Quality control step

This step allows to perform quality controls on the output runs. To do this Aozan uses Illumina reports, FastQC results and contamination detection results (using a reimplementation of FastQ Screen).

This step creates a report file including the thresholds fixed for quality controls with :

Note: The quality control step is the longest step, it can last several hours/days. If Aozan is stopped before the end of this step, it is possible to relaunch it. Restore points allow get back at the last sample processed.

Configuration parameters

The next table contains the parameters of this step.

Aozan property Type Default value description
qc.step boolean True Enable the step. If True, at least one test must be enabled, otherwise no data will be collected for the QC report.
qc.step.end.email.template string Not set Path of the email template for the end of the qc step.
qc.report.save.raw.data boolean False Save raw data generated for the tests
qc.report.save.report.data boolean False Save report data in XML format (before applying the stylesheet)
qc.report.stylesheet string Not set Path to the XSL stylesheet to use
qc.report.tests.to.remove.in.basic.report string Not set A list of test (e.g. qc.test.lane.pf.cluster.count) separated by commas to remove from an additional HTML report. This second HTML report will have the same filename as the standard HTML report but with "-basic" suffix before the HTML extension.
qc.conf.threads integer The number of core available on the system The number of thread to use

An example of email sent to the end of Aozan with the quality control summary as attachment and an example of all data built for one run in quality control step.

Example on quality control run report

Aozan creates a html page to navigate in all documents and archives from a run.

page to navigate in all document from a run