https://github.com/aplbrain/neuroworkflows-demo
INCF Assembly 2023 Demonstration of Neuroworkflows
https://github.com/aplbrain/neuroworkflows-demo
Last synced: over 1 year ago
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INCF Assembly 2023 Demonstration of Neuroworkflows
- Host: GitHub
- URL: https://github.com/aplbrain/neuroworkflows-demo
- Owner: aplbrain
- License: apache-2.0
- Created: 2023-09-08T17:18:57.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2023-09-19T16:05:08.000Z (over 2 years ago)
- Last Synced: 2025-01-22T00:16:04.833Z (over 1 year ago)
- Language: Python
- Size: 1.86 MB
- Stars: 0
- Watchers: 4
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# BossDB x DataJoint x NextFlow Demo
This repo is a example of how to use nextflow to quickly run scalable and containerized workflows.
## Whats included
- Example of a containarized workflow that
- pulls volumetric data from the Kasthuri dataset using `intern`, the python SDK for `BossDB`
- finds segment centroids for from a segmentation volume using `cc3d`, a connected-components library optimized for 3D volumes
- and uploads the resultant annotations to a locally-deployed `DataJoint` database.
- Configuration settings and docker images to allow for easy customization or templating of this repo for other projects.
## Requirements
1. docker and docker-compose
2. Java `jdk` version 11 or above
2. POSIX compatible system to download and run `nextflow` in the command line.
## How to run
Simply run the `set-up.sh` script to install nextflow, add it to your path, and run the docker-compose YAML. This script will take around 5 minutes to build the docker images.
```bash
./set-up.sh
```
Then, run the nextflow workflow file located in the `incf-demo/workflow` directory.
```bash
cd incf-demo/workflow
nextflow run incf-demo.nf -with-report report.html
```
You can then examine the outputs generated by `nextflow` in the `work` directory, which should be generated upon workflow completion.
## Acknowledgements and References
- [Seung Lab's cc3d](https://github.com/seung-lab/connected-components-3d)
- [DataJoint](https://datajoint.com/)
- [BossDB](https://bossdb.org/)
- [Kasthuri Dataset](https://bossdb.org/project/kasthuri2015)