Bioinformatics Workshop on Tools for Reproducible Research
Roundtable Introduce Yourself
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training_reproducible_research
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Tutorials
Cheat sheet
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Bioinformatics Workshop on Tools for Reproducible Research
training_reproducible_research
Home
Tutorials
Tutorials
Introduction
Roundtable Introduce Yourself
Introduction Reproducible Research
Data Management
Ice breaker session
Git
Git
Introduction
Setup
Creating a git repository
Committing changes
Undoing and recovering
Ignoring files
Branching and merging
Tagging commits
Working remotly
Conflict
Extra material
Conda
Conda
Introduction
Setup
The basics
Projects
Extra material
Workflow Manager System
Workflow Manager System
Introduction
Snakemake
Snakemake
Introduction
Setup
The basics
Visualising workflow
The MRSA Workflow
Parameters
Logs
Temporary files
Targets
Shadow rules
Generalizing workflows
Extra material
Nextflow
Nextflow
Introduction
Setup
Getting started with nf-core
The basics
Executing workflows
Working with process
Workflow configuration
Optmising the MRSA workflow
Extra material
Containers
Containers
Introduction
Setup
The basics
Building a Docker image
Managing containers
Distributing your images
Packaging the case study
Singularity
Extra material
Notebook
Notebook
Context
Markdown
R Markdown
R Markdown
Introduction
Setup
The basics
Text
Code chunks
The YAML header
Rendering
The MRSA case study
Extra materiel
Jupyter
Jupyter
Introduction
Setup
The basics
Magics
Plotting
Widgets
Extensions
Converting notebooks
The MRSA case study
Extra material
Quarto
Quarto
Introduction
Setup
The basics
Rendering
Extensions
The MRSA case study
Comparison
Extra material
Making a project reproducible
Making a project reproducible
Review
Good praticies
And now ?
To end on a high note !
Take down
Final word
Cheat sheet
Cheat sheet
Bash
Git
Git official
Conda
Notebook
Docker
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Roundtable Introduce Yourself
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