Import workflows into TeSS Concept Maps
### Representative: Niall Beard
ELIXIR Training Platform
TeSS has been developing a new feature called Concept Maps (demo: https://tess.oerc.ox.ac.uk/concept_maps). Concept Maps provide a conceptual representation of data analysis pipelines. The Concept Map is a medium for educating researchers about the steps a typical Workflow comrpises of, and informing them about what tools, databases, standards, and other resources are available to use when constructing one.
Each step of a Training Workflow in TeSS is annotated with an EDAM term. There are two step types; Data and Operations.
- Data steps are annotated with an EDAM Data and EDAM Format term, and contain links to available databases through the FAIRSharing registry.
- Operation steps are annotated with an EDAM Operation term, and contain links to tools from the bio.tools registry.
This task will look at devising a way to import workflows (CWL or Galaxy) into TeSS to turn the Computational Workflows into Conceptual Training Workflows that can educate and inform bioinformatics researchers.
- Manually construct a Concept Map based on a Galaxy Workflow
- Make the Concept Map again, but this time - automatically, by:
- Annotating the Galaxy/CWL workflow with EDAM terms (Operation and Data).
- Parse the workflow (CWL or Galaxy) using Ruby.
- Create a connected graph representation of the workflow in memory.
- Use TeSS's existing modified Cytoscape JS plugin to plot the connected graph onto a canvas ready to be annotated, assigned resources from bio.tools, FAIRSharing, and TeSS, and saved.
Programmers, workflow experts. Cytoscape JS, CWL/Galaxy, Ruby programmers (other languages welcome) Expected hacking days: 4 days, 3 days, 2 days