Explanation of options when introducing new commands

[florence-bockting]

Description

In the Making a Snakefile section, the following command is introduced without explanation of its options:

snakemake -j1 -p hostname_login

Learners unfamiliar with Snakemake will not know what -j1 and -p do.

Suggested improvements

• Introduce snakemake --help early on as the go-to reference for available options.
• Use the long form of options on first use to make the command self-explanatory:

snakemake --jobs 1 --printshellcmds hostname_login

Short forms (-j1 -p) can be mentioned alongside as convenient shorthands once the meaning is established.