https://github.com/cellgeni/nf-scvi-metrics

Grid search to optimise hyperparameters for scVI
https://github.com/cellgeni/nf-scvi-metrics

Last synced: 5 months ago
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Grid search to optimise hyperparameters for scVI

• Host: GitHub
• URL: https://github.com/cellgeni/nf-scvi-metrics
• Owner: cellgeni
• License: mit
• Created: 2025-03-06T09:16:01.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2025-07-23T09:25:00.000Z (11 months ago)
• Last Synced: 2025-09-09T23:51:26.327Z (9 months ago)
• Language: Python
• Size: 37.1 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# scVI Hyperparameter Metrics Pipeline  

This pipeline performs a grid search to optimize hyperparameters for `scVI`. The grid is constructed by combining elements from predefined lists of model input parameters. After running `scVI` with each set of parameters, integration metrics are calculated using `scib-metrics`.  

## Repository Contents  

- **`main.nf`** – The Nextflow pipeline that orchestrates the entire workflow.  

- **`nextflow.config`** – Configuration file that:  

  - Submits processes to LSF on Sanger's HPC.  

  - Ensures the correct environment is set via a Singularity container (absolute path).  

  - Defines global default parameters.  

- **`examples/inputs.py`** – Example `.py` file specifying the path to `anndata` and configurations for `scVI` and `scib-metrics`.  

- **`examples/run_scVI_metrics.sh`** – Example script to execute the pipeline. 

- **`Dockerfile`** – Defines a Docker image with `scVI` and `scib-metrics` version `0.2.2`.  

## Pipeline Arguments  

- **`--input_file`** – Path to a `.py` file specifying:  

  - The path to `anndata`.  

  - Configuration details for `scVI` and `scib-metrics`. 

### Optional parameters:

* `--help` — Display this help message

* `--umap` — Set this flag to calculate umap