4. PipelinesΒΆ

In Sequana parlance, a pipeline is an application based on Snakemake that consists of a Snakefile and a configuration file.

For snakemake tutorial, you can have a look at the Snakemake page or online-tutorials (e.g. http://slowkow.com/notes/snakemake-tutorial/)

Pipelines can be initialised and run via a command line interface called sequana but we would recommend to use Sequanix: GUI for snakemake workflows instead.

The following sections are dedicated to each pipeline.