.. include:: ../links.inc

.. _running:

Running Jobs
============

Once we have the :ref:`code-less configuration file <codeless>`, we can use the
command line interface to extract the features. This is achieved in a two-step
process: ``run`` and ``collect``.

The ``run`` command is used to extract the features from each element in the
dataset. However, depending on the storage interface, this may create one file
per subject. The ``collect`` command is then used to collect all of the
individual results into a single file.

Assuming that we have a configuration file named ``config.yaml``, the following
commands will extract the features:

.. code-block:: bash

    junifer run config.yaml

The ``run`` command accepts the following additional arguments:

* ``--help``: Show a help message.
* ``--verbose``: Set the verbosity level. Options are ``warning``, ``info``,
  ``debug``.
* ``--element``: The *element* to run. If not specified, all elements will be
  run. This parameter can be specified multiple times to run multiple elements.
  If the *element* requires several parameters, they can be specified by
  separating them with ``,``. It also accepts a file (e.g., ``elements.txt``)
  containing complete or partial element(s).

Example of running two elements:
--------------------------------

.. code-block:: bash

    junifer run config.yaml --element sub-01 --element sub-02

You can also specify the elements via a text file like so:

.. code-block:: bash

    junifer run config.yaml --element elements.txt

And the corresponding ``elements.txt`` would be like so:

.. code-block:: text

    sub-01
    sub-02

Example of elements with multiple parameters and verbose output:
----------------------------------------------------------------

.. code-block:: bash

    junifer run --verbose info config.yaml --element sub-01,ses-01

You can also specify the elements via a text file like so:

.. code-block:: bash

    junifer run --verbose info config.yaml --element elements.txt

And the corresponding ``elements.txt`` would be like so:

.. code-block:: text

    sub-01,ses-01

In case you wanted to run for all possible sessions (e.g., ``ses-01``,
``ses-02``, ``ses-03``) but only for ``sub-01``, you could also do:

.. code-block:: bash

    junifer run --verbose info config.yaml --element sub-01

or,

.. code-block:: bash

    junifer run --verbose info config.yaml --element elements.txt

and then the ``elements.txt`` would be like so:

.. code-block:: text

    sub-01


.. _collect:

Collecting Results
==================

Once the ``run`` command has been executed, the results are stored in the output
directory. However, depending on the storage interface, this may create one file
per subject. The ``collect`` command is then used to collect all of the
individual results into a single file.

Assuming that we have a configuration file named ``config.yaml``, the following
commands will collect the results:

.. code-block:: bash

    junifer collect config.yaml

The ``collect`` command accepts the following additional arguments:

* ``--help``: Show a help message.
* ``--verbose``: Set the verbosity level. Options are ``warning``, ``info``,
  ``debug``.