Add `--help` option to nextflow_conversion branch

[hyunhwan-bcm]

Description

We need to implement a --help option for the Nextflow script in the nextflow_conversion branch. This will provide users with information about the pipeline's usage, available parameters, and their descriptions.

Proposed Implementation

1. Add a new process or function to handle the --help option.
2. When --help is invoked, display information about:
   • Basic usage
   • Input parameters (e.g., params.input_vcf, params.input_hpo, params.run_id)
   • Output directories and files
   • Reference files and their purposes
   • Brief descriptions of main processes (e.g., VCF processing, annotation, feature engineering, prediction)

Example Help Output

Usage: nextflow run main.nf [options]

Options:
  --input_vcf           Path to input VCF file
  --input_hpo           Path to input HPO file
  --run_id              Unique identifier for this run
  --ref_ver             Reference genome version (hg38 or hg19)
  --outdir              Output directory
  --no_filter_exonic    Skip exonic filtering (default: false)

Reference Files:
  --ref_loc             Path to reference location file
  --ref_to_sym          Path to reference to symbol file
  --ref_sorted_sym      Path to reference sorted symbol file
  --ref_exonic_filter_bed  Path to exonic filter BED file

VEP Annotation:
  --vep_dir_cache       Path to VEP cache directory
  --vep_dir_plugins     Path to VEP plugins directory
  --vep_custom_gnomad   Path to custom gnomAD file for VEP
  --vep_custom_clinvar  Path to custom ClinVar file for VEP
  --vep_custom_hgmd     Path to custom HGMD file for VEP

(Add more parameters as needed)

For detailed information about each process, please refer to the documentation.

Tasks

• [ ] Implement --help option in the main Nextflow script
• [ ] Generate comprehensive help text covering all important parameters and processes
• [ ] Ensure help text is properly formatted and easy to read
• [ ] Test the --help option to verify it displays correctly
• [ ] Update documentation to mention the new --help option

Additional Notes

• Consider using Nextflow's built-in parameter validation and help generation features if available.
• Ensure the help text is kept up-to-date as the pipeline evolves.

[ZaahidShaik]

Made PR for this issue.