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Bioflows is an easy to use package for running bioinformatics workflows.
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README.md

Project Title

Travis Coverage Docs License
Conda

Overview

bioflows is an user-friendly python implementation of a workflow manager. The user is expected to not have any programming knowledge and needs to only provide a control file in a YAML format, chosen for its human readability. The goal here is to provide users with a simple and straight-forward interface for processing NGS datasets with many samples using standard bioinformatics pipelines, e.g RNA-seq, GATK variant calling etc. The tool is developed to alleviate some of the primary issues with scaling up pipelines, such as file naming, management of data, output and logs.

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.

Prerequisites

This package requires the conda-forge and the compbiocore conda channels to have a higher priority than that of defaults. So your .condarc should look like

channels
 - compbiocore
 - conda-forge
 - defaults

Installing

Installation is simple using conda environments

conda install -c compbiocore bioflows

This will install bioflows and all the necessary bioinformatics tools that are part of the standard workflows.

Tests

Deployment

Contributing

Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests to us.

Release History

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