captcr-snakemake

Author: [email protected] Orginal repo: https://github.com/arnavaz/cap-tcr

This repository is to automate the pughlab captcr pipeline using a snakemake workflow The pipeline consists of barcode extraction, running mixcr, running QC, and clonetracking

Intallation requirements

1. python-3.4.3 or higher
2. Biopython (python package)
3. pandas (python package)
4. numpy (python package)
5. matplotlib (python package)
6. R/3.6 or higher
7. ggplot2 (R-package)
8. ggalluvial (R-package)
9. randomcoloR (R-package)

Run with example data

# clone the repo
salloc -c 1 -t 2:00:00 --mem=6G -p build

git clone https://github.com/LupienLab/cap-tcr.git

# Update config file
vi config.yaml

# Run Snakemake or submit a job
snakemake -s Snakefile --cores 1