BioFlow-Insight

Description

This repository contains the software BioFlow-Insight written in Python. BioFlow-Insight automatically analyses the code of Nextflow workflows and extracts useful information, particularly in the form of visual graphs depicting the workflow's structure and representing its different steps.

BioFlow-Insight is easily installable as a Python package (see here). It is also accesible as a web service (see here).

Table of Contents

• BioFlow-Insight
  • Description
  • Table of Contents
  • Installation
  • Usage
  • Contributing
  • License

Installation

BioFlow-Insight is easily installable as a Python package.

To install it using pip, use the following command :

pip install bioflow-insight

TODO

Usage

BioFlow-Insight automatically analyses the code of Nextflow workflows and extracts useful information, particularly in the form of visual graphs depicting the workflow's structure and representing its different steps.

For an explanation of the different elements composing a Nextflow workflow, see its documentation.

The 3 different graphs generated by BioFlow-Insight are :

1. The specification graph which represents all elements of the workflow, including processes and operations, and their interactions through channels. Within the specification graph, we define two types of operations: those without inputs and those with inputs (called branch operations).
2. The second graph represents operations without any inputs, along with processes and their dependencies. This graph, called the dependency graph without branch operations, is obtained by removing the branch operations and linking the remaining elements if a path exists between them in the original specification graph.
3. The final graph, called the process dependency graph, represents only processes and their dependencies. Similar to the latter, this graph is constructed by removing all operations, leaving only processes, and linking them based on their dependencies in the original specification graph.

To examplify BioFlow-Insight utilisation, let's use the rnaseq-nf workflow proposed by Nextflow (its source code can be found here).

In this example, we are going to use the BioFlow-Insight source code. After cloning both repositories (this one and the rnaseq-nf workflow), the working directory should look like this :

Contributing

Guidelines for contributing to the project, including how to report issues and submit pull requests.

License

This project is licensed under the MIT License