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

Commit 55d7c62a authored by Frédéric Escudié's avatar Frédéric Escudié
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......@@ -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>
......
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