ELIXIR WES Implementation: WES-ELIXIR
GA4GH Workflow Execution Service implementation for CWL workflows
Provides a Flask microservice implementing the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification.
WES-ELIXIR is an implementation of the GA4GH WES OpenAPI specification based on Flask and Connexion. It allows clients/users to send workflows for execution, list current and previous workflow runs, and get the status and/or detailed information on individual workflow runs. It interprets workflows and breaks them down into individual tasks, for each task emitting a request that is compatible with the GA4GH Task Execution Service (TES) OpenAPI specification. Thus, for end-to-end execution of workflows, a local or remote instance of a TES service such as TESK or funnel is required.
The service is backed by a MongoDB database and optionally uses JWT token-based authorization, e.g. through ELIXIR AAI. While currently only workflows written in the Common Workflow Language are supported (leveraged by CWL-TES, we are planning to abstract workflow interpretation away from API business logic on the one hand and task execution on the other, thus hoping to provide an abstract middleware layer that can be interfaced by any workflow language interpreter in a pluggable manner.
Note that the project is currently still under active development. Nevertheless, a largely FUNCTIONAL PROTOTYPE is available as of October 2018, hosted at the CSC in Helsinki.
WES-ELIXIR is part of ELIXIR, a multinational effort at establishing and implementing FAIR data sharing and promoting reproducible data analyses and responsible data handling in the Life Sciences. Infrastructure and IT support are provided by ELIXIR Finland at the CSC, the TESK service is being developed and maintained by ELIXIR UK at the EBI in Hinxton, and WES-ELIXIR itself is being developed by ELIXIR Switzerland at the Biozentrum in Basel and the Swiss Institute of Bioinformatics.
(TBC)
Updated on 15 Feb 2023