DOC Fix typos & syntax

ngless-toolkit · Nov 3, 2020 · 79846a7 · 79846a7
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diff --git a/ChangeLog b/ChangeLog
@@ -8,7 +8,7 @@ Version 1.2.0 2020-07-12 by luispedro
 	* Enable specifying *all* module resources by URL with download on first
 	use
 	* Fix CIGAR reinjection bug
-	* Remove old motus/specI moduels
+	* Remove old motus/specI modules
 	* No longer ship JS libraries (also do not expand them in-place)
 
 Version 1.1.0 2020-01-25 by luispedro

diff --git a/docs/sources/Functions.rst b/docs/sources/Functions.rst
@@ -408,7 +408,7 @@ lazily: i.e., the first time you use them, NGLess will download and cache them.
 NGLess will also index any database used the first time it is used.
 
 The option ``block_size_megabases`` turns on low memory mode (see the
-corresponding section in the `mapping documentation <mapping.html>`__)
+corresponding section in the `mapping documentation <Mapping.html>`__)
 
 The option ``mode_all=True`` can be passed to include all alignments of both
 single and paired-end reads in the output SAM/BAM.

diff --git a/docs/sources/Mapping.rst b/docs/sources/Mapping.rst
@@ -5,7 +5,7 @@ Mapping is one of the major functions of NGLess. Here we describe, in more
 detail, some of its functionality.
 
 Mapping is implemented using `bwa <http://bio-bwa.sourceforge.net/>`__. As of
-version 0.6, NGLess uses *bwa 0.7.15*.
+version 1.2, NGLess uses *bwa 0.7.17* by default.
 
 By default, bwa is called with default parameters. If the ``mode_all`` argument
 is set to true, then ``-a`` is passed to ``bwa``.

diff --git a/docs/sources/configuration.rst b/docs/sources/configuration.rst
@@ -2,8 +2,8 @@
 Configuration
 =============
 
-.. note:: ngless' results do not change because of configuration or command
-    line options. **The ngless script always has complete information on what
+.. note:: NGLess' results do not change because of configuration or command
+    line options. **The NGLess script always has complete information on what
     is computed**. What configuration options change are details of *how* the
     results are computed such as where to store intermediate files and how many
     CPU cores to use.
@@ -60,7 +60,7 @@ if writing to a file or pipe), ``yes`` (synonym of ``force``).
 ``print-header``: whether to print ngless banner (version info...).
 
 ``user-directory``: user writable directory to cache downloads (default is
-system dependent, on Linux, typically ``$HOME/.local/share/ngless/``.
+system dependent, on Linux, typically it is ``$HOME/.local/share/ngless/``).
 
 ``user-data-directory``: user writable directory to cache data (default is a
 ``data`` directory inside the ``user-directory`` [see above]).