Projects quality control tests

User can add project tests to be performed in this steps, if the demultiplexing statistic file is available. The order of the parameters in the Aozan configuration file will be reused in the report generated by this step. Each test can use several parameters and contains always an "enable" property to activate the test. Usually a property named "interval" exists for each test, however if this property is not set, the value will be computed but not checked if it is the correct interval. The project tests reuse data collected from samples tests and other quality control tests on detection contamination and analysis undetermined clusters. Please report to those documentation pages for more information. You will find below all the parameters for all the available tests in Aozan:

Configuration project statistics quality tests

Aozan property Type Default value Description
qc.test.project.sample.count.enable boolean False Enable project sample count test
qc.test.project.genome.names.enable boolean False Enable genomes project names test
qc.test.project.lane.count.enable boolean False Enable project lane count test
qc.test.project.is.indexed.enable boolean False Enable project is indexed test
qc.test.project.min.raw.cluster.count.enable boolean False Enable project minimum raw cluster count test
qc.test.project.min.raw.cluster.count.interval integer interval Not set Interval for valid values
qc.test.project.max.raw.cluster.count.enable boolean False Enable project maximum raw cluster count test
qc.test.project.max.raw.cluster.count.interval integer interval Not set Interval for valid values
qc.test.project.raw.cluster.count.enable boolean False Enable project raw cluster count test
qc.test.project.raw.cluster.count.interval integer interval Not set Interval for valid values
qc.test.project.min.pf.cluster.count.enable boolean False Enable project minimum passing filter cluster count test
qc.test.project.min.pf.cluster.count.interval integer interval Not set Interval for valid values
qc.test.project.max.pf.cluster.count.enable boolean False Enable project maximum passing filter cluster count test
qc.test.project.max.pf.cluster.count.interval integer interval Not set Interval for valid values
qc.test.project.pf.cluster.count.enable boolean False Enable project project passing filter cluster count
qc.test.project.pf.cluster.count.interval integer interval False Interval for valid values
qc.test.project.recoverable.raw.cluster.percent.enable boolean False Enable project recoverable raw cluster percent test
qc.test.project.recoverable.raw.cluster.percent.interval double interval Not set Interval for valid values
qc.test.project.recoverable.pf.cluster.percent.enable boolean False Enable project recoverable passing filter cluster percent test
qc.test.project.recoverable.pf.cluster.percent.enable double interval False Interval for valid values
qc.test.project.fastqscreen.sample.overcontamination.count.enable boolean False Enable project FastQ Screen sample overcontamination count test
qc.test.project.fastqscreen.sample.overcontamination.count.enable integer interval False Integer for valid values
qc.test.project.fastqscreen.report.enable link False Enable link to detection contamination project report compilation samples data

Optional general configuration

User can change property on project test configuration.

Aozan property Type Default value description
qc.conf.fastqscreen.project.xsl.file string Not set Path to a specific stylesheet file to edit the fastqscreen report html, instead of the file per default
qc.conf.fastqscreen.project.contamination.percent.threshold double 0.10 Threshold to count sample with value for test (qc.test.sample.fastqscreen.mapped.percent.enable, mapped read on data set genome contamination.)

An example of table built with projects tests.

example on report with run data