Maintenance - Mise à jour mensuelle Lundi 6 Avril 2020 entre 7h00 et 9h00

Commit 8827871c authored by Maria Bernard's avatar Maria Bernard

adding part of informations of https://hebdo.framapad.org/p/ng6doc, in Add...

adding part of informations of https://hebdo.framapad.org/p/ng6doc, in Add workflow, Add Analysis and Format sections.
parent ebc4cde0
......@@ -414,7 +414,7 @@ class MyComponent (Analysis):
<td>string</td>
<td>false</td>
<td>"any"</td>
<td>The file format is checked before running the workflow. To create customized format,
<td>The file format is checked before running the workflow. Available format are "any", "bam", "fasta", "fastq", and "sff". To create customized format,
refere to the <a href="./format.html">Add a file format</a> documentation.</td>
</tr>
......@@ -554,7 +554,7 @@ class MyComponent (Analysis):
<td>string</td>
<td>false</td>
<td>"any"</td>
<td>The file format is checked before running the workflow. To create customized format,
<td>The file format is checked before running the workflow. Available format are "any", "bam", "fasta", "fastq", and "sff". To create customized format,
refere to the <a href="./format.html">Add a file format</a> documentation.</td>
</tr>
......@@ -672,7 +672,7 @@ class MyComponent (Analysis):
<td>string</td>
<td>false</td>
<td>"any"</td>
<td>The file format is checked before running the workflow. To create customized format,
<td>The file format is checked before running the workflow. Available format are "any", "bam", "fasta", "fastq", and "sff". To create customized format,
refere to the <a href="./format.html">Add a file format</a> documentation.</td>
</tr>
......@@ -790,7 +790,7 @@ class MyComponent (Analysis):
<td>string</td>
<td>false</td>
<td>"any"</td>
<td>The file format is checked before running the workflow. To create customized format,
<td>The file format is checked before running the workflow. Available format are "any", "bam", "fasta", "fastq", and "sff". To create customized format,
refere to the <a href="./format.html">Add a file format</a> documentation.</td>
</tr>
......
......@@ -329,14 +329,14 @@ class MyWorkflow (NG6Workflow):
<tr>
<td>read1</td>
<td>"Read 1 data file path.</td>
<td>Read 1 data file path.</td>
<td>true</td>
<td>inputfile list</td>
</tr>
<tr>
<td>read2</td>
<td>"Read 2 data file path.</td>
<td>Read 2 data file path.</td>
<td>false</td>
<td>inputfile list</td>
</tr>
......@@ -461,7 +461,7 @@ class MyWorkflow (NG6Workflow):
<td>true</td>
<td>None</td>
<td>The name of the parameter. The parameter value is accessible
within the workflow object through the attribute named <code>self.parameter_name</code>.</td>
within the workflow object through the attribute named <code>self.parameter_name</code> NB: "-" in parameter name will be automatically replace by "_", so <code>--name-param</code> become <code>self.name_param</code> in the code.</td>
</tr>
<tr>
......@@ -622,7 +622,7 @@ class MyWorkflow (NG6Workflow):
<td>string</td>
<td>false</td>
<td>"any"</td>
<td>The file format is checked before running the workflow. To create customized format,
<td>The file format is checked before running the workflow. Available format are "any", "bam", "fasta", "fastq", and "sff". To create customized format,
refere to the <a href="./format.html">Add a file format</a> documentation.</td>
</tr>
......@@ -853,11 +853,11 @@ class WF(NG6Workflow):
<h3>add_multiple_parameter()</h3>
<h4>Example</h4>
The following example creates a multiple parameter named <code>library</code> which contains two input files <code>R1</code> and <code>R2</code>
and a <code>sequencer</code> parameter. </p>
The following example creates a multiple parameter named <code>library</code> which contains two input files <code>R1</code> (which is mandatory) and <code>R2</code>
and a <code>sequencer</code> parameter. The parameter <code>R1</code> is required only if a <code>library</code> is defined.</p>
<div>
<pre class="pre-hl "><code class="python">self.add_multiple_parameter("library", "Library.", required=True)
<pre class="pre-hl "><code class="python">self.add_multiple_parameter("library", "Library.", required=False)
self.add_input_file("R1", "Path to R1 file.", required=True, add_to="library")
self.add_input_file("R2", "Path to R2 file.", add_to="library")
self.add_parameter("sequencer", "The sequencer type.", choices=["HiSeq2000",
......@@ -944,7 +944,7 @@ self.add_parameter("sequencer", "The sequencer type.", choices=["HiSeq2000",
<div id="exclusion_rules" class="subgroup">
<h2>Exclusion rules</h2>
<p>There is a possibility to exclude some rules from each others. To do so, the method <code>add_exclusion_rule()</code> is available. </p>
<p>There is a possibility to exclude some rules from each others. To do so, the method <code>add_exclusion_rule()</code> is available. It only works with simple parameter. </p>
<h3>add_exclution_rule()</h3>
<h4>Example</h4>
......@@ -1057,10 +1057,12 @@ self.add_exclution_rule("fasta_file", "fastq")</code></pre>
</tbody>
</table>
</div>
You must choose between args and kwargs options. kwargs dictionnary allow you to define subset of component options instead of all of them thanks to the args list.
<h2>get_resource()</h2>
<p>The method <code>get_resource()</code>, giving a specific resource, returns the defined value within the <code>resource</code>
section of the jflow configuration file.</p>
section of the jflow configuration file : <code>application.properties</code>.</p>
<h3>Options</h3>
<p>There is one required argument : resource.</p>
<div class="table-responsive">
......
......@@ -78,7 +78,10 @@
<section id="where" class="group">
<h1>Where to add a new format</h1>
<p>In the <code>workflows/</code> directory, ng6 provides a <code>formats.py</code> file where new formats can be added.</p>
<p>In the <code>workflows/</code> directory, ng6 provides a <code>formats.py</code> file where new formats can be added.
It already includes "any", "bam", "fasta", "fastq", and "sff" formats.
</p>
<pre class="pre-hl "><code class="ini">ng6/
├── bin/
├── docs/
......
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