.. _docs_user_guide:

User Guides
============

.. grid:: 1

    .. grid-item-card:: 

        .. dropdown:: :material-outlined:`bolt;2em` Usage changes v5.x onward
            :color: success

                .. include:: /gp5_0.inc

.. grid:: 2

    .. grid-item-card:: 

        The latest GenPipes release is version |genpipes_version|            

        :ref:`GenPipes<docs_about>` offers several validated bioinformatics pipelines to analyze many kinds of
        genomics data, including DNA, Long-read DNA, RNA, SARS-CoV2, Ch-IP, Amplicon, Nanopore,
        and Methylation sequencing. 

        *Happy genomic analysis with GenPipes!* 

    .. grid-item-card:: 

        .. dropdown:: :material-outlined:`dangerous;2em` DRAC Server Access
            :color: primary

            .. include:: /server_access.inc

        .. include:: /common/new_wizard_dropdown.txt  

        .. tab-set::

            .. tab-item:: New Users

                Check out :ref:`GenPipes Tutorials<doc_list_tutorials>`, use the :ref:`Quick Start<docs_quickstart_gp>` Guide or try the new :ref:`GenPipes Wizard tool<docs_gp_wizard>` to get started. 

            .. tab-item:: Seasoned Users

                Refer to the latest GenPipes :ref:`release notes<docs_release_notes>`. For usage, latest pipelines, and supported protocol options, see :ref:`Pipeline Reference Guide<docs_pipeline_ref>`. 

.. grid:: 2

    .. grid-item-card:: 

        .. toctree::
            :maxdepth: 2
            :caption: Quick Start 
            :name: sec-qs

            quickstart_gp
            gp_checklist

    .. grid-item-card:: 

        .. toctree::
            :maxdepth: 2
            :caption: Wizard 
            :name: sec-wz

            gp_wizard      

.. grid:: 1

    .. grid-item-card:: 

        .. toctree::
            :maxdepth: 2
            :caption: Pipeline Reference 
            :name: sec-pipe-ref

            pipeline_ref