Snakemake workflow for neoantigen prediction.
This workflow is still in development
This snakemake pipeline implements the GATK best-practices workflow
Clone this repository to your local system 需要写一个脚本判断是否有conda，如果没有自动下载安装并创建snakemake环境
Configure the workflow accoreding to your needs via editing the files config.yaml， sample.tsv
This workflow will download reference genomes and annotation automatically. Test your configuration by performing a dry-run via
snakemake --use-conda -n
Execute the workflow locally via
snakemake --use-conda --cores N
using N cores or run it in a cluster environment via
snakemake --use-conda --cluster qsub --jobs 100
After execution, you can create a self-contained interactive HTML report with all results via:
snakemake --report report.HTML