API reference
=============

Top-level
---------

.. autosummary::
   :toctree: _autosummary
   :recursive:

   capellini.config
   capellini.pipeline

Stages
------

.. autosummary::
   :toctree: _autosummary
   :recursive:

   capellini.stages.preflight
   capellini.stages.dada2
   capellini.stages.ncbi_mapping
   capellini.stages.mmseqs2
   capellini.stages.spacepharer
   capellini.stages.procs
   capellini.stages.network

Utilities
---------

.. autosummary::
   :toctree: _autosummary
   :recursive:

   capellini.utils.io
   capellini.utils.taxonomy
   capellini.utils.transforms
   capellini.utils.network_utils