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fairagro / M4.4_UC6_ARC

UC6 workflow in ARC proof-of-concept
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ARC for UC6

ARC validation CI

In this repository, we will create an annotated research context ARC with assays, studies, workflows and runs of these workflows for Use Case 6 of FAIRagro. Use Case 6 deals with ETL functions for semiautomated data integration into crop simulation modelling.

The ARC contians a modularised CWL workflow that can be executed locally with cwltool. To facilitate writing CWL, a minimal templating system that helps to generate CWL will be used or developed. Once the finalised ARC has undergone a test to verify that the workflow is running as intended, it will also be made accessible via the PLANTdataHUB. The ARC will serve as a test case for the further development of a Scientific Workflow Infrastructure (SciWIn).

Usage

git clone https://github.com/fairagro/M4.4_UC6_ARC.git
cd runs
cwltool ../workflows/main.cwl main_inputs.yml

Workflow

The Workflow contained in main.cwl is split into multiple small chunks. A visualisation can be found here:

Workflow