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.
Before running the subworkflow, ensure you have the following installed:
- Nextflow (version 21.04.0 or higher)
- Java (version 8 or higher)
- Docker or Singularity for containerized execution
- Git
Clone the repository to your local machine:
git clone https://github.com/WangLab-ComputationalBiology/SCRATCH-TCR.git
cd SCRATCH-TCR
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>
--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. Usedocker
orsingularity
depending on your containerization preference. Alternatively, you can create an HPC-aware profile for your institution.
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
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
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
For more detailed documentation and advanced usage, refer to the Nextflow documentation and the comments within the subworkflow script (main.nf
).
Contributions are welcome! Please submit a pull request or open an issue to discuss any changes.
This project is available under the GNU General Public License v3.0. See the LICENSE file for more details.
For questions or issues, please contact: