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docs/jflow-core-workflow.html

@@ -569,7 +569,10 @@ self.add_parameter("sequencer", "The sequencer type.", choices=["HiSeq2000",
 				<div class="page-header">
 			    	<h1>Overloading <i>process</i></h1>
 			    </div>
-		    	<p>The <code>process()</code> method defines the actions to do by the workflow.</p>
+		    	<p>The <code>process()</code> method defines the actions done by the workflow.</p>
+		    	<p>In process you can add components with the method <code>add_component()</code>. 
+		    	A component is class which represents a step in the workflow defined by a set of commands.
+		    	The components sequence and their parallelisation are managed by the input and output linkage between components.</p>
 		    	<pre class="pre-hl "><code class="python">def process(self):
     """ 
     Run the workflow
@@ -582,8 +585,6 @@ self.add_parameter("sequencer", "The sequencer type.", choices=["HiSeq2000",
     
     # align reads against indexed genome
     bwa = self.add_component("BWA", [indexed_ref, self.read_1, self.read_2])</code></pre>
-				<img src="./img/workflow_alignment.png">
-				<p>The components sequence and their parallelisation are managed by the input and output linkage between components.</p>
    				<h2>The add_component() method</h2>
    				<p>This method is used to add a component to the workflow.</p>
    				<div class="table-responsive">
@@ -635,8 +636,14 @@ self.add_parameter("sequencer", "The sequencer type.", choices=["HiSeq2000",
 				<div class="page-header">
 			    	<h1>Other available methods</h1>
 				</div>
-				<div id="pre_process" class="subgroup"><h2>Overloading pre process</h2></div>
-				<div id="post_process" class="subgroup"><h2>Overloading post process</h2></div>
+				<div id="pre_process" class="subgroup">
+					<h2>Overloading pre process</h2>
+					<p>This method is executed brefore process and cannot be used to add components.</p>
+				</div>
+				<div id="post_process" class="subgroup">
+					<h2>Overloading post process</h2>
+					<p>This method is executed after process and cannot be used to add components.</p>
+				</div>
 			</section>
 		  </div>
 		</div>