1.3 Program

1.3.1 May 3-4: Containers

1.3.1.1 Day 1: Docker

• Containers: introduction and history.
• Docker hub: find existing containers.
• Fetch (and build) an image from public registries (Docker Hub, Quay.io, etc.)
• Discover relevant base images
• Run Docker container based on an existing image (also run it interactively).
• Build an image from an existing recipe:
  • Sections and keywords.
  • Build options (e.g. cache or build variables).
• Write a Docker recipe and build an image from it.

1.3.1.2 Day 2: Docker + Singularity

• Docker:
  • Work with volumes and ports.
  • Upload image to registries.
• Singularity:
  • Singularity versus Docker.
    • Differences, pros and cons for each system.
  • Fetch (and build) a Singularity images.
    • Build from existing public registries.
    • Build from local Docker instances.
  • Run a Singularity container (interactively).
  • Understanding and working with volumes.
  • Singularity build recipes.
  • Advanced features: services, etc.

1.3.2 May 10-11: Nextflow

1.3.2.1 Day 3: Understand the code, run, modify

• Introduction to Nextflow.
• Scripting.
• Basic concepts:
  • Channels, processes and workflows.
• The work folder and its structure.
• The log file.
• Resuming pipelines.

1.3.2.2 Day 4: Write and share

• Decoupling configuration and main script.
• Run Nextflow with containers.
• Run Nextflow on a computing cluster (e.g. HPC):
  • Definition of computing requirements and queues.
  • Profiles.
• Modules, subworkflows, and how to reuse the code.
• Share Nextflow pipelines.