Commit 0a56981e authored by Maria Bernard's avatar Maria Bernard

adding supplementary documentation in quickstart.html, core-analysis.html, core-workflow.html

parent 8827871c
......@@ -113,7 +113,7 @@
<span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
In a NG6Workflow, the developper can also add instances of <code>jflow.component.Component</code> object. It is recommended to use <code>Component</code>
when the result of the execution has not to be presented to the final user (for example indexing a reference file) and <code>Analysis</code> when
results must be presented to the user, like a fastqc report.
results must be presented to the user, like a fastqc report. The differences are the necessity of developping <span style="text-decoration: underline;">define_analysis()</span>, and <span style="text-decoration: underline;">post_process()</span> functions and a <span style="text-decoration: underline;">template HTML</span> file for <code>Analysis</code> component.
</div>
</section>
......@@ -212,7 +212,7 @@ class MyComponent (Analysis):
<p>
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 given to the method by using their
keywords.
keywords. Arguments <code>cmd_format</code> and <code>argpos</code> may simplified the <code>process()</code> function (see <a href="#process">Analysis.process()</a> ).
</p>
<div id="parameters" class="subgroup">
......@@ -493,8 +493,11 @@ class MyComponent (Analysis):
<div id="output_parameters" class="subgroup">
<h2>Outputs</h2>
<p>Just like inputs, outputs can be added to handle a single file or a list of files. Thus, the <code>add__input_file()</code> method can be used to force
the component to produce one and only one file, where the <code>add__input_file_list()</code> method allows the component to produce as many files as possible.</p>
<p>Just like inputs, outputs can be added to handle a single file or a list of files. Thus, the <code>add_output_file()</code> method can be used to force
the component to produce one and only one file, where the <code>add_output_file_list()</code> method allows the component to produce as many files as possible.
There are also two specific functions <code>add_output_file_endswith()</code> and <code>add_output_file_pattern()</code>.
<br /><br />
</p>
<h3>add_output_file()</h3>
<h4>Example</h4>
......@@ -510,7 +513,7 @@ class MyComponent (Analysis):
</div>
<h4>Options</h4>
<p>The two positional arguments <code>name</code> and <code>help</code> are always present </p>
<p>The two positional arguments <code>name</code> and <code>help</code> are always present.</p>
<div class="table-responsive">
<table class="table table-bordered table-striped">
......@@ -610,7 +613,7 @@ class MyComponent (Analysis):
<h4>Options</h4>
<p>The two positional arguments <code>name</code> and <code>help</code> are always present </p>
<p>The two positional arguments <code>name</code> and <code>help</code> are always present.</p>
<div class="table-responsive">
<table class="table table-bordered table-striped">
......@@ -662,7 +665,7 @@ class MyComponent (Analysis):
<li><code>{fullpath}</code>, <code>{FULL}</code> for full input file path,</li>
<li><code>{basename}</code>, <code>{BASE}</code> for base input file name,</li>
<li><code>{fullpath_woext}</code>, <code>{FULLWE}</code> for full input file path without extension,</li>
<li><code>{basename_woext}</code>, <code>{BASEWE}</code> for base input file name without extension.</li>
<li><code>{basename_woext}</code>, <code>{BASEWE}</code> for base input file name without extension. note that ".gz" is not considered as an extension.</li>
</ul>
</td>
</tr>
......@@ -736,8 +739,7 @@ class MyComponent (Analysis):
<p>
This method is very different from <code>add_output_file_list()</code> because it should only be used when
the number of output files returned by the component is unknown. Three options are required:
<code>name</code>, <code>help</code> and <code>pattern</code>.
</p>
<code>name</code>, <code>help</code> and <code>pattern.</code></p>
<div class="table-responsive">
<table class="table table-bordered table-striped">
......
......@@ -413,6 +413,7 @@ class MyWorkflow (NG6Workflow):
<div class="alert alert-info" role="alert">
<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.
<br /> ex : <code><span style="text-decoration: line-through;"> if self.param_name is not None :</span></code> becomes <code>if self.param_name != None :</code>
</div>
<div id="parameters" class="subgroup">
......
......@@ -66,22 +66,22 @@
<nav class="col-xs-3 bs-docs-sidebar">
<ul id="sidebar" class="nav nav-stacked fixed">
<li><a href="#introduction" class="active">Introduction</a></li>
<li><a href="#first_step">Step #1</a></li>
<li><a href="#first_step">Step 1: folder tree</a></li>
<li><a href="#second_step">Step #2</a>
<li><a href="#second_step">Step 2: first component</a>
<ul class="nav nav-stacked">
<li><a href="#QilluminaFilter_analysis">QilluminaFilter analysis</a></li>
<li><a href="#QilluminaFilter_template">QilluminaFilter template</a></li>
</ul>
</li>
<li><a href="#third_step">Step #3</a>
<li><a href="#third_step">Step 3: second component</a>
<ul class="nav nav-stacked">
<li><a href="#QFastQC_analysis">QFastQC analysis</a></li>
<li><a href="#QFastQC_template">QFastQC template</a></li>
</ul>
</li>
<li><a href="#fourth_step">Step #4</a></li>
<li><a href="#fifth_step">Step #5</a></li>
<li><a href="#fourth_step">Step 4: workflow </a></li>
<li><a href="#fifth_step">Step 5: workflow test</a></li>
</ul>
</nav>
......@@ -932,6 +932,8 @@ Available sub commands:
</div>
<p>
Our quickstart workflow inherit from NG6Workflow class which inherit from BasicNG6Workflow class, so it also inherit of required arguments which are :
<code>--project-name</code>, <code>--name</code>, <code>--description</code>, <code>--data-nature</code>, <code>--sequencer</code>, <code>--species</code>, <code>--type</code>, </code>--admin-login</code> and at least one <code>--sample</code>
The <code>quickstart</code> workflow is already implemented in the NG6 sources.
</p>
......
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