/
pipe_setup.rst
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/
pipe_setup.rst
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Pipe Setup
==========
Pipe Settings Location
----------------------
The Default *CUT&RUN-Flow* settings used by the system are located in
*CUT&RUN-Flow's* installation directory. This is by default located
in the user's ``$HOME`` directory as such:
.. code-block:: bash
# PIpe Defaults Configuration:
$NXF_HOME/assets/rennelab/CnR-flow/nextflow.config # Pipe Executor, Dependency, Resource, etc. Configuration
#Default: $HOME/.nextflow/assets/rennelab/CnR-flow/nextflow.config
It is recommended that dependency configuration and other pipe-level
settings be configured here. An example of this file is provided
in :ref:`Pipe nextflow.config`.
.. note:: If any settings are provided in both the
above :ref:`Pipe nextflow.config` file and the
:ref:`Task nextflow.config` file located in the task directory,
the task-directory settings will take precedence. For more
information on Nextflow configuration precedence, see
:manpage:`config`.
Dependencies
------------
The following external dependencies are utilized by *CUT&RUN-Flow*:
.. csv-table:: Dependencies
:header-rows: 1
:file: ../../build_info/dependencies.tsv
:delim: tab
:name: dependencies_table
Dependency Config
-----------------
Conda/Bioconda
++++++++++++++
| *CUT&RUN-FLow* comes preconfigured to use the Conda_ package manager,
along with tools from the Bioconda_ [Bioconda_Citation]_ package
suite for automated dependency handling. Nextflow_ automatically
acquires, stores, and activates each conda environment as it is
required in the pipeline. For more information on Nextflow's,
usage of conda, see :manpage:`conda`.
.. include:: ../../build_info/config_zz_auto_conda_config.txt
:literal:
Modules
++++++++++++++
| *CUT&RUN-FLow* comes with an alternative "easy" configuration option
utilizng `Environment Modules <Envrionment_Modules>`_. Each conda
dependency paramater has an equivalent "module" paramater. Each module
will then be loaded at runtime for the appropriate steps of the pipeline.
For more information on Nextflow's use of Environment Modules,
see :manpage:`process` ("modules section").
.. include:: ../../build_info/config_zz_auto_module_config.txt
:literal:
Executable System Calls
++++++++++++++++++++++++
| To accommodate custom module or local setups, each required
dependency system call can be customized:
.. include:: ../../build_info/config_zz_auto_call_config.txt
:literal: