https://github.com/solida-core/ride
https://github.com/solida-core/ride
bioinformatics genomics rna-seq-analysis snakemake
Last synced: 5 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/solida-core/ride
- Owner: solida-core
- License: gpl-3.0
- Created: 2019-02-21T13:59:15.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2024-03-26T11:00:05.000Z (about 2 years ago)
- Last Synced: 2025-01-25T08:27:27.158Z (over 1 year ago)
- Topics: bioinformatics, genomics, rna-seq-analysis, snakemake
- Language: Python
- Size: 561 KB
- Stars: 0
- Watchers: 4
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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.
---
## 📦 Requirements
- Conda / Miniconda
- Snakemake ≥ 8.x
- Bash shell (Linux/macOS)
---
## 📥 Clone the Repository
Before installing the environment, clone the pipeline:
```bash
git clone https://github.com/solida-core/ride.git
cd ride
````
---
## 🔧 Setup
Install the Conda environment:
```bash
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:
```bash
make install prefix=/path/to/conda/envs/rna_seq_de_analysis
```
To update the environment:
```bash
make update
```
Show all available Make targets:
```bash
make help
```
---
## ⚙️ 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](config/README.md) for a detailed description of all configuration files and their expected formats.
---
## 🚀 Running the Pipeline
Launch the workflow with:
```bash
./run_ride.sh [options]
```
By default, each execution creates:
```
runs//
```
### 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//
• name → runs//
• path → used exactly as provided
-P PROFILE Snakemake profile directory (e.g. profiles/slurm)
-p PARAMS Additional Snakemake parameters (passed verbatim)
```
### Examples
```bash
# Default run (creates runs//)
./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"
````
---
## 🗂️ 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`
---
## 📊 Output Summary
RIDE produces:
* Trimmed reads and QC reports
* STAR alignments
* kallisto quantification
* DESeq2 differential expression results
* Snakemake HTML report
* Execution summary table
---
## 🛠️ Makefile Targets
```makefile
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
```
---
## 👤 Author
Maintained by Rossano Atzeni — CRS4 Bioinformatics Unit
---
## 📄 License
Distributed under the MIT License (see `LICENSE`).