Add example configuration

LUMC · Oct 31, 2024 · 8464350 · 8464350
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diff --git a/docs/source/expression.rst b/docs/source/expression.rst
@@ -10,11 +10,13 @@ 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.
+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.
+The input for this module is one BAM file and one STAR count table
+specified in a PEP configuration file, as is shown below.
 
 .. csv-table:: Example input for the expression module
    :delim: ,

diff --git a/docs/source/fusion.rst b/docs/source/fusion.rst
@@ -13,7 +13,11 @@ For each fusion event that remains after filtering, we also generate a figure us
 
 Input
 -----
-The input for this module is a single bam file, generated by STAR per sample, specified in a PEP configuration file, as is shown [here](../test/pep/chrM-bam.csv).
+The input for this module is a single bam file, generated by STAR per sample, specified in a PEP configuration file, as is shown below.
+
+.. csv-table:: Example input for the expression module
+   :delim: ,
+   :file: ../../test/pep/chrM-bam.csv
 
 Output
 ------
@@ -24,6 +28,13 @@ The output of this module are a JSON file with an overview of the most important
 Configuration
 -------------
 
+Example
+^^^^^^^
+.. literalinclude:: ../../test/data/config/fusion.json
+   :language: json
+
+Configuration options
+^^^^^^^^^^^^^^^^^^^^^
 .. list-table:: Configuration options
    :header-rows: 1
 

diff --git a/docs/source/itd.rst b/docs/source/itd.rst
@@ -26,8 +26,12 @@ Configuration
 -------------
 The configuration for this module is tailored to the provided reference files, be very careful if you want to modify any of these settings.
 
+.. literalinclude:: ../../test/data/config/itd.json
+   :language: json
+
+Configuration options
+^^^^^^^^^^^^^^^^^^^^^
 .. list-table:: Configuration options
-   :header-rows: 1
 
   * - Option
     - Description

diff --git a/docs/source/qc-seq.rst b/docs/source/qc-seq.rst
@@ -25,6 +25,13 @@ The output of this module are one set of merged FastQ files per sample, as well
 
 Configuration
 -------------
+Example
+^^^^^^^
+.. literalinclude:: ../../test/data/config/qc-seq.json
+   :language: json
+
+Configuration options
+^^^^^^^^^^^^^^^^^^^^^
 The only configurable option for this module is adapter sequences for
 `cutadapt <https://cutadapt.readthedocs.io/en/stable/>`_ to remove.
 

diff --git a/docs/source/snv-indels.rst b/docs/source/snv-indels.rst
@@ -37,6 +37,17 @@ The output of this module are a JSON file with an overview of the most important
 Configuration
 -------------
 
+Example
+^^^^^^^
+.. literalinclude:: ../../test/data/config/snv-indels.json
+   :language: json
+
+Note that the `vep-cache` entry is missing for this example file, which means
+that the online API of VEP will be used. For the best performance, please
+specify a `vep-cache` folder as well.
+
+Configuration options
+^^^^^^^^^^^^^^^^^^^^^
 .. list-table:: Configuration options
    :header-rows: 1
 
@@ -82,6 +93,9 @@ Configuration
   * - blacklist
     - File of blacklisted variants
     - yes
+  * - vep-cache
+    - Folder containing the VEP cache
+    - no
   * - vep_include_consequence
     - List of `VEP consequences <http://www.ensembl.org/info/genome/variation/prediction/predicted_data.html>_` to report
     - yes