Execution

This section guides you through running the workflow to compute relative abundance metrics for various microbial species.

Clone the repository

Clone the GitHub repository to access the scripts and configuration files needed for the workflow:

git clone https://github.com/pankajchejara23/16S-workflow

Download dataset

Navigate to the cloned repository and download the dataset using the provided script:

cd 16S-workflow
sh ./scripts/downloader.sh

Create processing environment

Set up the required Conda environment using the environment file:

conda env create -f ../envs/environment.yml
conda activate qiime2_snakemake

Configure Snakemake workflow

The config.yaml file is preconfigured for this workflow. If needed, edit the file to customize parameters for your specific use case.

Execute

Run the Snakemake workflow using the following command:

Snakemake --cores 4