RIDE – RNA-Seq Differential Expression Pipeline

RIDE is a reproducible and modular Snakemake pipeline for RNA-Seq differential expression analysis.
It performs trimming, alignment, quantification, QC, and DE analysis using STAR, kallisto, and DESeq2.
Each run is fully isolated and includes a snapshot of the configuration for complete traceability.

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📦 Requirements

• Conda / Miniconda
• Snakemake ≥ 8.x
• Bash shell (Linux/macOS)

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📥 Clone the Repository

Before installing the environment, clone the pipeline:

git clone https://github.com/solida-core/ride.git
cd ride

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🔧 Setup

Install the Conda environment:

make install

By default, the environment is created in the standard Conda locations (eg: $HOME/anaconda/envs/ride) You can specify a custom installation prefix using the prefix parameter:

make install prefix=/path/to/conda/envs/rna_seq_de_analysis

To update the environment:

make update

Show all available Make targets:

make help

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⚙️ Configuration

Before running the pipeline, you must edit the configuration files to match your dataset, reference genomes, and analysis parameters.

At minimum, you should review:

• config/config.yaml

• config/samples.tsv

• config/units.tsv

• config/reheader.tsv (optional but recommended)

📁 Configuration details

See config/README.md for a detailed description of all configuration files and their expected formats.

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🚀 Running the Pipeline

Launch the workflow with:

./run_ride.sh [options]

By default, each execution creates:

runs/<timestamp>/

Available options

Usage: run_ride.sh [-h] [-n] [-s SNAKEFILE] [-c CONFIG_FILE] [-w WORKDIR] [-P PROFILE] [-p "PARAMS"]
Launch the RIDE Snakemake workflow.

Options:
-h                Show this help message and exit
-n                Run in dry-run mode (equivalent to --dry-run)
-s SNAKEFILE      Snakefile to use (default: workflow/Snakefile)
-c CONFIG_FILE    Configuration file (default: config/config.yaml)

-w WORKDIR        Run directory:
                    • empty  → runs/<timestamp>/
                    • name   → runs/<name>/
                    • path   → used exactly as provided

-P PROFILE        Snakemake profile directory (e.g. profiles/slurm)
-p PARAMS         Additional Snakemake parameters (passed verbatim)

Examples

# Default run (creates runs/<timestamp>/)
./run_ride.sh

# Custom run name
./run_ride.sh -w test_run

# Use a different configuration file
./run_ride.sh -c config/hg38.yaml -w experiment_A

# Run with a Snakemake cluster profile
./run_ride.sh -P slurm_profile

# Pass extra Snakemake options
./run_ride.sh -p "--cores 40 --latency-wait 60"

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🗂️ Project Structure

config/            # Configuration files
workflow/          # Snakefile, rules, scripts, envs
run_ride.sh        # Launcher
Makefile           # Environment automation
environment.yaml   # Conda environment
runs/              # Output run directories

Each run directory contains a copy of the configuration and all workflow outputs:

• logs
• QC reports
• STAR / kallisto outputs
• DESeq2 results
• summary.tsv
• report.html

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📊 Output Summary

RIDE produces:

• Trimmed reads and QC reports
• STAR alignments
• kallisto quantification
• DESeq2 differential expression results
• Snakemake HTML report
• Execution summary table

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🛠️ Makefile Targets

make help        # Show help
make install     # Install the Conda environment
make update      # Recreate the environment
make clean       # Remove the environment
make run         # Execute the pipeline via the launcher

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👤 Author

Maintained by Rossano Atzeni — CRS4 Bioinformatics Unit

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📄 License

Distributed under the MIT License (see LICENSE).