cgat-showcase

cgat-showcase is a repository containing an example pipeline constructed to demonstrate how the cgat-core workflow management system can be used to create common workflows required in bioinformatics analysis.

Within this repository is an example pipeline pipeline_transdiffexprs.py that performs pseudoalignment of fastq files with kallisto and differential expression using DESeq2. It can be run locally on your own machine or distributed across a cluster depending on your requirements.

Documentation on how to run this pipeline can be found here and documentation on how to build your own custom workflow from scratch can be found here.

Installation

The following sections describe how to install the cgat-showcase pipeline.

We recommend installing using conda and the steps are described below::

conda install -c cgat cgatshowcase

Alternatively, the pipeline can be installed using pip::

pip install cgatshowcase

However, you will require certain software to run the pipeline. More detail on installation can be found on the Installation documentation.