Module Biokepi (.ml)

module Biokepi: sig .. end

Top-level entry point into the library

Biokepi provides different levels of abstraction to construct (Ketrew) pipelines:

• Biokepi.EDSL: very high-level embedded domain specific language that encode very consise complex pipelines and uses OCaml type-system to verify properties on them. The EDSL expressions can be “compiled” to Ketrew worfklows, to JSON, to Graphviz "dot" graphs, … Biokepi.Pipeline is an earlier, soon to be deprecated, implementation of the same idea.
• Biokepi.Tools: is a lower-level library of functions producing Ketrew-workflow-nodes.

The above modules use:

• some extensions to the Ketrew workflow EDSL see Biokepi.KEDSL,
• and an abstraction of the computing infrastructure of the user of the library: Biokepi.Machine.

Finally the Biokepi.Setup module provides (optional) tools to create a proper Biokepi.Machine.t that fits your computing environment (OS environment, cluster schedulers, installation of tools, fetching of reference data, etc.).

module EDSL: sig .. end

module Machine: Biokepi_run_environment.Machine

module Setup: sig .. end

module KEDSL: Biokepi_run_environment.Common.KEDSL

module Metadata: Biokepi_run_environment.Metadata

module Tools: Biokepi_bfx_tools

module Pipeline: Biokepi_pipeline_edsl.Pipeline