.. _rstoutput:

Output files
============

LIRICAL accepts phenopackets or YAML files as input (see :ref:`rstrunning`). In either case, LIRICAL
can output results in several data formats:

* an `HTML` file with a detailed summary of its analysis results,
* a tab-separated value (`TSV`) file for review in a table editor (e.g. Excel) or for using in bioinformatic pipelines, or
* a JSON file for downstream bioinformatic pipeline.

The HTML report is generated by default. Use the ``-f | --output-format`` option to request other data formats
(e.g. ``--output-format html --output-format json`` to get `HTML` and `JSON` files).


.. toctree::
    :maxdepth: 1

    LIRICAL HTML output <lirical-html>
    LIRICAL TSV output <lirical-tsv>
    LIRICAL JSON output <lirical-json>