Snakemake version of Decontamination of small-RNA sequencing samples from mouse

Snakemake reimplementation of decont, a training by @tdido, developed for educational purposes to illustrate what a Workflow Management System (WMS) is and why working with one is interesting.

It is assumed that you have previously worked with the bash version of decont and therefore already have a conda environment manager installed.

Usage

1. Download decont_snk from GitHub

Use the git clone command to create a local copy of the repository.

git clone https://github.com/villena-francis/decont_snk

2. Set up the environment

This pipeline requires a conda package manager and bioconda. It is also essential to install Snakemake, which in this case, will be set up in a Conda environment:

conda create -n snakemake_env snakemake graphviz -y

3. Run the workflow

First, navigate to the decont_snk directory, activate the Conda environment snakemake_env, and execute the Snakemake command with the arguments specified below.

# Activate the environment
conda activate snakemake_env
# Dry Run
snakemake --use-conda -j unlimited -n

The -n argument performs a dry run, meaning Snakemake will display which rules would be executed without actually running them.

The following command is an interesting way to visualize the pipeline as a directed acyclic graph (DAG), showing the dependencies between rules.

snakemake --dag | dot -Tpdf > dag.pdf

This is why graphviz was installed in the environment.

Now we can run the pipeline for real by removing the dry-run flag -n from the previous command.

snakemake --use-conda -j unlimited

🚧 Under construction 🚧