/SCRATCH-TCR

SCRATCH subworkflow for integrating scRNA and scRNA data

Primary LanguageNextflowGNU General Public License v3.0GPL-3.0

SCRATCH TCR Subworkflow

Introduction

This repository contains a Nextflow subworkflow for analyzing TCR sequencing data. The subworkflow integrates various processes to handle and analyze the provided input files, ensuring reproducibility and scalability.

Prerequisites

Before running the subworkflow, ensure you have the following installed:

Installation

Clone the repository to your local machine:

git clone https://github.com/WangLab-ComputationalBiology/SCRATCH-TCR.git
cd SCRATCH-TCR

Usage

To run the subworkflow, use the following command:

nextflow run main.nf -profile [docker/singularity] --input_vdj_contigs <path/to/vdj_contigs> --input_exp_table <path/to/exp_table> --input_annotated_object <path/to/annotated_object> --project_name <project_name>

Parameters

  • --input_vdj_contigs: Path to the VDJ contigs input file (required).
  • --input_exp_table: Path to the expression table input file (required).
  • --input_annotated_object: Path to the annotated object input file (required).
  • --project_name: Name of the project for organizing results (required).
  • -profile: Execution profile. Use docker or singularity depending on your containerization preference. Alternatively, you can create an HPC-aware profile for your institution.

Example

nextflow run main.nf -profile docker --input_vdj_contigs data/vdj_contigs.csv --input_exp_table data/exp_table.csv --input_annotated_object data/annotated_object.RDS --project_name Test

Configuration

The subworkflow can be configured using the nextflow.config file. Modify this file to set default parameters, profiles, and other settings. An institution profile should be created whenever running the pipeline in an HPC environment, please refer to Step-by-step guide to writing an institutional profile

Output

Upon successful completion, the results will be available in a directory named after your project (<project_name>). You can open the report in your browser:

Done! Open the following report in your browser -> <path/to/launchDir>/<project_name>/report/index.html

Documentation

For more detailed documentation and advanced usage, refer to the Nextflow documentation and the comments within the subworkflow script (main.nf).

Contributing

Contributions are welcome! Please submit a pull request or open an issue to discuss any changes.

License

This project is available under the GNU General Public License v3.0. See the LICENSE file for more details.

Contact

For questions or issues, please contact: