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docs/jflow-core-workflow.html

@@ -190,7 +190,7 @@ class Alignment (Workflow):
        	"The sequencer type.", 
        	choices = ["HiSeq2000", "ILLUMINA","SLX","SOLEXA","454","UNKNOWN"], 
        	default="HiSeq2000")</code></pre>
-			    	</div>					
+			    	</div>
 					
 					<h3>Options</h3>
 					
@@ -314,6 +314,66 @@ class Alignment (Workflow):
 	  		<section id="process" class="group">
 				<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>
+		    	<pre class="pre-hl "><code class="python">def process(self):
+    """ 
+    Run the workflow
+    """
+    indexed_ref = self.reference_genome
+    if not os.path.exists( self.reference_genome + ".bwt" ): # reference is not indexed
+        # index the reference genome
+        bwaindex = self.add_component("BWAIndex", [self.reference_genome])
+        indexed_ref = bwaindex.databank
+    
+    # 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">
+					<table class="table table-bordered table-striped">
+						<thead>
+							<tr>
+								<th>Name</th>
+								<th>Type</th>
+								<th>Required</th>
+								<th>Default value</th>
+								<th>Description</th>
+							</tr>
+						</thead>
+						<tbody>
+							<tr>
+								<td>component_name</td>
+								<td>str</td>
+								<td>true</td>
+								<td> - </td>
+								<td>The class name of the component used.</td>
+							</tr>
+							<tr>
+								<td>args</td>
+								<td>list</td>
+								<td>false</td>
+								<td>[]</td>
+								<td>The component's arguments (see <a href="./jflow-core-component.html#define_parameters">here</a> for more details).</td>
+							</tr>
+							<tr>
+								<td>kwargs</td>
+								<td>dict</td>
+								<td>false</td>
+								<td>{}</td>
+								<td>The component's keyword arguments (see <a href="./jflow-core-component.html#define_parameters">here</a> for more details).</td>
+							</tr>
+							<tr>
+								<td>component_prefix</td>
+								<td>str</td>
+								<td>false</td>
+								<td>"default"</td>
+								<td>This prefix is used with the component name as a unique identifiant. This is necessary when you use the same component several time in the workflow.</td>
+							</tr>
+						</tbody>
+					</table>
 				</div>
 			</section>