Please document the program properly, step by step

[marade]

The current documentation says we need query files and a config file in certain formats, but when I execute mora --help there are no flags for those. Some of the other instructions suggest I need to produce a certain kind of SAM file first, but there are no instructions for that as well.

[AfZheng126]

To see details on the config file, look at "Using the full pipeline with Snakemake" under wiki. Here I describe how to update your config file. You can also look at Snakemake's documentation on how it reads configuration files. If you want to just use Mora as a Rust algorithm, then you need to first prepare a SAM or a BAM file of the reads via some other program like minimap2 etc.

[marade]

Thanks for telling me that here, but what I'm seeking is for that to more clear on the front page. The Snakemake stuff is hidden at the very bottom. There's no documentation on which aligners and invocations are acceptable. The wiki page isn't mentioned at all, and there's only a reference to a wiki page from another program. I'm experienced enough to figure this stuff out for myself, but many people will be lost because the front page is sparse with details.