.. _profiles:

Profiles
========

To select one or multiple profiles, please use the ``-profile`` option. For example:

::

    $>  nextflow run scilus/nf-mouse_flow --input input_folder -profile singularity --atlas atlas_directory -resume 

Profiles available
------------------

``singularity``
    When this profile is used, MouseFlow will use Singularity containers.

``docker``
    When this profile is used, MouseFlow will use Docker containers.

``run_preqc``
    When this profile is used, MouseFlow will run the preqc step.
    Combined with --use_preqc, it will run the preqc step and use the preqc results to run the pipeline.