data wrangling for
computational genomics


CGPipe is a bioinformatics pipeline development language. It is very similar in spirit (and practice) to the venerable Makefile, but geared towards execution in an HPC environment. Like Makefiles, CGPipe pipelines establish a series of build targets, their required dependencies, and a recipe (shell script) used to build the outputs. Unlike Makefiles, CGPipe pipelines are scripts that can incorporate logic and flow control in the setup and execution of the build-graph.

CGPipe is distributed as a self-executing fat-JAR file. This means that for installation, all one needs is a working copy of Java and the cgpipe file.

For more information, please see the following documentation: