fixed referencing in docs

README.md

@@ -41,12 +41,15 @@ snakemake
 
 Expected runtime: 25 min
 
+For more information on different installation options, check out the 
+[documentation](https://gagneurlab-drop.readthedocs.io/en/latest/installation.html)
+
 ## Set up a custom project
 Install the drop module according to [installation](#installation) and initialize the project in a custom project directory.
 ### Prepare the input data
 Create a sample annotation that contains the sample IDs, file locations and other information necessary for the pipeline.
 Edit the config file to set the correct file path of sample annotation and locations of non-sample specific input files.
-The requirements are described in the [documentation](https://drop-rna.readthedocs.io/en/latest/prepare.html).
+The requirements are described in the [documentation](https://gagneurlab-drop.readthedocs.io/en/latest/prepare.html).
 
 ### Execute the pipeline
 Once these files are set up, you can execute a dry run from your project directory

docs/source/index.rst

@@ -1,8 +1,10 @@
 DROP - Detection of RNA Outliers Pipeline
 ==========================================
 
-DROP is intended to help researchers use RNA-Seq data in order to detect genes with aberrant expression, aberrant splicing and mono-allelic expression. It consists of three independent modules for each of those strategies. 
-After installing DROP, the user needs to fill in the config file and sample annotation table (Preparing Input Data). Then, DROP can be executed in multiple ways (Executing the Pipeline).
+DROP is intended to help researchers use RNA-Seq data in order to detect genes with aberrant expression,
+aberrant splicing and mono-allelic expression. It consists of three independent modules for each of those strategies.
+After installing DROP, the user needs to fill in the config file and sample annotation table (:ref:`prepare`).
+Then, DROP can be executed in multiple ways (:ref:`pipeline`).
 
 .. toctree::
    :maxdepth: 2

docs/source/pipeline.rst

@@ -1,3 +1,5 @@
+.. _pipeline:
+
 Pipeline Commands
 =================
 
@@ -39,8 +41,8 @@ DROP's steps are computationally heavy, therefore it is a good idea to run them
 If the ``--cores`` flag is not specified, snakemake will use a single core by default.
 
 
-Executing parts of the pipeline
--------------------------------
+Executing subworkflows
+----------------------
 
 Every single module can be called independently.
 
@@ -62,7 +64,7 @@ An example for calling the aberrant expression pipeline with 10 cores would be
 
     snakemake aberrantExpression --cores 10
 
-Rerunning the Pipeline
+Rerunning the pipeline
 ----------------------
 
 When DROP is updated or jobs fail, the following commands can be used to rerun and troubleshoot.