Existing Building Blocks and Workflows

This section provides a list of available PerMedCoE building blocks (BB), existing workflows and links to further user documentation.

Building blocks are executed using the permedcoe base package. In PerMedCoE, a BB is considered a unit of work, like a black box that performs a particular computation. Consequently, it has inputs and outputs, and can be instantiated into applications and piped as required. Combinations of several building blocks can be used to execute different workflows.

The permedcoe package enables BB execution using a variety of workflow managers, such as PyCOMPSs, Snakemake or Nextflow.