Additional Flags to Run_One

[LeeBergstrand]

          Thanks for making this basic run_one command CLI! In future, for users to be able to use the run_one command effectively, I think we will need to add flags for additional basic run options, in particular

• the type of Nanopore reads (nano-raw vs. nano-hq),
• ~the medaka model name, and~ now the model type is determined automatically.
• the minimum coverage cutoffs for contigs
• minimum length and quality scores for long read QC

There are other options available in rotary, but it could become cumbersome to add them all as flags in the run_one command. Maybe users who want fine-level control over their runs would need to use the run command instead -- thoughts?

Overall, I think the current run_one CLI is OK for this PR, but we might want to add a TODO to add more flags to run_one in the future -- sounds good?

_Originally posted by @jmtsuji in https://github.com/jmtsuji/rotary/pull/46#discussion_r1363332764_

[LeeBergstrand]

"Maybe users who want fine-level control over their runs would need to use the run command instead -- thoughts?"

@jmtsuji I think that this is the approach we should take. We would have standardized settings run for the run_one command with a high-quality and low-quality flag for the nanopore data (the newest flow cells versus the older ones). If users want to tune the setting, they can use the run command.

[LeeBergstrand]

Or add a config file that maps between the flow cell version and recommended settings and add a flag for the flow cell version in a parameter.