Why do we learn to use the shell?
The shell allows users to automate repetitive tasks and capture small data manipulation steps that are normally not recorded to make research reproducible
The Problem
- 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
The Shell
- 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
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