fix: fixed and issue with BASECALLING and QC where reads were not properly counted and processed

	- Minor fixx for modkit: changed chrMT to chrM;
	- Minor fix for pycoqc: added "--sample 0" parameter; this is due to wrong reporting of reads per barcodes;
	- Minor fix for calculate_coverage: added a stageInMode that prevents the wrongfull coverage allocation per barcode in QC process.
	- New referece file is being used in this version of the pipeline - "chm13v2.0.fa" available at https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/analysis_set/chm13v2.0.fa.gz