Bionode-watermill: A (Not Yet Streaming) Workflow Engine
Table of Contents
- What is bionode-watermill
- Example pipelines
- Why bionode-watermill?
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.
- Lots of modularity - tasks can be recycled as many times as you want!
- Reusability - tasks can be reused many times within and between pipelines.
- Automated Input/Output handling - no need to worry about input/output location, bionode-watermill does that for you.
- Ability to run programs using Unix shell - As demonstrated by
myTask. So, there is no need to reinvent the wheel, you can use your previous scripts and programs within bionode-watermill framework.
- Streamable tasks (still not implemented - Issue #79)
Who is this tool for?
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.
npm install bionode-watermill
npm install bionode-watermill -g
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.
- Toy pipeline with shell/node
- Simple capitalize task
- Simple SNP calling
- SNP calling with filtering and fork
- Mapping with bowtie2 and bwa (with tutorial)
This blog post compares the available tools to deal with NGS workflows, explaining the advantages of each one, including bionode-watermill.
Feel free to submit your pipeline to us
Just make a PR for us, that adds a pipeline under
You can check some of the already existing examples here.