This package can help you generate Snakemake workflows, enabling you to perform upstream RNA-seq analysis in one step.

Author :qinti

Install the package using pip:

mamba env create - n RNAseq -f environment.yml
pip install RNAseqt

Run the command to initialize a project:

RNAseqt /path/to/project

Edit the congfig.yaml:

vim congfig.yaml
# samples 
# reference

Run the workflow of RNAseq upstream

snakemake -n
snakemake --core 32