RSE Tools Tech Group
đź‘‹ Welcome to the NBIS RSE Tools Tech Group!
These blog posts are short walkthroughs on various Research Software Engineering (RSE) tools useful in bioinformatics. We aim to share a demonstration of a tool every two weeks.
Want to discuss or need help? Start a discussion on our Discussions page or reach out on the #tech-group-rse-tools channel on NBIS Slack.
Walkthroughs
Targets: A workflow manager in R
R
Targets
Workflow management
Reproducibility
5-Minute Tool Tips Showcase
Containers
Pixi
Wave
SSH
Terminal
Git
Obsidian
An introduction to the Snakemake workflow manager
Snakemake
Workflow management
Reproducibility
nf-test: A Nextflow testing framework
Nextflow
Testing
nf-core
Dotfile Management with Git
Git
Version control
Terminal
Introduction to Blender
Blender
b3d
visualization
computer graphics
Working with nf-core modules
Nextflow
Workflow management
nf-core
Introduction to Configure and Make
HPC
Software installation
Bioinformatics
Terminal
Tips and Tricks
Working Reproducibly
Reproducibility
Documentation
Version control
Package management
Workflow management
Reintroduction to Pixi
Pixi
Package management
Command runner
GitHub Pull Requests and Code Reviews
GitHub
Pull Requests
Code Reviews
Copilot and VSCode - protecting sensitive data
Copilot
VSCode
AI
IDE
Secure Data Environment
Tips and Tricks
Working with R packages
R
Package management
Bioconductor
Version control
Introduction to GitHub Actions
GitHub Actions
Continuous integration
Nextflow best practices
Nextflow
Nextflow foundations
Nextflow
Pixi tools on HPC centers
Pixi
HPC
Secure Data Environment
Introduction to Docker
Docker
Containers
Package management
Introduction to Container Registries
Docker
GitHub
Seqera
Various Tips and Tricks
Terminal
Quarto
Nano
MacOS
Nextflow
Conda
PacMan
R
Dardel
VSCode
Tips and Tricks
When to use Nextflow?
Nextflow
README’s in GitHub
GitHub
Documentation
Self-promotion
Introduction to VSCode
VSCode
Remote development
IDE
Introduction to Pixi
Pixi
Package management
Command runner
Introduction to Apptainer
Apptainer
Singularity
Containers
Package management
Quarto to Confluence
Quarto
Literate programming
Confluence
Introduction to Gitpod
Git
GitHub
Version control
Gitpod
Introduction to Quarto
Quarto
Literate programming
Introduction to Git
Git
Version control
Collaboration on GitHub
Git
GitHub
Version control
Collaboration
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