builder usage is available at http://pb.opensource.epam.com built on master branch and http://pb.opensource.epam.com:10000 built on dev branch

This demo application demonstrates major capabilities of a Pipeline Builder

Description of the demo application is available at Demo application overview

Installation and Usage

Install pipeline-builder the usual way:

npm install --save pipeline-builder

Then require it

const pipeline = require('pipeline-builder');
console.log(pipeline.VERSION);

Refer to the API docs and tutorials for more details

WDL Parser/Visualizer limitations

The following WDL features, that require more specific parsing or visualization, are not supported at the moment:

• Order of steps (workflow, call, if, scatter, while) in generated WDL code
• Declarations in a [call, if, scatter and while] blocks are not supported

Contribution

Ensure that the latest git (e.g Git For Windows) and Node.js v6 LTS are installed. You're also encouraged to use Yarn package manager to guarantee that package versions are consistent across all build machines. Gulp.js v3 is used as a build framework.

# grab the project
git clone https://github.com/epam/pipeline-builder.git

# install necessary Node.js modules
cd pipeline-builder
yarn global add gulp-cli
yarn install

# test and build everything
gulp

# or just start webpack development server with live reload
gulp serve