Feature request: Support Multiple Output Formats (CSV, TSV, JSON)

[berntpopp]

• Description: The pipeline currently outputs results in a single format (TSV). To increase flexibility and usability, the pipeline should support additional output formats, such as CSV and JSON. Users should be able to specify the desired output format via a command-line argument or configuration file.
• Tasks:
  • Implement support for CSV and JSON output formats.
  • Add a command-line argument or config option to specify the desired output format.
  • Update the documentation to reflect the new output format options.
  • Ensure that the pipeline output is consistent across all formats.

[berntpopp]

Actually, the current summarized output is only an html file as a summary_report.
The intermediate steps generate different file formats.
We could introduce a function that generates summary outputs in different tabular or machine-readable file formats along the HTML output.