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https://github.com/augustdev/nf-shard
Nextflow runs monitoring and organisation UI
https://github.com/augustdev/nf-shard
nextflow nf-shard nf-tower
Last synced: 3 days ago
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Nextflow runs monitoring and organisation UI
- Host: GitHub
- URL: https://github.com/augustdev/nf-shard
- Owner: AugustDev
- License: mit
- Created: 2023-09-03T16:08:21.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-09-20T03:46:20.000Z (3 months ago)
- Last Synced: 2024-12-06T15:06:31.185Z (16 days ago)
- Topics: nextflow, nf-shard, nf-tower
- Language: TypeScript
- Homepage: https://main.d29s1tosoaghp.amplifyapp.com/
- Size: 2.07 MB
- Stars: 55
- Watchers: 4
- Forks: 9
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# nf-shard
nf-shard is an open source user interface for monitoring Nextflow runs, searching historical runs and analysing metrics. It was designed as drop-in replacement for community [nf-tower](https://github.com/seqeralabs/nf-tower), however it does not aim to replace Enterprise nf-tower.
[](https://www.youtube.com/watch?v=Fzq9cqozwEU)
## Usage in Nextflow
Once nf-shard is running to integrate it into your Nextflow project you should add similar snippet to your `nextflow.config`. The exact form of this snippet will be displayed once you start nf-shard.
```nextflow
tower {
enabled = true
accessToken = "non-empty"
endpoint = "http://localhost:3000/api"
}
```
## Run
Following instructions allows to run `nf-shard` locally. To run nf-shard you PostgreSQL database.
### Method 1 - docker-compose
docker-compose will spin up PostgreSQL database and the server.
```bash
git clone [email protected]:AugustDev/nf-shard.git
cd nf-shard
docker-compose --profile all up
```
If you have PostgreSQL running externally then you only need to launch the server. In this case update your `.env` with `POSTGRES_URI` and run
```bash
git clone [email protected]:AugustDev/nf-shard.git
cd nf-shard
docker-compose --profile server up
```
Add tower server details in your Nextflow config.
```nextflow
tower {
enabled = true
accessToken = "non-empty"
endpoint = "http://localhost:3000/api"
}
```
Done! If you navigate to `http://localhost:3000` and run Nextflow workflow you should be able to see progress in the UI.
Note - `accessToken` can by any non-empty string.
### Method 2 - yarn
If you already have running PostgreSQL database, you can run build the project using yarn package manager. To specify your database login edit `.env`. If you are developer you would prefer using this approach.
```
yarn
yarn migrate
yarn build
yarn run
```
Not that `yarn migrate` requires connection to databse, so you should update `.env` file.
To run PostgreSQL for local development you can use
```
docker-compose --profile db up
```
Since connection to PostgreSQL now happens outside of docker, you should update your `.env` to specify `localhost`
```
POSTGRES_URI=postgresql://postgres:yourpassword@localhost:5432/postgres?schema=public
```
### Method 3 - Vercel
One click deployment using Vercel requires having PostgreSQL access. Video instructions below. In the video I use [Neon.tech](https://neon.tech/) free PostgreSQL version, but any provider works.
[](https://vercel.com/new/clone?repository-url=https%3A%2F%2Fgithub.com%2FAugustDev%2Fnf-shard%2F&env=POSTGRES_URI&project-name=nf-shard&repository-name=nf-shard&demo-title=nf-shard&demo-description=Monitor%20Nextlfow%20pipelines.%20Group%20runs%20into%20workspaces&demo-url=https%3A%2F%2Fmain.d29s1tosoaghp.amplifyapp.com%2F&build-command=yarn%20generate%20%26%26%20yarn%20build%20%26%26%20npx%20prisma%20migrate%20deploy&output-directory=build)
[](https://www.youtube.com/watch?v=luqc2vmKvKY)
## Stack
- NextJS/React/Typescript
- PostgreSQL
- Prisma ORM
I was picking the a stack with large communities to maximise open source contribution from the Nextflow community.
## Features
- [Slack integration](https://www.youtube.com/watch?v=8lWLgvROQ8Q)
- Indexed search by workflow ID, run name, user name, tag, projeect name, before date, after date.
- Search supports multiple `AND` conditions.
- Ability to attach multiple tags for each workflow. Tags are visible in the UI and can be used in search.
- Workspaces
- List of historical runs
- Run details
- `nf-tower` plugin compatible API.
- Store and submit pipeline jobs from Shard UI (beta requires deploying [shard-worker](https://github.com/AugustDev/shard-worker))
## Roadmap
- Authentication
- Dedicated plugin
- Upload/view execution logs
- Download reports
- [tRPC](https://trpc.io/) client/server communication
## Development
Useful during development
```
docker buildx build --platform linux/amd64 -t nf-shard:semver . --load
docker run -it nf-shard:semver /bin/sh
```
## Author
Augustinas Malinauskas