Update cmpb content in docs #5 #11

docs/source/cmpb/about-pipeline.rst

@@ -2,18 +2,15 @@ About ``CMPB``
 ==============
 
 The CarveMe + ModelPolisher based (CMPB) pipeline curates a model using refineGEMs and ModelPolisher.
-The starting point is either the input files for CarveMe (future update) or an already built model. If the model is/was 
-built with CarveMe a correction is performed. After that the model is gap filled. The gap fill step can be either done 
-with a manually created file or automatically. Afterwards ModelPolisher is used to enhance the annotation content 
-(future update). Further annotation enhancement is done by adding Pathways as Groups from KEGG and using the SBOannotator 
-via the refineGEMs connection to get more specific SBO term annotations. Afterwards the model is cleaned up with 
-MassChargeCuration and, optionally, with BOFdat. Both tools are accessed via refineGEMs. A further option for the clean 
-up is the removal of duplicates. There are optional steps to analyse the model with FROG (future update) or MEMOTE. The 
-default analysis steps include model statistics, growth analysis and auxotrophy tests. For each step the model version and, 
-optionally, the according MEMOTE report can be saved.
-
-Overview of the CMPB Pipeline
------------------------------
+The starting point is either the input files for CarveMe (future update) or an already built model.
+
+This pipeline aims at minimising the user's workload by concatenating steps that could be done individually with the 
+integrated tools.
+
+.. _cmpb-overview:
+
+Overview of the ``CMPB`` Pipeline
+---------------------------------
 
 The following image shows an overrview of the steps of the pipeline:
 
@@ -23,3 +20,45 @@ The following image shows an overrview of the steps of the pipeline:
   :alt: Workflow from CaveMe to close-to-final model
 
   Workflow from CaveMe to close-to-final model
+
+The following steps are executed in the workflow:
+
+.. hint::
+  All steps can also be performed individually.
+
+  Many of the steps of the pipeline can be fine tuned and turned off/on. 
+  Check the :doc:`configuration file <cmpb-config>` for a full list of all parameters.
+
+- Step 0: Possible inputs
+
+  - Model (e.g. created with CarveMe)
+  - Data to create a model with CarveMe (future update)
+
+- Step 1.A: If the model is/was built with CarveMe a correction is performed as CarveMe adds valuable information for example in the notes and not the corresponding fields of the SBML document. 
+- Step 1.B: The model is gap filled. The gap fill step can be either done with a manually created file or automatically. 
+- Step 2: ModelPolisher is used to enhance the annotation content (future update). 
+- Step 3: Annotations
+
+  - Adding pathways as Groups from KEGG
+  - Using SBOannotator to get more specific SBO term annotations
+
+- Step 4: Model cleanup
+
+  - Using MassChargeCuration
+  - Optionally: Using BOFdat
+  - Optionally: Removing duplicates
+
+- Step 5: Model analyses
+
+  - Model statistics
+  - Analysing growth
+  - Testing for amino acid auxotrophies
+  - Optionally: Analysing with FROG (future update)
+  - Optionally: Analysing with MEMOTE
+
+| For each step the model version and, optionally, the according MEMOTE report can be saved.
+| All tools are accessed via refineGEMs unless stated otherwise. Steps or tools marked as future update will be added soon.
+
+.. note::
+
+    All accessible functions are listed in the :ref:`Contents of SPECIMEN` section.

docs/source/cmpb/run-pipeline.rst

@@ -5,7 +5,7 @@ This page explains how to run the complete ``CMPB`` (CarveMe + ModelPolisher bas
 and how to collect the neccessary data.
 
 For more information about the steps of the pipeline, 
-see :ref:`Overview of the CMPB Pipeline`.
+see :ref:`cmpb-overview`.
 
 ``CMPB``: Quickstart 
 --------------------
@@ -16,7 +16,7 @@ see :ref:`Overview of the CMPB Pipeline`.
     The CarveMe connection will be added in a future update.
 
 The pipeline can either be run directly from the command line or its functions can be called from inside a Python script.
-The input in both cases is a `configuration file <cmpb-config.html>`__ that contains all information needed (data file paths and parameters) to run it.
+The input in both cases is a :doc:`configuration file <cmpb-config>` that contains all information needed (data file paths and parameters) to run it.
 
 The configuration can be downloaded using the command line: