workflow doc ok

docs/jflow-core-workflow.html

@@ -581,25 +581,27 @@ self.add_exclution_rule("fasta_file", "fastq")</code></pre>
 			</section>
 			
 	  		<section id="process" class="group">
-		    	<h1 class="page-header">Overloading <i>process</i></h1>
-		    	<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
-    """
-    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>
-   				<h2>The add_component() method</h2>
-   				<p>This method is used to add a component to the workflow.</p>
+		    	<h1 class="page-header">Process</h1>
+		    	<p>The <code>process()</code> method is in charge to build the workflow by adding components (using the method <code>add_component()</code>) and 
+		    	linking their inputs and their outputs. A component is a class representing a workflow step. See the 
+		    	<a href="./jflow-core-component.html">Add a component</a> documentation for more information.</p>
+
+   				<h2>add_component()</h2>
+   				<p>The <code>add_component()</code> method add a component to the workflow by building a <code>jflow.component.Component</code>
+   				object and returning it. All attributs defined within this object, such as the outputs, are then available from the workflow and 
+   				can be used as inputs of other components.</p>
+   				<h3>Example</h3>
+   				<p>In the following example, the first component <code>BWAIndex</code> is built and returned in the <code>bwaindex</code> object.
+   				The output <code>bwaindex.databank</code> is accessible as an object attribut and can be used as input of the <code>BWAmem</code>
+   				component. This example is extracted from the <a href="./jflow-quickstart.html">Quick start</a>.</p>
+					<div>
+				    <pre class="pre-hl "><code class="python"># index the reference genome
+bwaindex = self.add_component("BWAIndex", [self.reference_genome])
+# align reads against the indexed genome
+bwamem = self.add_component("BWAmem", [bwaindex.databank, self.reads])</code></pre>
+				    	</div>
+   				<h3>Options</h3>
+   				<p>There is one positional argument : component_name. All other options are keyword options.</p>
    				<div class="table-responsive">
 					<table class="table table-bordered table-striped">
 						<thead>
@@ -614,10 +616,10 @@ self.add_exclution_rule("fasta_file", "fastq")</code></pre>
 						<tbody>
 							<tr>
 								<td>component_name</td>
-								<td>str</td>
+								<td>string</td>
 								<td>true</td>
-								<td> - </td>
-								<td>The class name of the component used.</td>
+								<td>None</td>
+								<td>The component class name to add to the workflow.</td>
 							</tr>
 							<tr>
 								<td>args</td>
@@ -635,10 +637,11 @@ self.add_exclution_rule("fasta_file", "fastq")</code></pre>
 							</tr>
 							<tr>
 								<td>component_prefix</td>
-								<td>str</td>
+								<td>string</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>
+								<td>The prefix is used to name the component at the execution. The prefix allows to add multiple components of the same class within
+								the same workflow.</td>
 							</tr>
 						</tbody>
 					</table>
@@ -646,14 +649,17 @@ self.add_exclution_rule("fasta_file", "fastq")</code></pre>
 			</section>
 			
 	  		<section id="other_methods" class="group">
-		    	<h1 class="page-header">Other available methods</h1>
+		    	<h1 class="page-header">Other methods</h1>
 				<div id="pre_process" class="subgroup">
-					<h2>Overloading <i>pre process</i></h2>
-					<p>This method is executed brefore process and cannot be used to add components.</p>
+					<h2>Pre process</h2>
+					<p><code>pre_process()</code> is executed before to run the <code>process</code> method. Unlike <code>process</code>, this method does not allow
+					to add components, but can be useful when implementing an application requiring to prepare some data before running the workflow (insert / recover
+					information from a database, add metadata to the workflow, ...).</p>
 				</div>
 				<div id="post_process" class="subgroup">
-					<h2>Overloading <i>post process</i></h2>
-					<p>This method is executed after process and cannot be used to add components.</p>
+					<h2>Post process</h2>
+					<p><code>post_process()</code> is executed right after the <code>process</code> method and cannot be used to add components. This method can
+					be useful to perform some database transactions and to synchronize data.</p>
 				</div>
 			</section>
 		  </div>