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.
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.
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
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.
Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests to us.