1. Introduction to HPC Containers

Slides: Brief Introduction to CSC HPC Environments

Slides: Introduction to Apptainer containers

Slides: Tykky Container Wrapper

Tutorials and exercises

1. Tutorial1 - Tykky container wrapper

2. Building and Using HPC Containers

Slides: Basic Usage of Apptainer Containers

Slides: Building Apptainer/Singularity container images

Tutorials and exercises

1. Tutorial1 - Running applications in containers

2. Tutorial2 - Creating Apptainer containers from definition files

3. Tutorial3(bonus) - Building Apptainer container images in sandbox mode (Bonus tutorial)

3. Working with Docker Containers

Slides: Basic introduction to Docker containers

Slides: Working with containerised applications

Tutorials and exercises

1. Tutorial1 - Hello-world Docker example

2. Tutorial2 - Converting a local Docker image to Apptainer

3. Tutorial3 - Analysis with containerised BLAST software

4. Tutorial4(bonus) - Sharing images using registries

5. Tutorial5(bonus) - WGS analysis with DeepVariant container

4. Containers in web applications and workflows

Slides: Rstudio and Jupyter Notebooks

Slides: Brief Introduction to Bio-workflows

Slides: Running Nextflow and Snakemake workflows at CSC

Tutorials and exercises

1. Tutorial1 - Launch custom Jupyter notebook

2. Tutorial2 - Hello-world Nextflow example

3. Tutorial3 - Containerised FastQC in Nextflow

4. Tutorial4 - Run nf-core pipelines at CSC

5. Tutorial5 - High-throughput Snakemake workflows

6. Tutorial6 - Custom Rstudio on Puhti

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