limbo1996 / GATK-snakemake-pipeline

DNA-seq and Neoantigens prediction

Snakemake workflow for neoantigen prediction.

This workflow is still in development

This snakemake pipeline implements the GATK best-practices workflow

Step 1 Clone repository

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

Step 2 Edit files

Configure the workflow accoreding to your needs via editing the files config.yaml， sample.tsv

Step 3 Execute the process

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

Step 4 Inspection results

After execution, you can create a self-contained interactive HTML report with all results via:

snakemake --report report.HTML