https://github.com/fairagro/M4.4_UC6_ARC

UC6 workflow in ARC proof-of-concept
https://github.com/fairagro/M4.4_UC6_ARC

common-workflow-language cwl fairagro

Last synced: about 1 year ago
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UC6 workflow in ARC proof-of-concept

• Host: GitHub
• URL: https://github.com/fairagro/M4.4_UC6_ARC
• Owner: fairagro
• Created: 2024-07-02T11:07:02.000Z (almost 2 years ago)
• Default Branch: main
• Last Pushed: 2024-08-15T08:49:12.000Z (almost 2 years ago)
• Last Synced: 2024-08-15T10:25:21.590Z (almost 2 years ago)
• Topics: common-workflow-language, cwl, fairagro
• Language: Common Workflow Language
• Homepage:
• Size: 3.64 MB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 6
• Metadata Files:
  • Readme: README.md
  • Changelog: Changelog.md

Awesome Lists containing this project

README

          
# ARC for UC6

![ARC validation](https://gist.githubusercontent.com/JensKrumsieck/4ebee77ce2479ec4c5946f469afb835a/raw/badge.svg) [![CI](https://github.com/fairagro/M4.4_UC6_ARC/actions/workflows/arc-validation.yml/badge.svg)](https://github.com/fairagro/M4.4_UC6_ARC/actions/workflows/arc-validation.yml)

In this repository, we will create an annotated research context [ARC](https://www.nfdi4plants.de/content/learn-more/annotated-research-context.html) with assays, studies, workflows and runs of these workflows for [Use Case 6](https://github.com/fairagro/uc6_csmTools/tree/main) of FAIRagro.

Use Case 6 deals with ETL functions for semiautomated data integration into crop simulation modelling.

The ARC contians a modularised [CWL](https://www.commonwl.org/) workflow that can be executed locally with [cwltool](https://github.com/common-workflow-language/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

```bash

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](./.github/workflow.svg)