snakemake-rnaseq

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Usage

Run the test pipeline with testing config:

# run the workflow
docker compose run --rm rnaseq
snakemake --cores 4 --use-conda --configfile ../.test/config/config.yaml

# generate the report
snakemake --configfile ../.test/config/config.yaml --report results/report.html

# exit the container
exit

Run the test pipeline by overriding config values via CLI:

snakemake --cores 4 --use-conda \
  --config raw_data_dir="../.test/test_data" \
          output_dir="results" \
          references_dir="references" \
          samplesheet="../.test/config/samplesheet.csv" \
          comparison="../.test/config/comparison.csv"

Note: These paths act as defaults in config.yaml but can be overridden dynamically via CLI with --config.

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Configuration

See config/README.md for detailed instructions on configuring config.yaml, samplesheet.csv, and comparison.csv.

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Web

You can run the web interface directly with Docker, without installing Node.js or npm locally.

Copy results to web/public

Before starting the web server, copy the analysis results into the web/public directory.
(Modify results if your output folder name is different.)

cp -r ./workflow/results/04_multiqc_reports ./web/public/04_multiqc_reports
cp -r ./workflow/results/05_results ./web/public/05_results
cp ./workflow/results/05_results/images.js ./web/src/assets/images.js

Run with Docker

docker run -it --rm \
  -p 5173:5173 \
  -v $(pwd)/web:/app \
  -w /app \
  node:20-alpine \
  sh -c "npm install && npm run dev -- --host"

# 'Ctrl + C' to exit

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Requirements

• Docker
• Docker Compose
• Snakemake ≥ 9.1.10