.. only:: wgts_build

   OICR Genomics WGTS Pipeline documentation
   ==========================================

   .. toctree::
      :maxdepth: 1
      :caption: Accredited Pipelines

      informatics-pipelines/informatics-pipelines
      informatics-pipelines/wgts

   .. toctree::
      :maxdepth: 1
      :caption: Data Review and Reporting

      data-review-reporting/data-review-and-reporting
      data-review-reporting/wgts-report
      data-review-reporting/report-tips

   .. toctree::
      :maxdepth: 1
      :caption: Software

      Requisition System <https://oicr-gsi.readthedocs.io/projects/requisition-system/stable>
      infrastructure


.. only:: tar_build

   OICR Genomics TAR Pipeline documentation
   ==========================================

   .. toctree::
      :maxdepth: 1
      :caption: Accredited Pipelines

      informatics-pipelines/informatics-pipelines
      informatics-pipelines/tar

   .. toctree::
      :maxdepth: 1
      :caption: Data Review and Reporting

      data-review-reporting/data-review-and-reporting
      data-review-reporting/tar-report
      data-review-reporting/report-tips

   .. toctree::
      :maxdepth: 1
      :caption: Software

      Requisition System <https://oicr-gsi.readthedocs.io/projects/requisition-system/stable>
      infrastructure


.. only:: pwgs_build

   OICR Genomics pWGS Pipeline documentation
   ===========================================

   .. toctree::
      :maxdepth: 1
      :caption: Accredited Pipelines

      informatics-pipelines/informatics-pipelines
      informatics-pipelines/pwgs

   .. toctree::
      :maxdepth: 1
      :caption: Data Review and Reporting

      data-review-reporting/data-review-and-reporting
      data-review-reporting/plasma-report
      data-review-reporting/report-tips

   .. toctree::
      :maxdepth: 1
      :caption: Software

      Requisition System <https://oicr-gsi.readthedocs.io/projects/requisition-system/stable>
      infrastructure


.. only:: not wgts_build and not tar_build and not pwgs_build

   OICR Genome Sequence Informatics documentation
   ===============================================

   GSI is a team of bioinformaticians and software developers at `Ontario Institute for Cancer Research`_ that develop, maintain, and operate the core analysis infrastructure, analyze genomic data produced at the institute, and support collaborators and researchers with their bioinformatics analysis. To support these activities, we have developed a large suite of open-source software that can be found under our Github organizations: `oicr-gsi`_ and `miso-lims`_.


   .. _Ontario Institute for Cancer Research: https://oicr.on.ca

   .. _oicr-gsi : https://github.com/oicr-gsi

   .. _miso-lims : https://github.com/miso-lims


   Contact us
   -----------

   Contact us through the Github issue tracker on any project.



   .. toctree::
      :maxdepth: 1
      :caption: Accredited Pipelines

      informatics-pipelines/informatics-pipelines
      informatics-pipelines/assays
      informatics-pipelines/wgts
      informatics-pipelines/tar
      informatics-pipelines/pwgs

   .. toctree::
      :maxdepth: 1
      :caption: Data Review and Reporting

      data-review-reporting/data-review-and-reporting
      data-review-reporting/wgts-report
      data-review-reporting/tar-report
      data-review-reporting/plasma-report
      data-review-reporting/report-tips


   .. In most cases, we can use Intersphinx to link between the main project and the subproject
   .. But not in toctree. For some reason.

   .. toctree::
      :maxdepth: 1
      :caption: Research Use Only Pipelines

      ruo-pipelines/ruo-assays

   .. toctree::
      :maxdepth: 1
      :caption: Software

      Requisition System <https://oicr-gsi.readthedocs.io/projects/requisition-system/stable>
      infrastructure

   +----------------+----------------------+
   | **Change Log** | `Github commit log`_ |
   +----------------+----------------------+

   .. _Github commit log : https://github.com/oicr-gsi/oicr-gsi/commits/main/source/index.rst