Rules
=====
- Paired End

  - Classification

    - Viral

      .. toctree::
        paired_end/classification/viral/summary.rst

      - Identification

        .. toctree::
          paired_end/classification/viral/identification/summary.rst

    - Report

      - Transcripts

        - Pca

          .. toctree::
            paired_end/classification/report/transcripts/pca/summary.rst

        - Count Table

          .. toctree::
            paired_end/classification/report/transcripts/count_table/summary.rst

        - Revigo

          .. toctree::
            paired_end/classification/report/transcripts/revigo/summary.rst

        - Html Table

          .. toctree::
            paired_end/classification/report/transcripts/html_table/summary.rst

      - Taxonomic Counts

        - Pieplot

          .. toctree::
            paired_end/classification/report/taxonomic_counts/pieplot/summary.rst

        - Barplot

          .. toctree::
            paired_end/classification/report/taxonomic_counts/barplot/summary.rst

        - Alpha Diversity

          .. toctree::
            paired_end/classification/report/taxonomic_counts/alpha_diversity/summary.rst

        - Count Table

          .. toctree::
            paired_end/classification/report/taxonomic_counts/count_table/summary.rst

      - Summary

        .. toctree::
          paired_end/classification/report/summary/summary.rst

    - Contig Based

      .. toctree::
        paired_end/classification/contig_based/summary.rst

    - Transcripts

      .. toctree::
        paired_end/classification/transcripts/summary.rst

    - Differential Analysis

      .. toctree::
        paired_end/classification/differential_analysis/summary.rst

      - Filter Significant

        .. toctree::
          paired_end/classification/differential_analysis/filter_significant/summary.rst

    - Read Based

      .. toctree::
        paired_end/classification/read_based/summary.rst

  - Mapping

    - Mapper

      .. toctree::
        paired_end/mapping/mapper/summary.rst

  - Assembly

    - Report

      - Quality Report

        .. toctree::
          paired_end/assembly/report/quality_report/summary.rst

      - Assembly Graph

        .. toctree::
          paired_end/assembly/report/assembly_graph/summary.rst

    - Assembler

      .. toctree::
        paired_end/assembly/assembler/summary.rst

  - Reads

    - Report

      - Quality Report

        .. toctree::
          paired_end/reads/report/quality_report/summary.rst

    - Preprocess

      - Joined

        .. toctree::
          paired_end/reads/preprocess/joined/summary.rst

      - Deduplicated

        .. toctree::
          paired_end/reads/preprocess/deduplicated/summary.rst

      - Decontaminated

        .. toctree::
          paired_end/reads/preprocess/decontaminated/summary.rst

      - Subsampled

        .. toctree::
          paired_end/reads/preprocess/subsampled/summary.rst

      - Trimmed

        .. toctree::
          paired_end/reads/preprocess/trimmed/summary.rst

- Shared

  - Consensus

    - Caller

      .. toctree::
        shared/consensus/caller/summary.rst

  - Mapping

    - Report

      - Quality Report

        .. toctree::
          shared/mapping/report/quality_report/summary.rst

      - Methylation

        .. toctree::
          shared/mapping/report/methylation/summary.rst

    - Postprocess

      - Deoverlapped

        .. toctree::
          shared/mapping/postprocess/deoverlapped/summary.rst

      - Read Group

        .. toctree::
          shared/mapping/postprocess/read_group/summary.rst

      - Deduplicated

        .. toctree::
          shared/mapping/postprocess/deduplicated/summary.rst

      - Sorted

        .. toctree::
          shared/mapping/postprocess/sorted/summary.rst

      - Realigned

        .. toctree::
          shared/mapping/postprocess/realigned/summary.rst

      - Filtered

        .. toctree::
          shared/mapping/postprocess/filtered/summary.rst

    - Merged

      .. toctree::
        shared/mapping/merged/summary.rst

    - Index

      .. toctree::
        shared/mapping/index/summary.rst

    - Mapper

      - Indices

        .. toctree::
          shared/mapping/mapper/indices/summary.rst

  - Reference

    - Report

      - Phylogenetic Tree

        .. toctree::
          shared/reference/report/phylogenetic_tree/summary.rst

      - Comparison

        .. toctree::
          shared/reference/report/comparison/summary.rst

    - Download

      .. toctree::
        shared/reference/download/summary.rst

    - Alignment

      .. toctree::
        shared/reference/alignment/summary.rst

    - Attributes

      - Desc

        .. toctree::
          shared/reference/attributes/desc/summary.rst

    - Index

      - Dict

        .. toctree::
          shared/reference/index/dict/summary.rst

      - Fai

        .. toctree::
          shared/reference/index/fai/summary.rst

    - Phylogeny

      .. toctree::
        shared/reference/phylogeny/summary.rst

  - Variant

    - Report

      - Summary

        .. toctree::
          shared/variant/report/summary/summary.rst

      - Calling

        .. toctree::
          shared/variant/report/calling/summary.rst

    - Caller

      .. toctree::
        shared/variant/caller/summary.rst

  - Reads

    - Preprocess

      - Conversion

        .. toctree::
          shared/reads/preprocess/conversion/summary.rst

- Single End

  - Mapping

    - Mapper

      .. toctree::
        single_end/mapping/mapper/summary.rst

  - Reads

    - Report

      - Quality Report

        .. toctree::
          single_end/reads/report/quality_report/summary.rst

    - Preprocess

      - Decontaminated

        .. toctree::
          single_end/reads/preprocess/decontaminated/summary.rst

      - Trimmed

        .. toctree::
          single_end/reads/preprocess/trimmed/summary.rst


