Results

SCUFL2 Workflow Bundle

• A ZIP file that contains several files that together define the workflow to execute
  • One file per (nested) workflow
  • Workflow Bundle document that ties together
    • "Main workflow" and "Preferred profile"
• Profiles for choosing implementation activity and configurations
  • Separate file per profile
  • Separate file per configuration
    • Can be shared across profiles
• JSON-LD based configurations - flexible for each activity
• XML schemas for workflow structure files
  • structured XML that can be validated
  • ..also parseable as RDF/XML
• Everything has a URI
  • Unique UUID-based identifier pr workflow version
  • Declared relative within ZIP - but can be made absolute
  • Annotation target for any workflow object
  • URI service - minimally describe any worfklow component

SCUFL2 API

• Java API for programmatically loading, saving and creating SCUFL2 Workflow Bundles
• Each workflow element is a Java bean
• Support for load/save different formats, scufl1, t2flow, wfbundle, wfdesc, shiwa-iwir

wfdesc

• Abstract workflow language that only deals with the pipeline
• Easier to query
• Hooks for annotation on a Research Object level
• Hooks for describing provenance of workflow run
• Same identifiers as in SCUFL2
• Not complete enough for execution - no control logic or iteration
• Inspiration for Commons workflow language

Common Workflow Language

• Work in progress
• Definition for executable workflow language across bioinformatics workflow systems.
• Specifies how to invoke command line tools
• Dataflow-driven

RO Bundle

• Evolution from UCF container to RO bundle
  • Details how to describe metadata, provenance and annotations
• Formal specification: https://w3id.org/bundle
  • To be proposed as an RFC
• A wfbundle is also a ro bundle
  • how to store annotations

Databundle

Workflow results can be stored as a DataBundle - extension of robundle.

Used for provenance of workflow runs -
https://github.com/taverna/taverna-prov#structure-of-exported-provenance

Databundle contains a wfbundle

TODO: Can a wfbundle contain/also be a databundle for example input/output/run?

Identifiers

• http://taverna.incubator.apache.org/ns/
• \cite{Starlinger_2012}