Implement code review suggestions
- The Snakefile isn't commented. It should have comments describing the input/output and purpose of each rule => DONE
- The user can't chose between references-based and references-free metrics. They should be able to do by editing the config file. I'll add an if/else in the rule all in the Snakefile => DONE, user can now chose one, both or neither kind of metrics (open to add more kinds of metrics)
- The pipeline doesn't differenciate between long and hi-fi reads. I'll modify the config file and the rule all in the Snakefile => DONE, I can now make assemblers specific to long or hi-fi reads, and chose which to apply to which kind of read independently
- The user might be confused when installing the pipeline : add in an "Installation" section in the readme, and add in a picture of the pipeline diagram => DONE
Edited by MAURICE Nicolas