Add chapter on concepts

docs/source/concepts.rst

+Concepts
+========
+
+PSOT is a system that executes bioinformatic tools on a file with protein
+sequences and converts the results into easy to process json documents. It
+contains a live mode that writes the results of already finished tools into
+a directory, which can be polled and further processed, e.g. by a website
+that displays results as they become ready.
+
+Vocabulary
+----------
+
+Module
+    A module implements a bioinformatic tool and the corresponding json converter.
+    It is defined in a module manifest.
+
+Profile
+    A profile is a set of modules that are executed during an execution of PSOT.
+    Profiles can override default parameters of modules.
+
+Workflow
+--------
+
+1. Load all module manifests and profiles
+2. Create an execution directory
+3. Generate a nextflow script for the choosen profile in the execution directory
+4. Run the nextflow script
+5. Remove the execution directory
+
+Structure of the Nextflow Script
+----------------------------
+
+1. Run all analyses in parallel
+2. Convert all analyses in parallel
+3. In live mode: generate a json document for each module and each sequence within the live directory
+4. Join all json files into a single one containing all information
+5. Split the large json file into separate files for each sequence
+

docs/source/index.rst

@@ -10,6 +10,7 @@ Welcome to PSOT - protein sequence observation tool's documentation!
    :maxdepth: 2
    :caption: Contents:
 
+   concepts
    modules
 
 

docs/source/modules.rst

 .. highlight:: yaml
+
 Modules
 =======
 
@@ -45,3 +46,4 @@ A module manifest has the following structure::
 	    dbxref: UniProtKB/Swiss-Prot
 
 These parameters can be overridden in the profile.
+