up: basecalling, nextflow.config, nextflow parameters and readability

 - Updated multiple variables in nextflow.config to match them across the different processes and workflows;
 - Added profiles in nextflow to facilitate the steps;
 - Added --kit-name configuration (params.barcoding_kit) to improve trimming during basecalling;
 - Changed descriptions across variables in nextflow.config;
 - Improved output directory name to include the projects' name (params.project_name);
 - Updated params.basecall_speed to use latest available simplex/modification model for basecalling;
 - Reorganized demux process to be included in the basecalling process to improve code readability;
 - Corrected few typos.