RAPPEL : Opération de maintenance > ForgeMIA indisponible le 20 Janvier entre 7h et 12h

Commit d072f2bf authored by Frédéric Escudié's avatar Frédéric Escudié
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......@@ -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>
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