Naming Conventions

For sanity and consistency, it’s good practice to be intentional with how you name things. Below is the recommended conventions for different kinds of files.

Github repos

• Style: dashes in place of spaces
• Example: this-is-a-kebab-case-name

Directories on the server

• Style: snake-case (all lowercase with _ in place of spaces)
• Example: this_is_a_snake_case_name

Shell scripts

• Style: All uppercase for variable names
• Example: WORKDIR=path/to/somewhere

R scripts

• Style: snake-case for object and function names
• Example: cod_pedigree <- read.table("cod_pedigree.txt")

Programs

Analysis log

Use a github formatted markdown file to keep track of your analysis logs. You can use RMarkdown to generate this markdown file.