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https://github.com/cellgeni/nf-metacells

https://github.com/cellgeni/nf-metacells

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Repository

Basic Info
  • Host: GitHub
  • Owner: cellgeni
  • Language: Python
  • Default Branch: main
  • Size: 63.5 KB
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Created over 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme

README.md

nf-metacells

This project uses Nextflow to run SEACells analysis on single-cell RNA/ATAC sequencing data.

Project Structure

/lustre/scratch127/cellgen/cellgeni/aljes/nf-metacells/ ├── main.nf ├── nextflow.config ├── example/ │ ├── run_seacells.sh │ └── samples.csv └── README.md

Usage

To run the SeaCells analysis, use the provided script in the example directory:

bash bash example/run_seacells.sh

Parameters

The following parameters can be configured in the main.nf script:

  • --filelist: Path to the CSV file containing sample information.
  • --seacells.enabled: Enable SeaCells analysis.
  • --seacells.gamma: Gamma parameter for SeaCells.
  • --seacells.type: Type of data (e.g., gex).
  • --seacells.n_top_genes: Number of top genes to consider.
  • --seacells.n_components: Number of components for dimensionality reduction.
  • --seacells.celltype_label: Label for cell types.
  • --seacells.convergence_epsilon: Convergence epsilon for the algorithm.
  • --seacells.min_iterations: Minimum number of iterations.
  • --seacells.max_iterations: Maximum number of iterations.

Example

An example script is provided to demonstrate how to run the analysis:

```bash

!/bin/bash

Run the SeaCells example

nextflow run main.nf \ --filelist samples.csv \ --seacells.enabled \ --seacells.gamma 75 \ --seacells.type gex \ --seacells.ntopgenes 2000 \ --seacells.ncomponents 50 \ --seacells.celltypelabel celltype \ --seacells.convergenceepsilon 0.00001 \ --seacells.miniterations 10 \ --seacells.max_iterations 50 \ -resume ```

Owner

  • Name: Cellular Genetics Informatics
  • Login: cellgeni
  • Kind: organization
  • Location: United Kingdom

Wellcome Sanger Institute

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