| layout | title | subtitle |
|---|---|---|
slides |
The Unix Shell |
Motivation |
The shell allows users to automate repetitive tasks and capture small data manipulation steps that are normally not recorded to make research reproducible
- Running the same workflow on several samples can be unnecessarily labour intensive
- Manual manipulation of data files:
- is often not captured in documentation
- is hard to reproduce
- is hard to troubleshoot, review, or improve
- Workflows can be automated through the use of shell scripts
- Built-in commands allow for easy data manipulation (e.g. sort, grep, etc.)
- Every step can be captured in the shell script and allow reproducibility and easy troubleshooting