feat: refactored basecalling, updated coverage merge, enhanced modkit, unified...

feat: refactored basecalling, updated coverage merge, enhanced modkit, unified tuple IDs and updated containers

main.nf:
	- Updated the use of ‘channel.from’ between steps;
	- Refactored ‘fast5_path’ and ‘pod5_path’ channel construction to use tuple ID across inputs;
	- The new ID format is now derived from the directory structure and filename (this will be altered in future updates);
	- Implemented the logic for selecting basecalling configuration (basecall_arg_val), which was previously defined in ‘BASSECALLING.nf’;
	- Improved logging in step selection and execution parameters;
	- Resolved a pipeline break caused when the modkit subworkflow expected 1 input but received 2 channels instead;
	- Improved readability and code organization.
Basecalling:
	- Updated Dorado to the latest version (v1.3.0);
	- Removed internal ‘basecall_arg_val’ computation from ‘BASECALLING.nf’; now receives the argument computed once in ‘main.nf’;
	- Refactored demultiplexed BAM sorting;
	- Improved structure and indentation of the shell block.
Modkit:
	- Updated Modkit to the latest version (v0.6.0);
	- Modkit pileup now explicitly sets ‘--modified-bases 6mA 5mC 5hmC’ and ‘--reference ${reference_file}’ reflecting changes made in modkit v0.6.0.
Container (debian-nanopore.def):
	- Added a dedicated step to install NumPy/Pandas versions compatible with pycoQC (v3.0.0);
	- Switched jq installation to a pinned GitHub binary using ‘JQ_VERSION’;
	- Updated versions.txt to track new and updated software versions.
Collapse Strands (EXPERIMENTAL):
	- Added initial draft of a ‘COLLAPSE_STRANDS’ process/subworkflow for future strand-collapsing logic;
	- Kept in the repo as an experimental block for future development, as it will be modified and fixed to address duplication issues in modifications across opposite strands.