Running poretitioner from command line

[kdoroschak]

The previous version of the pipeline could only be run by directly invoking python commands for each step (this was done in a jupyter notebook).

This could be good for some applications, but most bioinformatics software can be directly called on the command line & that should be the default way to run this.

Prerequisites:

• Determine a good format for the config file (currently using yaml, not attached to it in the slightest)
• Define configuration parameters (initial set of parameters here: Document & validate allowed configuration parameters for segmenter #27)
• Determine which sub-commands we want (probably just poretitioner segment; poretitioner filter; poretitioner classify; poretitioner quantify?)

Not sure what further steps should include (unfamiliar with this area)