Bohra
-------
`Bohra <https://github.com/MDU-PHL/bohra>`_ is a microbial genomics pipeline.

Bohra is made available on the cluster as a shared :doc:`Apptainer <apptainer>` container image. 

You can use the :code:`apptainer/bohra` module which will add convenient aliases to the :code:`bohra` binary, which will run within the container.

See the `Bohra wiki <https://github.com/MDU-PHL/bohra/wiki>`_ for usage information.

.. code-block:: bash

    module load apptainer/bohra
    # The following is required to use aliases in a non-interactive/SLURM batch script:
    shopt -s expand_aliases
    bohra test
    bohra run ......