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Maintenance - Mise à jour mensuelle Lundi 6 Février entre 7h00 et 9h00
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genotoul-bioinfo
jflow
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d072f2bf
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d072f2bf
authored
Feb 24, 2015
by
Frédéric Escudié
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docs/jflow-core-workflow.html
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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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