Estimate-host-reads NF conversion

[jihanyehia]

• Added Nextflow license to Metagenomics 3rd-party licenses
• Updated pipeline doc and workflow documentation

[jihanyehia]

• Refactored main.nf to improve parameter validation and streamline workflow execution.
• Introduced new modules for parsing host tables, managing software versions, and updating assay tables.
• Enhanced the KRAKEN2_DB process to support custom FASTA files and pre-built databases.
• Updated the generate_protocol process to use a Python script for better flexibility.
• Migrated to workflow output and removed unnecessary publishDir directives from several processes to simplify output management.
• Added JSON schema for parameter validation.
• Created new conda environment files for dp_tools and kraken2.
• Updated workflow documentation to reflect changes.