Commit 67ba07d9 authored by Gerald Salin's avatar Gerald Salin

#37

parent a6e392b2
......@@ -100,7 +100,7 @@
<section id="what" class="group">
<h1 class="page-header">What is an Analysis</h1>
<p>
An analysis presents the results of the execution of one or multiple softwares, which can be external scripts or python code, using NGS data.
An analysis presents the results of the execution of one or multiple software, which can be external scripts or python code, using NGS data.
It is represented by two main objects :
</p>
<ul>
......@@ -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. 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.
results must be presented to the user, like a fastqc report. The differences are the necessity to develop <span style="text-decoration: underline;">define_analysis()</span>, <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>
......@@ -121,16 +121,16 @@
<section id="analysis-architecture" class="group">
<h1 class="page-header">Where to add a new Analysis</h1>
<p>
The new analysis must be added in a Python package. Two different locations are possible in order to be imported by ng6:
The new analysis must be added in a Python package. Two different locations are possible in order to be imported by ng6 :
</p>
<ul>
<li><code>workflows.components</code>: the analysis will be visible by all workflows,</li>
<li><code>workflows.myWorkflow.components</code>: the analysis will only be available for<code>myWorkflow</code>.</li>
</ul>
<p>
The template file presenting the results of the analysis must be added in ui/nG6/pi1/analyzes/. The tempalte file must
The template file presenting the results of the analysis must be added in ui/nG6/pi1/analyzes/. The template file must
have the same name as the Python class of the Analysis.
The following code represent the structure of the source, and the location where to add specific files.
The following code represents the structure of the source, and the location where to add specific files.
</p>
<pre class="pre-hl "><code class="ini">nG6/
......@@ -971,7 +971,7 @@ class MyComponent (Analysis):
Overloading <code>process()</code> can be omitted. NG6 offers, for analyzes and components with easy command lines,
an automatic built of the <code>process()</code> method.
In this case, options <code>argpos</code> and <code>cmd_format</code> must be provided by the developper for each parameter.
Also, two other methods of must be overloaded. <code>get_command()</code>, which must returns
Also, two other methods must be overloaded. <code>get_command()</code>, which must returns
the execution path and <code>get_abstraction()</code> which returns the abstraction name to use.
</div>
......@@ -1256,7 +1256,7 @@ fastaTrim.pl --length 50 splC.fasta > splC_trim.fasta</code></pre>
<h3>MultiMap</h3>
<p>The <code>MultiMap</code> abstraction allows to map n input file lists to n output file lists, all of the same lenght.</p>
<p>The <code>MultiMap</code> abstraction allows to map n input file lists to n output file lists, all of the same length.</p>
<h4>Example</h4>
<pre class="pre-hl "><code class="python">fastq_list = ["splA.fastq", "splB.fastq", "splC.fastq"]
......
......@@ -106,7 +106,7 @@
<p><a class="btn btn-primary" href="./core-workflow.html" role="button">View details &raquo;</a></p>
</div>
<div class="col-lg-6">
<p><a class="btn btn-primary" href="./core-component.html" role="button">View details &raquo;</a></p>
<p><a class="btn btn-primary" href="./core-anaysis.html" role="button">View details &raquo;</a></p>
</div>
</div>
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