.. _rstyaml:

YAML input format
=================

The recommended input format for running LIRICAL is the `Phenopacket <https://github.com/phenopackets>`_, but
LIRICAL also supports `YAML <https://en.wikipedia.org/wiki/YAML>`_, which is a simple, human readable format that
is commonly used for configuration files.

YAML
----
LIRICAL uses default values for many configuration options, and a simple YAML configuration file would
include the following information::

    ## LIRICAL Analysis Template.
    # These are all the possible options for running LIRICAL. Use this as a template for your own set-up.
    ---
    sampleId: NF2-example
    hpoIds: ['HP:0002321', 'HP:0000365', 'HP:0000360', 'HP:0009589', 'HP:0002858']
    negatedHpoIds: ['HP:0009736']
    age: P20Y6M
    sex: FEMALE
    vcf: /path/to/example.vcf


In YAML, lines that begin with ``#`` are comments, and the three dashes
indicate the start of the contents of the file.

1. ``sampleId`` is the identifier of the individual being analyzed.
2. ``hpoIds`` is a list of HPO term representing the clinical manifestations observed in the individual being analyzed.
3. ``negatedHpoIds`` a list of HPO terms that represent abnormalities that were **excluded** in the proband.
4. ``age`` age of the individual entered using the ISO8601 duration notation. E.g. ``P20Y6M`` for an individual with age of 20 years and 6 months.
5. ``sex`` sex of the individual, either ``MALE`` or ``FEMALE``.
6. ``vcf`` is the path to the file we want to analyze.
   Note that the VCF file must contain the sample corresponding to ``sampleId`` and
   the CLI must include ``--assembly`` and ``-e19 | -e38`` options to run with a VCF file.

You can use the example file as a starting point for your own configuration file.
An example YAML file can also be found
in the `examples <https://github.com/TheJacksonLaboratory/LIRICAL/tree/master/lirical-cli/src/examples>`_ folder.