Small Python cleanups. Everything passes flake8 now.

[terrycojones]

Hi Jesse. Here are some very small suggested Python clean-ups for you, if you'd like them. They're all trivial. I don't use snakemake but I think the import snakemake is correct. I added it because it stops tools like flake8 from complaining about the unknown name and also editors from flagging it as unknown.

[jbloom]

@terrycojones, thanks! I had one question: what does E option mean in set -Eeuo pipefail in bash? I could not find an explanation for this one by Google-ing.

[terrycojones]

The -E is a bit obscure I guess. It's like set -e but causes a failure if an error is encountered in code executed in trap. Of course you don't have any traps, but you also don't have any pipes, so pipefail also isn't necessary. The -E is mentioned on the page your script points to https://vaneyckt.io/posts/safer_bash_scripts_with_set_euxo_pipefail/ (which I read years ago, after tracking down a nasty problem that was due to using -e but not realizing that it for some reason didn't apply in pipes). After that I got myself into the habit of always sticking set -Eeuo pipefail at the top of all bash scripts.

[terrycojones]

Actually, man bash has a short and clear explanation: -E If set, any trap on ERR is inherited by shell functions, command substitutions, and commands executed in a subshell environment. The ERR trap is normally not inherited in such cases.