Course material for Containers and Workflows in Bioinformatics

1. Introduction to CSC HPC environment and containers

1.1 Slides:Introduction to CSC HPC environment

1.2 Slides:Fundamentals of containers

1.3 Tutorials and exercises

  1. Tutorial1 - Getting familiar with Puhti

  2. Tutorial2 - Hello world Singularity

  3. Tutorial3 - Hello-world Docker example

2. Using Pre-existing Images for Bioapplications

2.1 Slides: Using container images in HPC environment

2.2 Slides:Containerised bio applications

2.3 Tutorials and exercises

  1. Tutorial1 - Using existing Singularity images

  2. Tutorial2 - BLAST example

  3. Tutorial3 - WGS analysis with DeepVariant container

3. Running Singularity on HPC Environment

3.1 Slides: Converting docker images to singularity images

3.2 Slides: Building singularity container images

3.3 Tutorials and exercises

  1. Tutorial1 - Conversion of Docker Images to singularity

  2. Tutorial2 - Converting of local Docker images to singularity

  3. Tutorial3 - Efficient conversion of Docker images to singularity

  4. Tutorial4(bonus) - Sharing images using registries

  5. Tutorial5 - Creating singularity containers from definition files

  6. Tutorial6(Bonus) - Building Singularity container images in sandbox mode

4. Nextflow on HPC

4.1 Slides: Introduction to workflows with nextflow

4.2 Slides: Workflows with singularity containers

4.3 Tutorials and exercises

Tutorial1 - Hello-world example

Tutorial2 - FastQC example

Tutorial3 - Nextflow example with containers

Tutorial4 - nf-core pipeline

Tutorial5 - Run nf-core pipeline with hyperqueue executor

5. Snakemake on HPC

5.1 Tutorials and exercises

Tutorial1 - Sankemake toy example

Tutorial2 - Sankemake tykky example

Tutorial3 - Sankemake with singularity containers

Tutorial4 - Sankemake with hyperqueue executor

Information

This project has received funding from the European High-Performance Computing Joint Undertaking (JU) under grant agreement No 951732.

All material (C) 2020-2021 by CSC -IT Center for Science Ltd.
This work is licensed under a Creative Commons Attribution-ShareAlike 3.0
Unported License, http://creativecommons.org/licenses/by-sa/4.0/

 

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