Commit 99aec608 authored by Penom Nom's avatar Penom Nom

documentation update

parent 43e19d2d
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<!DOCTYPE html>
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<h1>Where to add a new format</h1>
<p>In the <code>workflows/</code> directory, jflow provides a <code>formats.py</code> file where new formats can be added.</p>
<pre class="pre-hl "><code class="ini">jflow/
├── bin/
├── docs/
├── src/
├── workflows/
│ ├── components/
│ ├── extparsers/
│ ├── __init__.py
│ ├── formats.py [ file where to add new jflow formats ]
│ └── types.py
├── applications.properties
└── README</code></pre>
<h1>How to add a new format</h1>
<p>In jflow a format is represented by a function named by the desired format name. The function should take only
one argument, whose value is the file path given by the user. The function is in charge to open and check the
content of the file. If an error occurred or if the value does not meet the expected criteria, a
<code>jflow.InvalidFormatError</code> should be raised with the suitable error message. This message will
be used by jflow to inform the final user of the error.</p>
<p>In the following example, the <code>fasta</code> function checks if the 10 first lines of the input file are in
a fasta format:</p>
<pre class="pre-hl "><code class="python">def fasta(ifile):
try:
reader = seqio.FastaReader(ifile, wholefile=True)
nb_seq = 0
for id, desc, seq, qualities in reader:
nb_seq += 1
# only check the first 10 sequences
if nb_seq == 10: break
except:
raise jflow.InvalidFormatError("The provided file '" + ifile + "' is not a fasta file!")</code></pre>
<span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
Jflow provides <code>jflow.seqio</code> and <code>jflow.featureio</code> libraries where several file formats handler are available.
<h1>How to use a new format</h1>
<p>The new created format can then be used in all <code>add_input_*</code> functions of the class <code>jflow.workflow.Workflow</code>
and <code>jflow.component.Component</code> as following:</p>
<pre class="pre-hl "><code class="python">[...]
def define_parameters(self, function="process"):
self.add_input_file("reference_genome", "Which genome should the read be align on", file_format="fasta", required=True)
[...]</code></pre>
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Next Generation Sequencing Information System.
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<h2>Add new analysis</h2>
<p>Your workflow requires new analysis, learn how to add new ones.</p>
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<h2>Add new workflows</h2>
<p>Learn how to add new workflows.</p>
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