bionode.io

bionode-watermill

> Bionode-watermill: A (Not Yet Streaming) Workflow Engine

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Table of Contents

* What is bionode-watermill
* Main features
* Who is this tool for?
* Installation
* Documentation
* Tutorial
* Example pipelines
* Why bionode-watermill?
* Contributing

What is bionode-watermill

Bionode-watermill is a workflow engine that lets you assemble and run
bioinformatic pipelines with ease and less overhead. Bionode-watermill
pipelines are
essentially node.js scripts in which tasks are the modules that will be
assembled in the final pipeline using orchestrators.

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* Modularity
* Reusability
* Automated Input/Output handling
* Ability to run programs using Unix shell
* Node.js integration
* Streamable tasks (still not
implemented - Issue #79)

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Bionode-watermill is for biologists who understand it is important to
experiment with sample data, parameter values, and tools. Compared to other
workflow systems, the ease of swapping around parameters and tools is much
improved, allowing you to iteratively compare results and construct more
confident inferences. Consider the ability to construct your own
Teaser
for your data with a simple syntax, and getting utmost performance out of the box.

Bionode-watermill is for programmers who desire an efficient and
easy-to-write methodology for developing complex and dynamic data pipelines,
while handling parallelization as much as possible. Bionode-watermill is an npm
module, and is accessible by anyone willing to learn a little JavaScript. This
is in contrast to other tools which develop their own DSL
(domain specific language), which is not useful outside the tool. By leveraging
the npm ecosystem and JavaScript on the client, Bionode-watermill can be built
upon for inclusion on web apis, modern web applications, as well as native
applications through Electron. Look forward to
seeing Galaxy-like applications backed by a completely configurable Node API.

Installation

Local installation:

``npm install bionode-watermill`

Global installation:

`npm install bionode-watermill -g`

Documentation

Our documentation is available here.
There you may find how to use bionode-watermill to construct and run
your
pipelines. Moreover, you will also find the description of the API to help
anyone
willing to contribute.

Tutorial

- Try bionode-watermill tutorial!

Example pipelines

- Toy pipeline with shell/node
- Simple capitalize task
- Simple SNP calling
- SNP calling with filtering and fork
- Mapping with bowtie2 and bwa (with tutorial)

Why bionode-watermill?

This blog post
compares the available tools to deal with NGS workflows, explaining the
advantages of each one, including bionode-watermill.

Contributing

Just make a PR for us, that adds a pipeline under ./examples/pipelines/`.
You can check some of the already existing examples here.