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

Commit 90f7d465 authored by Philippe Bardou's avatar Philippe Bardou
Browse files

No scroll in the <pre><code>

New css for <code>
Update fixed nav bar
parent 2b4717cd
......@@ -147,14 +147,13 @@ footer {
margin-top: -50px;
}
/* pre highlight */
.pre-hl {
word-break: normal;
word-wrap: normal;
}
/* pre code highlight */
.pre-hl code {
white-space: inherit;
font-weight: bold;
}
code {
background-color: #f3f2ff;
color: #428bca;
}
\ No newline at end of file
......@@ -31,7 +31,7 @@
<body role="document">
<!-- Fixed navbar -->
<!-- Fixed navbar -->
<div class="navbar navbar-inverse navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
......@@ -47,12 +47,16 @@
<ul class="nav navbar-nav">
<li><a href="./index.html">About</a></li>
<li><a href="./jflow-install.html">Install</a></li>
<li><a href="./jflow-quickstart.html">Quick start</a></li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation<span class="caret"></span></a>
<ul class="dropdown-menu" role="menu">
<li><a href="./jflow-core.html">Architecture</a></li>
<li><a href="./jflow-core-workflow.html">Adding workflow</a></li>
<li><a href="./jflow-core-component.html">Adding component</a></li>
<li><a href="./jflow-plugin.html">Plugin insertion</a></li>
<li><a href="./jflow-type.html">Adding data type</a></li>
<li><a href="./jflow-format.html">Adding file format</a></li>
</ul>
</li>
<li class="active"><a href="./example1.html">Example</a></li>
......@@ -62,7 +66,7 @@
</div><!--/.nav-collapse -->
</div>
</div>
<div class="container theme-showcase" role="main">
<!-- Jumbotron -->
......
......@@ -44,7 +44,7 @@
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation<span class="caret"></span></a>
<ul class="dropdown-menu" role="menu">
<li><a href=".jflow-architecture">Architecture</a></li>
<li><a href="./jflow-core.html">Architecture</a></li>
<li><a href="./jflow-core-workflow.html">Adding workflow</a></li>
<li><a href="./jflow-core-component.html">Adding component</a></li>
<li><a href="./jflow-plugin.html">Plugin insertion</a></li>
......
......@@ -23,7 +23,7 @@
<body role="document">
<!-- Fixed navbar -->
<!-- Fixed navbar -->
<div class="navbar navbar-inverse navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
......@@ -39,12 +39,16 @@
<ul class="nav navbar-nav">
<li><a href="./index.html">About</a></li>
<li><a href="./jflow-install.html">Install</a></li>
<li><a href="./jflow-quickstart.html">Quick start</a></li>
<li class="dropdown active">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation<span class="caret"></span></a>
<ul class="dropdown-menu" role="menu">
<li><a href="./jflow-core.html">Architecture</a></li>
<li><a href="./jflow-core-workflow.html">Adding workflow</a></li>
<li><a href="./jflow-core-component.html">Adding component</a></li>
<li><a href="./jflow-plugin.html">Plugin insertion</a></li>
<li><a href="./jflow-type.html">Adding data type</a></li>
<li><a href="./jflow-format.html">Adding file format</a></li>
</ul>
</li>
<li><a href="./example1.html">Example</a></li>
......
......@@ -42,12 +42,16 @@
<ul class="nav navbar-nav">
<li><a href="./index.html">About</a></li>
<li><a href="./jflow-install.html">Install</a></li>
<li><a href="./jflow-quickstart.html">Quick start</a></li>
<li class="dropdown active">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation<span class="caret"></span></a>
<ul class="dropdown-menu" role="menu">
<li><a href="./jflow-core.html">Architecture</a></li>
<li><a href="./jflow-core-workflow.html">Adding workflow</a></li>
<li><a href="./jflow-core-component.html">Adding component</a></li>
<li><a href="./jflow-plugin.html">Plugin insertion</a></li>
<li><a href="./jflow-type.html">Adding data type</a></li>
<li><a href="./jflow-format.html">Adding file format</a></li>
</ul>
</li>
<li><a href="./example1.html">Example</a></li>
......@@ -63,6 +67,7 @@
<!--Nav Bar -->
<nav class="col-xs-3 bs-docs-sidebar">
<ul id="sidebar" class="nav nav-stacked fixed">
<li><a href="#where">Where adding a new workflow</a></li>
<li><a href="#workflow" class="active">Adding workflow</a></li>
<li><a href="#define_parameters">Define parameters</a>
<ul class="nav nav-stacked">
......@@ -83,21 +88,40 @@
<li><a href="#post_process">Post process</a></li>
</ul>
</li>
<li><a href="#where">Where adding the class</a></li>
</ul>
</nav>
<div class="col-xs-12 col-sm-9">
<section id="where" class="group">
<div class="page-header">
<h1>Where adding a new workflow</h1>
</div>
<p>Create a directory (named by the desired workflow name) in the <code>workflows/</code> directory.</p>
<pre class="pre-hl"><code class="python">jflow/
├── bin/
├── docs/
├── src/
├── workflows/
│ ├── components/
│ ├── extparsers/
│ ├── myWorkflowName ** create a directory name by the desired workflow namew **
│ │ └── __init__.py ** add your code in the __init__.py file (see below) **
│ ├── __init__.py
│ ├── formats.py
│ └── types.py
├── applications.properties
└── README</code></pre>
</section>
<section id="workflow" class="group">
<div class="page-header">
<h1>The <i>Workflow</i> class</h1>
</div>
In order to add workflow you must:
In order to add workflow you need to:
<ul>
<li>Inherit from the <i>Workflow</i> class</li>
<li>Implement the <b>get_description()</b> function to define the workflow description</li>
<li>Implement the <b>define_parameters()</b> function to add the workflow inputs and parameters</li>
<li>Implement the <b>process()</b> function by adding components and provide the component arguments</li>
<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>
</ul>
<div>
......@@ -110,9 +134,12 @@ class Alignment (Workflow):
return "Align reads against a reference genome"
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", required=True, file_format="fasta")
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, )
def process(self):
"""
......@@ -153,13 +180,7 @@ class Alignment (Workflow):
<div id="pre_process" class="subgroup"><h2>Overloading pre process</h2></div>
<div id="post_process" class="subgroup"><h2>Overloading post process</h2></div>
</section>
<section id="where" class="group">
<div class="page-header">
<h1>Where should the class be added</h1>
</div>
</section>
</div>
</div>
</div>
<hr>
......
......@@ -33,21 +33,24 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="#">Jflow</a>
<a class="navbar-brand" href="./index.html">Jflow</a>
</div>
<div class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li><a href="./index.html">About</a></li>
<li><a href="./jflow-install.html">Install</a></li>
<li class="active dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Core <span class="caret"></span></a>
<li><a href="./jflow-quickstart.html">Quick start</a></li>
<li class="dropdown active">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation<span class="caret"></span></a>
<ul class="dropdown-menu" role="menu">
<li><a href="./jflow-core.html">Jflow overview</a></li>
<li><a href="./jflow-core-component.html">Adding component</a></li>
<li><a href="./jflow-core.html">Architecture</a></li>
<li><a href="./jflow-core-workflow.html">Adding workflow</a></li>
<li><a href="./jflow-core-component.html">Adding component</a></li>
<li><a href="./jflow-plugin.html">Plugin insertion</a></li>
<li><a href="./jflow-type.html">Adding data type</a></li>
<li><a href="./jflow-format.html">Adding file format</a></li>
</ul>
</li>
<li><a href="./jflow-plugin.html">JS Plugin</a></li>
<li><a href="./example1.html">Example</a></li>
<li><a target="_blank" href="https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/jflow/index.php/Accueil">Sources</a></li>
<li><a href="mailto:support.genopole@toulouse.inra.fr">Contact</a></li>
......
......@@ -39,12 +39,16 @@
<ul class="nav navbar-nav">
<li><a href="./index.html">About</a></li>
<li class="active"><a href="./jflow-install.html">Install</a></li>
<li><a href="./jflow-quickstart.html">Quick start</a></li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation<span class="caret"></span></a>
<ul class="dropdown-menu" role="menu">
<li><a href="./jflow-core.html">Architecture</a></li>
<li><a href="./jflow-core-workflow.html">Adding workflow</a></li>
<li><a href="./jflow-core-component.html">Adding component</a></li>
<li><a href="./jflow-plugin.html">Plugin insertion</a></li>
<li><a href="./jflow-type.html">Adding data type</a></li>
<li><a href="./jflow-format.html">Adding file format</a></li>
</ul>
</li>
<li><a href="./example1.html">Example</a></li>
......@@ -54,7 +58,7 @@
</div><!--/.nav-collapse -->
</div>
</div>
<div class="container">
<div class="row">
<!--Nav Bar -->
......
......@@ -23,7 +23,7 @@
<body role="document">
<!-- Fixed navbar -->
<!-- Fixed navbar -->
<div class="navbar navbar-inverse navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
......@@ -39,12 +39,16 @@
<ul class="nav navbar-nav">
<li><a href="./index.html">About</a></li>
<li><a href="./jflow-install.html">Install</a></li>
<li><a href="./jflow-quickstart.html">Quick start</a></li>
<li class="dropdown active">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation<span class="caret"></span></a>
<ul class="dropdown-menu" role="menu">
<li><a href="./jflow-core.html">Architecture</a></li>
<li><a href="./jflow-core-workflow.html">Adding workflow</a></li>
<li><a href="./jflow-core-component.html">Adding component</a></li>
<li><a href="./jflow-plugin.html">Plugin insertion</a></li>
<li><a href="./jflow-type.html">Adding data type</a></li>
<li><a href="./jflow-format.html">Adding file format</a></li>
</ul>
</li>
<li><a href="./example1.html">Example</a></li>
......@@ -54,7 +58,6 @@
</div><!--/.nav-collapse -->
</div>
</div>
<div class="container">
<div class="row">
<!--Nav Bar -->
......
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>Jflow</title>
<!-- Bootstrap core CSS -->
<link href="css/bootstrap.min.css" rel="stylesheet">
<!-- Bootstrap theme -->
<link href="css/bootstrap-theme.min.css" rel="stylesheet">
<!-- Custom styles for this template -->
<link href="css/theme.css" rel="stylesheet">
<!-- Highlight code -->
<link href="css/tomorrow-night-eighties.css" rel="stylesheet">
<!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body role="document">
<!-- Fixed navbar -->
<div class="navbar navbar-inverse navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target=".navbar-collapse">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="./index.html">Jflow</a>
</div>
<div class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li><a href="./index.html">About</a></li>
<li><a href="./jflow-install.html">Install</a></li>
<li class="active"><a href="./jflow-quickstart.html">Quick start</a></li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation<span class="caret"></span></a>
<ul class="dropdown-menu" role="menu">
<li><a href="./jflow-core.html">Architecture</a></li>
<li><a href="./jflow-core-workflow.html">Adding workflow</a></li>
<li><a href="./jflow-core-component.html">Adding component</a></li>
<li><a href="./jflow-plugin.html">Plugin insertion</a></li>
<li><a href="./jflow-type.html">Adding data type</a></li>
<li><a href="./jflow-format.html">Adding file format</a></li>
</ul>
</li>
<li><a href="./example1.html">Example</a></li>
<li><a target="_blank" href="https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/jflow/index.php/Accueil">Sources</a></li>
<li><a href="mailto:support.genopole@toulouse.inra.fr">Contact</a></li>
</ul>
</div><!--/.nav-collapse -->
</div>
</div>
<div class="container">
<div class="row row-offcanvas row-offcanvas-right">
<div class="col-xs-12 col-sm-9">
</div>
</div>
<hr>
<footer>
<div class="container" style="text-align: center;">
<p>Copyright © 2015, INRA | Designed by <a target="_blank" href="http://bioinfo.genotoul.fr/">GenoToul Bioinfo platform</a> and <a target="_blank" href="http://www.sigenae.org/">Sigenae platform</a>.</p>
</div>
</footer>
</div>
<!-- Bootstrap core JavaScript
================================================== -->
<!-- Placed at the end of the document so the pages load faster -->
<script src="js/jquery.min.js"></script>
<script src="js/bootstrap.min.js"></script>
<!-- <script src="../../assets/js/docs.min.js"></script> -->
<!-- IE10 viewport hack for Surface/desktop Windows 8 bug -->
<!-- <script src="../../assets/js/ie10-viewport-bug-workaround.js"></script> -->
<!-- Highlight code -->
<script src="js/highlight.pack.js"></script>
<script>hljs.initHighlightingOnLoad();</script>
<script src="js/offcanvas.js"></script>
<script type='text/javascript'>
$('body').scrollspy({
target: '.bs-docs-sidebar',
offset: 150
});
</script>
</body>
</html>
\ No newline at end of file
......@@ -43,10 +43,10 @@
<li><a href="./index.html">About</a></li>
<li><a href="./jflow-install.html">Install</a></li>
<li><a href="./jflow-quickstart.html">Quick start</a></li>
<li class="active dropdown">
<li class="dropdown active">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation<span class="caret"></span></a>
<ul class="dropdown-menu" role="menu">
<li><a href=".jflow-architecture">Architecture</a></li>
<li><a href="./jflow-core.html">Architecture</a></li>
<li><a href="./jflow-core-workflow.html">Adding workflow</a></li>
<li><a href="./jflow-core-component.html">Adding component</a></li>
<li><a href="./jflow-plugin.html">Plugin insertion</a></li>
......@@ -66,7 +66,7 @@
<h1>Where adding a new type</h1>
<p>In the <code>workflows/</code> directory, jflow provides a <code>types.py</code> file where new types can be added.</p>
<pre class="pre-hl "><code class="python">jflow/
<pre class="pre-hl"><code class="python">jflow/
├── bin/
├── docs/
├── src/
......
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