add mash_dist documentation

Author: bfrgoncalves

docs/resources/reports/mash_dist_table.png

@@ -9,6 +9,7 @@ Pipeline reports
 .. include:: reports/fastqc.rst
 .. include:: reports/fastqc_trimmomatic.rst
 .. include:: reports/integrity_coverage.rst
+.. include:: reports/mash_dist.rst
 .. include:: reports/mlst.rst
 .. include:: reports/patho_typing.rst
 .. include:: reports/pilon.rst
@@ -18,6 +19,7 @@ Pipeline reports
 .. include:: reports/process_spades.rst
 .. include:: reports/process_viral_assembly.rst
 .. include:: reports/seq_typing.rst
+.. include:: reports/sistr.rst
 .. include:: reports/trimmomatic.rst
 .. include:: reports/true_coverage.rst
 

docs/resources/reports/sliding_window_mash_dist.png

@@ -0,0 +1,20 @@
+mash_dist
+---------
+
+Table data
+^^^^^^^^^^
+
+Plasmids table:
+    - **Mash Dist**: Number of plasmid hits
+
+.. image:: ../resources/reports/mash_dist_table.png
+    :align: center
+
+Plot data
+^^^^^^^^^
+
+- **Sliding window Plasmid annotation**: Provides annotation of plasmid
+  hits along the genome assembly. This report component is only available
+  when the ``mash_dist`` component is used.
+
+.. image:: ../resources/reports/sliding_window_mash_dist.png

docs/user/pipeline_reports.rst

@@ -0,0 +1,11 @@
+sistr
+-----
+
+Table data
+^^^^^^^^^^
+
+Typing table:
+    - **sistr**: The sequence typing result.
+
+.. image:: ../resources/reports/typing_table.png
+    :align: center