janis-pipelines 0.3.0

Contains classes and helpers to build a workflow, and provide options to convert to CWL / WDL

Janis

WARNING: this project is work-in-progress and is provided as-is without warranty of any kind. There may be breaking changes committed to this repository without notice.

Janis is a framework creating specialised, simple workflow definitions that are then transpiled to
Common Workflow Language or Workflow Definition Language.

Documentation is hosted here: https://janis.readthedocs.io/

Introduction

Janis is designed to assist in building computational workflows to generate a runnable workflow description (CWL | WDL).

Janis requires a Python installation > 3.6, and can be installed through PIP (project page) by running:

# Install janis and the bioinformatics tools
pip3 install janis-pipelines[bioinformatics]  

You can import Janis into your project with:

import janis as j  

Included tool definitions and types

Bioinformatics

The Janis framework can be extended to include a suite of Bioinformatics data types and tools. These can be installed with the bioinformatics install extra option.

pip3 install janis-pipelines[bioinformatics]  

Unix

Some basic unix tools have been wrapped and included as part of the base Janis module and are the basis for the examples. You can reference these unix tools through janis.unix.tools.

These can be referenced by janis.bioinformatics or janis_bioinformatics, the latter might be easier due to the way nested python imports work.

Example

Further information: Simple Workflow

Below we've constructed a simple example that takes a string input, uses the echo tool to log this to stdout, and capturing the stdout to output. to give you a basic idea of how to construct a pipeline.

import janis as j  
from janis.unix.tools.echo import Echo   
w = j.Workflow("workflow_identifier")  

inp = j.Input("input_identifier", j.String())  
step = j.Step("step_identifier", Echo())  
outp = j.Output("output_identifier")  

w.add_edges([(inp, step), (step, outp)])

# Will print the CWL, input file and relevant tools to the console  
w.translate("cwl")  

We can export a CWL representation to the console using .translate("cwl").

More examples

• Bioinformatics workflow tutorial: AlignSortedBam

• Unix Toolset: in janis/examples.

• Whole genome germline pipeline: janis-examplepipelines repository.

About

Further information: About

This project was produced as part of the Portable Pipelines Project in partnership with:

• Melbourne Bioinformatics (University of Melbourne)
• Peter MacCallum Cancer Centre
• Walter and Eliza Hall Institute of Medical Research (WEHI)

Support

Contributions

Further information: Development

This project is work-in-progress and is still in developments. Although we welcome contributions, due to the immature state of this project we recommend raising issues through the Github issues page for Pipeline related issues.

If you find an issue with the tool definitions, please see the relevant issue page:

• Pipeline-bioinformatics

Information about the project structure and more on contributing can be found within the documentation.