.. .. codeauthor:: Shaloo Shalini <shaloo_shalini@yahoo.com>

GenPipes v\ |genpipes_version|\  Documentation
==============================================

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        .. dropdown:: :material-outlined:`bolt;2em` Usage Changes (from v5.x)
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        **GenPipes** is a flexible, *Python-based*, open-source framework optimized
        for genomic analysis using *High-Performance Computing (HPC) cluster* 
        and *cloud* environments. It supports the development and deployment of multi-step, scalable,
        validated *genomic workflows*. Various :ref:`genomics applications<docs_gp_usecases>` utilize
        its :ref:`gene sequencing pipelines<docs_pipeline_ref>`.

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            GenPipes is developed and financed by the `Canadian Centre for Computational Genomics <https://www.computationalgenomics.ca>`_ (C3G).

            C3G is a core platform affiliated with `McGill University <https://www.mcgill.ca>`_, provides bioinformatics analysis and HPC services for life sciences research. 

            These services include:
            
            * Bespoke pipeline development
            * Fee-based analyses
            * Other suite of software solutions genomics     

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        This documentation serves both *new* and *experienced* genomics users.
        
        We welcome community :ref:`contributions<docs_contributing>` to GenPipes and its
        documentation. To understand its structure, refer to the :ref:`Site Map<docs_genpipes_archmap>`.

                
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        .. dropdown:: :material-outlined:`lock;2em` DRAC Server Access
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        .. dropdown::  :material-outlined:`coronavirus;2em` Fighting COVID-19
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            GenPipes offers two pipelines: :ref:`CoVSeq<docs_gp_covseq>` for short-read sequencing (e.g., Illumina) and :ref:`Nanopore_CoVSeq<docs_gp_nanopore_cov>` for long-read sequencing. These pipelines help researchers analyze viral sequences and detect mutations quickly, preventing the spread of new strains.

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        .. toctree::
            :maxdepth: 1
            :caption: Overview 
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            about/index
            get-started/gp_usecases
            faq/gp_faq

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         .. toctree::
            :maxdepth: 1
            :caption: Get Started
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            deploy/how_to_deploy_genpipes
            get-started/index
            tutorials/list_tutorials

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         .. toctree::
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            :caption: Reference
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            development/release_notes
            user_guide/user_guide 
            resources/compute_resources

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         .. toctree::
            :maxdepth: 1
            :caption: Support
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            support/how_to_get_support
            user_guide/gp_wizard

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         .. toctree::
            :maxdepth: 1
            :caption: Resources
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            resources/citation
            resources/publications
            resources/workshops

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         .. toctree::
            :maxdepth: 1
            :caption: Community
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            community/channels
            community/contributing

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         .. toctree::
            :maxdepth: 1
            :caption: Development
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            development/dev_guide
            development/gp_release_instructions

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         .. toctree::
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            :caption: Documentation
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            documentation/about
            documentation/genpipes_doc_archmap
            documentation/docs_changelog

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.. Indices and tables
.. ------------------
..
.. * :ref:`genindex`
.. * :ref:`modindex`
.. * :ref:`search`

.. _GitHub Issue 110: https://github.com/c3g/GenPipes/issues/110