sid-krish / rhometa

metagenome population recombination rate estimation pipeline
MIT License
12 stars 0 forks source link

Feedback on README.md and the CLI #9

Open cerebis opened 2 years ago

cerebis commented 2 years ago

The Readme

I see you have directed users to look at the console help (--help) for guidance, but this isn't sufficient.

README.md (or a wiki) really needs to spend some words explaining the use of each user-facing unit.

Conscientious reviewers will definitely checkout your repo and attempt to use rhometa. If there is difficulty, you will get negative feedback. Keep in mind, people will only devote so much time when trying a new tool.

Your documentation needs demo of each worfklow and a description of options each has, particularly for those that are mandatory. It's really helpful to offer wisdom on what are sensible values, too. The less a user has to specify initially the better, so long as the options are also explained. When they develop more expertise, they can always come back to twiddle.

Looking lookup_table_gen.nf, I think you really need to provide a nice work-through. How deep is enough, etc? You can also hand them a pre-made table and lessen how critical this section of your help will be, but I would still cosndier it super important that any user that wants to know all the finer points, can learn them.

Comments on Console Help

Your CLI options are frequently long abridged phrases, akin to verbose program variables. As there is little to no context for console commands (unlike a source-code file), long names aren't that enlightening to users. Long names should really just be use when disambiguating similar options.

Using lookup_table_gen.nf as talking point