index.md

title	author
Containers and Workflows in Bioinformatics	CSC Training

Course material for Containers and Workflows in Bioinformatics

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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

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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

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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

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4. Nextflow on HPC

4.1 Slides: Introduction to workflows with nextflow

4.2 Slides: Workflows with singularity containers

4.3 Tutorials and exercises

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5. Snakemake on HPC

5.1 Tutorials and exercises

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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/