Snakemake

Snakemake is a workflow management system that helps automate data analysis pipelines. Please read through the snakemake documentation to learn more.

Example Project Folder Structure

• .gitignore
• README.md
• LICENSE.md
• Directoryworkflow

  • Directoryrules

    • module1.smk
    • module2.smk
  • Directoryenvs

    • tool1.yaml
    • tool2.yaml
  • Directoryscripts

    • script1.py
    • script2.R
  • Directorynotebooks

    • notebook1.py.ipynb
    • notebook2.r.ipynb
  • Directoryreport

    • plot1.rst
    • plot2.rst
  • Snakefile
• Directoryconfig

  • config.yaml
  • some-sheet.tsv
• results
• resources