cat < README.md

🧬 Nextflow Project Template Generator

This repository contains a universal automation script to initialize a standardized, nf-core aligned folder structure for bioinformatics pipelines (specifically optimized for Single-Cell Analysis).

🚀 One-Line Usage

Open your terminal and run this command from anywhere to create a new project. Replace `path/to/project` with your desired location:

```bash curl -s https://raw.githubusercontent.com/MJBioInfo/nf-templates/main/folder_creation.sh | bash -s -- path/to/project ```

📂 Included Structure

The script automatically generates:

• workflows/: Main pipeline logic (`main.nf`).
• conf/data_params/: Dedicated space for your `dataset.yaml` files.
• data/: Folders for raw and reference data (ignored by Git).
• results/: Organized output structure for Seurat/AnnData objects.
• Configs: Pre-configured `.gitignore` and `nextflow.config`.

🛠️ Workflow Steps

1. Initialize: Run the curl command above.
2. Configure: Edit `conf/data_params/dataset_v1.yaml` with your data paths.
3. Execute: ```bash nextflow run workflows/main.nf -params-file conf/data_params/dataset_v1.yaml ```

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Status Badges: Portable Automation Single-Cell EOF