Reproducibility

• 1. Before we start
  • 1.1. Pasteur Virtual Machines (VMs)
  • 1.2. Data for the course
• 2. Versionning Control System
  • 2.1. git tutorial/exercices
• 3. Conda
  • 3.1. Conda tutorial/exercises
• 4. Containers
  • 4.1. Docker
  • 4.2. Singularity
• 5. Notebooks
  • 5.1. Introduction to notebooks with Jupyter Lab
• 6. Workflows
  • 6.1. Nextflow
  • 6.2. Snakemake
• 7. Development
  • 7.1. Project structure
  • 7.2. Licensing
  • 7.3. Coding
  • 7.4. Tests
  • 7.5. Documentation
  • 7.6. Automation
  • 7.7. Increase your software visibility
  • 7.8. Take Home Message
• 8. Project
  • 8.1. Introduction
  • 8.2. Input data
  • 8.3. Detailed steps