Documentation for get_cpu and get_memory

docs/jflow_advanced_configuration.html

@@ -271,9 +271,20 @@ cutadapt = /path/to/cutadapt</code></pre>
 			    	<h1 class="page-header">Components <small>section</small></h1>
 				  	<p>In a production environment, it can be useful to custom DMS options for each components. To do so, within the <code>components</code>
 				  	section in the jflow configuration file, add a line following the schema: [component_name].batch_options = [options].</p>
+				  	<p>Cpu and memory values are then avalaible in the component via the methods <code>get_cpu()</code> and <code>get_memory()</code> on local and SGE enviroment only/</p>
+				  	<h3>Local configuration</h3>
+					<p>you can provide option with format <code>mem=XX[K|M|G] cpu=XX"</code></p>
+<pre class="pre-hl "><code class="ini">[components]
+BWAIndex.batch_options = "mem=1G"
+BWAmem.batch_options = "mem=10G cpu=4"</code></pre>
+				  	
+				  	<h3>SGE configuration</h3>
+					<p>you can provide option as you would provide to SGE</code></p>
 				  	<pre class="pre-hl "><code class="ini">[components]
 BWAIndex.batch_options = -l mem=1G -l h_vmem=1G -q myflowq
 BWAmem.batch_options = -l mem=10G -l h_vmem=10G -q myflow2q</code></pre>
+					
+
 				</section>
 
 		  		<section id="workflows">

docs/jflow_core_component.html

@@ -1266,6 +1266,18 @@ fastq2fasta.py --input splC.fastq --fasta splC.fasta --qual splC.qual</code></pr
 						</table>
 					</div>
 				</div>
+				<div id="get_cpu" class="subgroup">
+					<h2>Get cpu</h2>
+					<p><code>get_cpu()</code> return the cpu value of <code>batch_options</code> configuration for this component (available for <b>local and sge only</b>). 
+					This option is usefull to set software parameter that needs more than one CPU.</p> 
+					<p>For more information about how to configure a component see advanced configuration</p>
+				</div>
+				<div id="get_memory" class="subgroup">
+					<h2>Get memory</h2>
+					<p><code>get_memory()</code> return the memory value of <code>batch_options</code> configuration for this component (available for <b>local and sge only</b>). 
+					This option is usefull to set software parameter that needs specific value of memory.</p> 
+					<p>For more information about how to configure a component see advanced configuration</p>
+				</div>
 			</section>
 			
 			<section id="external_components" class="group">