Consistent bystro config naming scheme

[wingolab]

Background:

A concise description of why we're pursuing this task.

The bystro configuration file uses different styles to name keys. It would make it easier if it was more consistent. I suggest lower case with underlines (e.g., snake_case) but recognize this is arbitrary.

Completion Criteria:

What is the goal, and how do we know this task is accomplished?

• Update the bystro perl code to use lower case with underlines.
• Convert the existing example genome builds to the lower case with underlines convention.

Implementation Summary

Give enough technical detail for a teammate to understand the proposed solution.

Examine the code base - probably at the build steps - to determine the scope of change that this might entail.

[akotlar]

For the perl codebase, the intention was to only use snake_case for CLI arguments, so converting entirely to camelCase will be far easier. Would this be workable?

[akotlar]

Thinking about this some more I don't think that will be satisfactory. I'll convert the perl codebase to snake_case in a series of PRs; we'll do it gradually to avoid breaking too much.

[wingolab]

The intention behind my suggestion was around the configuration file and any areas of the code that require adapting to a change from the existing name to one that uses lower case with underscores (e.g., snake_case). I didn't mean that we should change the entire Perl code base to use snake_case.

The bigger issue with the configuration files are their complexity, and what seems like some inconsistency between how track keys are used between different tracks (it was only one track's keys that behaved differently - not recalling it at the moment). This led me to look at configuration languages that 1) could enforce a schema; 2) allow the configuration to be split across several files for readability and maintenance ease; and, 3) would not make us change anything about the YAML and Perl code. I came across pkl that might be something worth considering. It seems like it was just released but the tutorial and docs made me think it would be a few days of work to adapt for our project.

[akotlar]

I like the suggestion and will look into pkl. I agree the configuration files are complex. Better documentation will help some as well.