In Sequana parlance, a pipeline is an application based on Snakemake that consists of a Snakefile and a configuration file. Each pipeline and its configuration file can be automatically downloaded using:
sequana --pipeline <name>
By default the previous command creates a directory named analysis where the pipeline and config file are stored. The pipeline must not be changed but the configuration file can be edited to change the options.
Although the configuration is documented and should be self content, additional help for users and developers can be found for each pipeline in the following links.
the following sections are in progress but should already give useful information about the pipelines that are available.