snakepipes_ATAC-seq

about author

author: 赵华男 | ZHAO Hua-nan

email: hermanzhaozzzz@gmail.com

Zhihu | BLOG

doc

snakepipes_ATAC-seq is a standard snakemake pipeline for ATAC-seq sequencing data

env

conda env create -f conda_env.yml

run

# run Jupyter notebook to abtain the config
# run this cmd
# or
# open notebook and run all cells
runipy step.01.GetFileName.ipynb
# dry run for test
snakemake -pr -j 10 -s step.02.Snakefile.smk.py -n
# run calculation
snakemake -pr -j 10 -s step.02.Snakefile.smk.py

project structure