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.