PRACS-AU25
Week overviews
Week 1: Omics data and OSC
Week 2: Project organization and Unix shell basics
Week 3: Working with files in the Unix shell
Week 4: Version control with Git and GitHub
Week 5: Software management at OSC
Week 6: Shell scripts and CLI tools
Week 7: Slurm batch jobs at OSC
Week 8: Catch-up (half-week)
Week 9: Workflow and data management
Week 10: Using generative AI
Week 11: R basics
Week 12: R + Markdown with Quarto (half-week)
Week 13: R – data visualization
Week 14: R – omics data (half-week)
Week 15: Nextflow nf-core pipelines
Week 16: Student presentations
Exercises
Week 3: Unix shell
Week 5: GitHub and software at OSC
Week 7: Shell scripts
Week 9: Workflow and data management
Week 11: R basics
Week 12: Quarto
Week 14: R for omics data
Week 15: nf-core pipelines
Assignments
GRADED
GA 1: Markdown and Unix shell basics (Week 2)
GA 2: Unix shell data tools and Git (Week 4)
GA 3: Shell scripts and software (Week 6)
GA 4: Slurm batch jobs (Week 8)
GA 5: Coding with generative AI (Week 10)
GA 6: Data analysis with R (Week 13)
UA 1: Pre-course survey (week 1)
UA 2: OSC account setup (week 1)
UA 3: GitHub account setup (week 4)
UA 4: Local VS Code installation (week 9)
UA 5: Post-course survey (week 16) [TBA]
Final project
General info
FP 1: Proposal (week 12)
FP 2: Draft (week 14)
FP 3: Oral presentation (week 16)
FP 4: Final submission (week 16)
Other
Reference material
Course references
Optional self-study material
Advanced Git and GitHub
Software management with Conda
Advanced shell scripting
Additional data management notes
SSH connections
About
Source Code
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Week 15 Exercises: Running nf-core pipelines
Author
Affiliation
Jelmer Poelstra
CFAES Bioinformatics Core, Ohio State University
Published
December 1, 2025
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