scMicropipe

A modular Nextflow pipeline for single-cell (scRNA-seq) data analysis, structured in independent sub-workflows for flexibility and reproducibility.

1. Pipeline structure

The scMicropipe pipeline follows a modular architecture implemented in Nextflow.

• The main script main.nf acts as an entry point and dispatches the execution based on the --cmd parameter.
• Each subcommand (DGE_matrix, Data_processing, Celltype_annotation, Integration, Functionality_analysis, Coexpression_modules ) is implemented as an independent workflow in the modules/ directory.
• The workflow is further divided into modular Nextflow processes, allowing clear separation of steps and easier maintenance.
• Helper Python scripts used during processing are located in the bin/ directory.
• A test/ directory is provided with example data to test the pipeline.

This structure ensures that the pipeline is:

• Easy to extend with new subcommands or modules.
• Highly reproducible and portable through the use of Nextflow and Docker.
• User-friendly: each subcommand can be run independently by specifying the appropriate parameters.

Below is the current directory structure:

├── main.nf                         # Main Nextflow script: dispatches to sub-workflow modules
├── config/
│ ├── containers.config             # Docker/Singularity container configuration
├── modules/                        # Modular Nextflow workflows by subcommand
│ ├── DGE_matrix/
│ │ └── main.nf                     # Generation of digital gene expression matrices
│ ├── Data_processing/
│ │ └── main.nf                     # scRNA-seq data filtering and processing
│ ├── Celltype_annotation/
│ │ └── main.nf                     # Cell type annotation and classification
│ ├── Integration/
│ │ └── main.nf                     # Dataset integration and batch effect correction
│ ├── Functionality_analysis/
│ │ └── main.nf                     # Functional analysis (e.g., GSEA, pathway analysis)
│ └── Coexpression_modules/
│ └── main.nf                       # Construction and analysis of coexpression modules
├── bin/                             
├── test/ 
├── README.md 
└── nextflow.config                 # Global configuration and default parameters