Snakemake workflow: SNP_GATK

A Snakemake workflow for calling snp

Getting started

Install miniforge

wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
bash Miniforge3-Linux-x86_64.sh

Install Snakemake

mamba create -c conda-forge -c bioconda -n env_name snakemake
mamba activate env_name
pip install snakemake-executor-plugin-slurm

Get the workflow

git clone https://github.com/r1cheu/snp_gatk.git
cd snp_gatk
sudo singularity build snp_gatk.sif snp_call.def
### we alse provide a pre-built singularity image

Prepare Samples

modify config/samples.tsv and config/units.tsv. or use the provided python script

python workflow/script/gen_input_csv.py -I /dir/path/to/fastq.gz \
    --fq1 .1.fastq.gz --fq2 .2.fastq.gz

Modify the config file

modify the config/config.yaml and cluster/config.yaml file to fit your needs. e.g. sif: /path/to/snp_gatk.sif, slurm_partition and slurm_account, etc.

Run the workflow

snakemake --profile cluster --cache --rerun-incomplete