up: modkit parameters to improve modification data analysis

- changed modkit extract full to modkit extract calls for testing (future updates will contain a new modified modkit extract full);
- implemented reference FASTA file in modkit extract calls;
- updated modkit.yaml with path to reference file used in modkit;
- implemented region delimiter to mitochondrial DNA using --region MT;
- implemented a filter-threshold of 0.9 for all bases;
- implemented bgzf compression of calls.tsv to improve storage management;
- implemented modkit sample-probs to analyse distribution of bases (cannonicals and modified) across the samples;
- added 6mA in nextflow.config to be basecalled concurrently with 5mC_5hmC.