.. hoge documentation master file, created by
   sphinx-quickstart on Fri Nov 27 13:56:38 2020.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

CaGMeJ
================================

| CaGMeJ(Cancer Genomic Medicine in Japan)はWGS解析パイプラインです。
| Parabricksを使うことでGPUによる高速なゲノム解析を可能とします。
| Parabricksについては https://docs.nvidia.com/clara/parabricks/v3.5/index.html を参考にしてください。


.. gallery?

.. toctree::
   :maxdepth: 1
   :caption: Quick Start-Up Guide

   dna_quick_start.rst
   rna_quick_start.rst

.. toctree::
   :maxdepth: 1
   :caption: Workflow

   dna_workflow.rst
   rna_workflow.rst

.. toctree::
   :maxdepth: 1
   :caption: DNA Analysis Documentation
   
   dna_mapping.rst
   mutation_call.rst
   cnv_detect.rst
   sv_detect.rst
   msi.rst
   hrd.rst
   genomon_pipeline.rst
   virus_count.rst
   hyperclust.rst

.. toctree::
   :maxdepth: 1
   :caption: RNA Analysis Documentation

   rna_mapping.rst
   fusion.rst
   expression.rst

.. toctree::
   :maxdepth: 1
   :caption: Quality Control

   qc.rst

.. toctree::
   :maxdepth: 1
   :caption: Sample Matching

   ngscheckmate.rst

.. toctree::
   :maxdepth: 1
   :caption: File Format

   cram.rst

.. toctree:: 
   :maxdepth: 1
   :caption: Users Guide ( DNA )
    
   dna_pipeline_csv.rst
   dna_pipeline_cfg.rst
   genomon_pipeline_cfg.rst
   dna_output_info.rst

.. toctree::
   :maxdepth: 1
   :caption: Users Guide ( RNA )

   rna_pipeline_csv.rst
   rna_pipeline_cfg.rst
   rna_output_info.rst

.. toctree::
   :maxdepth: 1
   :caption: Report

   pipeline_log.rst
   multiqc.rst

.. toctree::
   :maxdepth: 1
   :caption: Parabricks ( DNA )

   parabricks_fq2bam.rst
   parabricks_mutect.rst
   parabricks_deepvariant.rst
   parabricks_cnvkit.rst
   parabricks_bammetrics.rst


.. toctree::
   :maxdepth: 1
   :caption: Prepare Data

   annovar.rst

.. toctree::
   :maxdepth: 1
   :caption: Linux

   linux.rst

.. toctree::
   :maxdepth: 1
   :caption: Containers

   docker.rst

.. toctree::
   :maxdepth: 1
   :caption: Version Control

   github.rst

.. toctree::
   :maxdepth: 1
   :caption: Reference

   reference.rst

.. toctree::
   :maxdepth: 1
   :caption: Information

   releasenote.rst

.. toctree::
   :maxdepth: 1
   :caption: Contact

   contact.rst