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Commit 9033d508 authored by Jerome Mariette's avatar Jerome Mariette
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<nav class="col-xs-3 bs-docs-sidebar">
<ul id="sidebar" class="nav nav-stacked fixed">
<li><a href="#workflow-architecture" class="active">Where to add a new workflow</a></li>
<li><a href="#workflow" >Workflow definition</a></li>
<li><a href="#workflow" >The Workflow class</a></li>
<li><a href="#define_parameters">Define parameters</a>
<ul class="nav nav-stacked">
<li><a href="#simple_parameters">Simple parameters</a></li>
......@@ -86,13 +86,12 @@
<div class="col-xs-12 col-sm-9">
<section id="workflow-architecture" class="group">
<h1 class="page-header">Where to add a new workflow</h1>
<p>The new wokflow must be added as a new python package in the <code>workflows</code> package. The definition of
the workflows must be written in <code><a href="#workflow">__init__.py</a></code>.</p>
<p>User can optionaly add : </p>
<p>New wokflow must be added as a new python package in the <code>workflows</code> package. The implementation of
a workflows must be written in the package <code>__init__.py</code> file. The developper can also create: </p>
<ul>
<li><code><a href="./jflow-core-component.html">components</a></code> package to define specific components to this new workflow</li>
<li><code>lib</code> package to define specific libraries</li>
<li><code>bin</code> a folder with binaries used in the workflow.</li>
<li>a <code>components</code> package, where all the workflow specific components can be stored,</li>
<li>a <code>lib</code> package to import specific libraries within its workflow,</li>
<li>a <code>bin</code> folder with the binaries used in the workflow.</li>
</ul>
<pre class="pre-hl "><code class="text">jflow/
......@@ -100,11 +99,11 @@
├── docs/
├── src/
├── workflows/
│ ├── myWorkflowName/ ** workflow package to add **
│ │ ├── components/ ** workflow specific components **
│ │ ├── lib/ ** workflow specific libraries **
│ │ ├── bin/ ** workflow specific binairies **
│ │ └── __init__.py ** the workflow code **
│ ├── myworkflow/ ** the new workflow package **
│ │ ├── components/ ** specific components **
│ │ ├── lib/ ** specific libraries **
│ │ ├── bin/ ** specific binairies **
│ │ └── __init__.py ** the workflow implementation **
│ ├── components/
│ ├── extparsers/
│ ├── __init__.py
......@@ -115,64 +114,49 @@
</section>
<section id="workflow" class="group">
<h1 class="page-header">The <i>Workflow</i> definition</h1>
<p>The new workflow is a class defined in <code>__init__.py</code>. In order to add workflow you must: </p>
<h1 class="page-header">The Workflow class</h1>
<p>In jflow, a workflow is a class defined in the <code>__init__.py</code> file. In order to add a new workflow, the developper has to: </p>
<ul>
<li>Inherit from the <code>Workflow</code> class</li>
<li>Implement the <code>get_description()</code> function to define the workflow description</li>
<li>Implement the <code>define_parameters()</code> function to add the workflow inputs and parameters</li>
<li>Implement the <code>process()</code> function by adding components and provide the component arguments</li>
<li>Link components inputs and outputs (typing test is done)</li>
<li>implement a class inheriting from the <code>Workflow</code> class,</li>
<li>overload the <code>get_description()</code> method to provide the final user a description of the workflow,</li>
<li>overload the <code>define_parameters()</code> method to add the workflow inputs and parameters,</li>
<li>overload the <code>process()</code> method by adding components and setting their arguments,</li>
<li>link the components inputs and outputs.</li>
</ul>
<p>The class skeleton is given by</p>
<div>
<pre class="pre-hl "><code class="python">from jflow.workflow import Workflow
from jflow.parameter import InputFileList, InputFile
class Alignment (Workflow):
class MyWorkflow (Workflow):
def get_description(self):
return "Align reads against a reference genome"
return "a description"
def define_parameters(self, function="process"):
self.add_input_file_list("read_1", "Which read1 should be used",
file_format="fastq", required=True)
self.add_input_file_list("read_2", "Which read2 should be used",
file_format="fastq")
self.add_input_file("reference_genome", "Which genome should the read being align on",
file_format="fasta", required=True, )
# define the parameters
def process(self):
"""
Run the workflow
"""
# index the reference genome
bwaindex = self.add_component("BWAIndex", [self.refernce_genome])
# align reads against indexed genome
bwa = self.add_component("BWA", [bwaindex.databank, self.read_1, self.read_2])</code></pre>
# add and link the components</code></pre>
</div>
<p>The <code>get_name()</code> method can be overwritted to change the command name of the workflows. By default
the workflows will be called as the class name in lower case.</p>
</section>
<section id="define_parameters" class="group">
<h1 class="page-header">Define parameters</h1>
<p>
The define parameters function is used to add workflow inputs and outputs. Several methods are available to add different
types of parameters. The added parameter will be available as an object attibut, thus be accessible using <code>self.param_name</code>.
Each function defines hows the parameter will be described in the command line and in the interface.
The <code>define_parameters()</code> method is used to add workflow inputs and outputs. Several methods are available to add different
types of parameters. The added parameter, once defined, is available as an object attibut, thus it is accessible through
<code>self.param_name</code>.
</p>
<p>
Several types of parameters can be added, all described in the following sections. They all have two required positional
arguments name and help. All other arguments passed to those methods are keywords argument.
Several types of parameters can be added, all described in the following sections. All have two required positional
arguments: <code>name</code> and <code>help</code>. The other arguments are optional and can be provided by using the
keywords argument.
</p>
<div class="alert alert-danger" role="alert">
<span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
Do not use the <code>is</code> operator to evaluate a parameter. Use instead <code>==</code>.
</div>
<span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
The operator <code>is</code> is not supported to evaluate a parameter, the operator <code>==</code> must be prefered.
<div id="simple_parameters" class="subgroup">
<h2>Simple parameters</h2>
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