https://github.com/karchinlab/tcrtoolkit-bulk
A NextFlow pipeline for processing and analyzing TCRseq data
https://github.com/karchinlab/tcrtoolkit-bulk
Last synced: 11 months ago
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A NextFlow pipeline for processing and analyzing TCRseq data
- Host: GitHub
- URL: https://github.com/karchinlab/tcrtoolkit-bulk
- Owner: KarchinLab
- Created: 2024-05-18T14:52:49.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2025-07-23T18:50:16.000Z (11 months ago)
- Last Synced: 2025-07-23T20:48:26.859Z (11 months ago)
- Language: Nextflow
- Size: 10.3 MB
- Stars: 1
- Watchers: 3
- Forks: 1
- Open Issues: 16
-
Metadata Files:
- Readme: README.md
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README
# TCRtoolkit-Bulk: A T Cell Repertoire Analysis Platform
Thanks for checking out `TCRtoolkit-Bulk`, the platform for bulk T Cell Repertoire analysis! `TCRtoolkit-Bulk` is wrapped in NextFlow, written in python, and uses Docker to manage dependencies.
We currently support bulk TCRseq data from Adaptive Biotechnologies.
## Requirements
1. Nextflow
Nextflow can be used on any POSIX-compatible system (Linux, OS X, WSL). It requires Bash 3.2 (or later) and Java 11 (or later, up to 18) to be installed.
```{bash}
wget -qO- https://get.nextflow.io | bash
chmod +x nextflow
```
The nextflow executable is now available to run on the command line. The executable can be moved to a directory in your $PATH variable so you can run it from any directory.
2. Docker
`TCRtoolkit-Bulk` runs in Docker containers available [here](https://hub.docker.com/repository/docker/karchinlab/bulktcr/general). Depending on what operating system you are running (Linux, MacOS, WSL), please refer to the [Docker documentation](https://docs.docker.com/engine/install/) for installation instructions.
3. TCRtoolkit-Bulk
```{bash}
git clone https://github.com/KarchinLab/TCRtoolkit-Bulk.git
cd TCRtoolkit-Bulk
```
## Quick Start
Below is a minimal example of how to run the pipeline. The `minimal-example` dataset provided is a small subset of the dataset from this manuscript by [Tumeh and Ribas et al. (2014)](https://www.nature.com/articles/nature13954). Note that the results are simply for demonstration purposes and are not intended for biological interpretation.
```
## from the TCRtoolkit-Bulk directory
nextflow run main.nf \
--samplesheet test_data/minimal-example/samplesheet.csv \
--outdir out-minimal-dev \
--input_format adaptive \
--max_memory 10GB --max_cpus 4
```