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 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:

#!/bin/bash
# Run the SeaCells example

nextflow run main.nf \
  --filelist samples.csv \
  --seacells.enabled \
  --seacells.gamma 75 \
  --seacells.type gex \
  --seacells.n_top_genes 2000 \
  --seacells.n_components 50 \
  --seacells.celltype_label celltype \
  --seacells.convergence_epsilon 0.00001 \
  --seacells.min_iterations 10 \
  --seacells.max_iterations 50 \
  -resume