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.
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.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.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.