Add some documentation for the expression module

docs/source/expression.rst

@@ -0,0 +1,54 @@
+expression
+==========
+
+The `expression` module is responsible for determining gene expression levels
+from STAR bam and count files. Although the strandedness of the library
+preparation is important when determining, the module itself is strand
+agnostic. Instead, we take inspiration from STAR and produce output files for
+unstranded, forward stranded and reverse stranded libraries, and leave it to
+the user to select the relevant output for their samples.
+
+Tools
+-----
+This module relies on the STAR count files in combination with a set of housekeeping genes to normalize gene expression levels.
+
+Input
+-----
+The input for this module is one or more pairs of FastQ files per sample, specified in a PEP configuration file, as is shown below.
+
+.. csv-table:: Example input for the expression module
+   :delim: ,
+   :file: ../../test/pep/expression.csv
+
+Output
+------
+
+* Three files with the normalized gene expression levels, one for each strandedness.
+* A single MultiQC report which contains the same data.
+
+Configuration
+-------------
+The following options are available for the `expression` module
+
+
+Example
+^^^^^^^
+.. literalinclude:: ../../test/data/config/expression.json
+   :language: json
+
+Configuration options
+^^^^^^^^^^^^^^^^^^^^^
+.. list-table:: Configuration options
+
+  * - Option
+    - Description
+    - Required
+  * - housekeeping
+    - A list of genes to use for normalizing the expression
+    - yes
+  * - gtf
+    - A GTF file, to look up the ENSG for the housekeeping genes
+    - yes
+  * - bed
+    - A BED file with genomic regions (genes) to quantify
+    - yes

docs/source/index.rst

@@ -13,4 +13,5 @@ Contents
     snv-indels
     fusion
     itd
+    expression
     CHANGELOG 

test/test_docs.yml

@@ -6,6 +6,8 @@
   command: make -C docs/ html
   files:
     - path: docs/build/html/genindex.html
+      contains:
+        - "expression"
 
 - name: test-docs-links
   tags: