Change log

Release History

Version Date Description
0.1 2011-12-08 Aozan version 0.1
0.2 2011-12-09 Aozan version 0.2
0.3 2011-12-09 Aozan version 0.3
0.4 2011-12-09 Aozan version 0.4
0.5 2011-12-12 Aozan version 0.5
0.6 2011-12-16 Aozan version 0.6
0.7 2012-02-24 Aozan version 0.7
0.8 2012-05-16 Aozan version 0.8
0.9 2012-06-20 Aozan version 0.9
0.10 2012-10-08 Aozan version 0.10
1.0 2013-04-26 Aozan version 1.0
1.1 2013-09-02 Aozan version 1.1
1.1.1 2013-09-20 Aozan version 1.1.1
1.1.2 2013-09-24 Aozan version 1.1.2
1.1.3 2013-10-14 Aozan version 1.1.3
1.2 2013-12-09 Aozan version 1.2
1.2.1 2014-01-17 Aozan version 1.2.1
1.2.2 2014-01-28 Aozan version 1.2.2
1.2.3 2014-03-11 Aozan version 1.2.3
1.2.4 2014-03-14 Aozan version 1.2.4
1.2.5 2014-04-04 Aozan version 1.2.5
1.2.6 2014-05-06 Aozan version 1.2.6
1.2.7 2014-09-01 Aozan version 1.2.7
1.2.8 2014-09-11 Aozan version 1.2.8
1.3 2014-10-16 Aozan version 1.3
1.3.1 2014-12-12 Aozan 1.3.1 release
1.3.2 2014-12-30 Aozan 1.3.2 release
1.4 2015-03-05 Aozan 1.4 release
1.4.1 2015-03-19 Aozan 1.4.1 release
1.4.2 2015-04-14 Aozan 1.4.2 release
1.5 2015-04-29 Aozan 1.5 release
2.0-rc1 2015-10-01 Aozan 2.0-rc1 release
2.0-rc2 2015-10-29 Aozan 2.0-rc2 release
2.0-rc3 2015-10-29 Aozan 2.0-rc3 release
2.0-rc4 2015-10-29 Aozan 2.0-rc4 release
2.0-rc5 2015-10-31 Aozan 2.0-rc5 release
2.0-rc6 2015-11-01 Aozan 2.0-rc6 release
2.0-rc7 2015-11-03 Aozan 2.0-rc7 release
2.0-rc8 2015-11-17 Aozan 2.0-rc8 release
2.0-rc9 2015-11-18 Aozan 2.0-rc9 release
2.0-rc10 2016-01-06 Aozan 2.0-rc10 release
2.0-rc11 2016-01-27 Aozan 2.0-rc11 release
2.0-rc12 2016-02-01 Aozan 2.0-rc12 release
2.0-rc13 2016-04-05 Aozan 2.0-rc13 release
2.0-rc14 2016-07-04 Aozan 2.0-rc14 release
2.0-rc15 2016-07-11 Aozan 2.0-rc15 release
2.0-rc16 2016-07-14 Aozan 2.0-rc16 release
2.0-rc17 2016-08-23 Aozan 2.0-rc17 release
2.0-rc18 2016-08-25 Aozan 2.0-rc18 release
2.0-rc19 2016-10-03 Aozan 2.0-rc19 release
2.0-rc20 2016-10-28 Aozan 2.0-rc20 release
2.0 2017-02-14 Aozan 2.0 release
2.1 2017-11-08 Aozan 2.1 release
2.1.1 2017-11-23 Aozan 2.1.1 release
2.2 2017-12-10 Aozan 2.2 release
2.2.1 2017-12-21 Aozan 2.2.1 release

Release 0.1 – 2011-12-08

Type Changes By
Update Initial version. jourdren

Release 0.2 – 2011-12-09

Type Changes By
Add While a run is running on HiSeq, send the first base report when available. jourdren

Release 0.3 – 2011-12-09

Type Changes By
Add Add a hiseq.deny file that contains all the run ids to not process. jourdren
Fix Now save a file with the pid of aozan. Now send a mail with the lock error only when the lock pid no more exists. jourdren
Fix Remove temporary files (design, hiseq_log_ directory). jourdren
Fix Fix issue when zip design files. jourdren

Release 0.4 – 2011-12-09

Type Changes By
Fix Fix issue with pid checking of already running aozan process. jourdren

Release 0.5 – 2011-12-12

Type Changes By
Add Aozan has now a log file name aozan.log. jourdren
Add Trace exception in log file. jourdren
Fix Issue with pid of currently running instance of Aozan. jourdren
Fix Now get the good Basecall_Stats_FLOWCELLID path even for RTA 1.10.36. jourdren
Add Now show in log the new disk usage and disk free at the end of sync step and demux step. jourdren
Fix Demux space estimation. jourdren

Release 0.6 – 2011-12-16

Type Changes By
Fix Fix mail message when a run is discovered. jourdren
Update Don't show Aozan welcome message when there is nothing to do. jourdren
Fix Change Eoulsan version dependency. Prevent errors with Casava design CSV file with comma in cell value. jourdren

Release 0.7 – 2012-02-24

Type Changes By
Fix Fix typo in mail message when the end of run is discovered. jourdren
Update Now use Eoulsan 1.2-SNAPSHOT as dependency. New Casava sample sheet check: 1) Allow the use of a sample in several lanes; 2) new error if a sample is used by more than one project; 3) new warning if a sample exists in more than one lane; 4) new warning with the list of line where is a sample (if the number of lanes >1); 5) new errors if a sample is defined several time by with not the same sequence index. jourdren
Update In demux step, add Casava design warnings to log and to the success mail send to users. jourdren
Update The default number of threads is now the number of available processors/cores. jourdren

Release 0.8 – 2012-05-16

Type Changes By
Add Add support for Casava 1.8.2. jourdren
Add Add Quality control report step. jourdren

Release 0.9 – 2012-06-20

Type Changes By
Update When an exception is thrown, send a mail with the exception message and traceback. jourdren
Fix When checking critical space available on HiSeq computer at every Aozan startup do not send a message if the HiSeq data path is not reachable. jourdren
Fix In Casava design checking now only allow strings using ascii charset. jourdren
Fix Aozan qc test do not fail if data to test does not exist. jourdren
Fix FastQC don't throw exception if no read read. jourdren
Update No write the qc raw data before the xml qc report. jourdren
Update If an unexcepted exception is thrown in qc step, now send a mail. jourdren

Release 0.10 – 2012-10-08

Type Changes By
Add Jython is now bundled in Aozan. jourdren

Release 1.0 – 2013-04-26

Type Changes By
Add The quality control step now contains a optional module for assessing sample contamination using a re-implementation of FastQ Screen. perrin
Add Add quality control restoration points to avoid relaunch all the analysis if a fatal error occurs before the end. perrin
Add Now estimate the space needed for the current run and check if enough free space in directory for next step is available. perrin
Add Add a common logger for java and python code. perrin

Release 1.1 – 2013-09-02

Type Changes By
Add Add a new module for contamination detection that use partial FASTQ files to reduce computation time without lost of information. perrin
Add Add a collector for reading TileOutMetrics.bin InterOp binary files. perrin
Add Add a collector for reading ErrorOutMetrics.bin InterOp binary files. perrin
Add Add a collector for reading ExtractionOutMetrics.bin InterOp binary files. perrin
Update The contamination detection report is now available in two formats: HTML and CSV. perrin
Add Add contamination detection for paired-end runs. Two modes are available, one by mapping only the first read and the other one by mapping both reads. perrin
Add Add a debug mode in configuration Aozan file. perrin

Release 1.1.1 – 2013-09-20

Type Changes By
Update Aozan now use FastQC 0.10.1. perrin
Fix Now show values for Undetermined instead of NA. perrin

Release 1.1.2 – 2013-09-24

Type Changes By
Fix Fix missing closing tags in XSL files. perrin

Release 1.1.3 – 2013-10-14

Type Changes By
Fix The change directory to save mapper index can now be set instead of always use /tmp. perrin

Release 1.2 – 2013-12-09

Type Changes By
Add Add an optional blast search in the 'Overrepresented Sequences' FastQC module. For unidentified sequences, a blastn is launched and the first hit is added in the FastQC report. perrin
Add In Aozan configuration several FastQC parameters can now be set: a file with list of contaminants, the kmers size and if each cycles values must be displayed. perrin
Update In the CASAVA/bcl2fastq samplesheet validator, add a tab to check genome sample. perrin
Add Add an HiSeq data continuous synchronization mode. jourdren
Add Formatter file rules for eclipse or other IDE can be download on Aozan site. perrin

Release 1.2.1 – 2014-01-17

Type Changes By
Add Homogeization of the configuration settings names. Now use the new Settings class to retrieve a configuration value. perrin
Update In the test on demultiplexing data 'percentinlanesample', add a score that depends of the sample count in the lane. perrin
Update Update Guava library version dependency from 14.0.1 to 15.1. perrin

Release 1.2.2 – 2014-01-28

Type Changes By
Fix The mapping for contamination detection was launched in mono-thread mode. perrin

Release 1.2.3 – 2014-03-11

Type Changes By
Fix The alias genome names file used by FastQScreen is updated and no more rewritten. perrin
Add Now check main parameters from configuration before starting Aozan. perrin
Fix Launching steps when synchronization step is skipped without entry in infinite loop. The useful directory and archives for next steps are been created. perrin
Fix The QC report is now generated only if one 'qc.test' is enabled. Useful collectors are automatically called. perrin
Fix The 'From' field header in emails sent by Aozan was not set. jourdren

Release 1.2.4 – 2014-03-14

Type Changes By
Fix When check main paths in configuration, the paths are no more converted to lower case. jourdren
Update Add setting for bcl2fastq/casava compression format (.bz2, .gz, none, bzip2, gz, gzip). jourdren
Fix Remove blast database prefix configuration setting. perrin

Release 1.2.5 – 2014-04-04

Type Changes By
Fix Now check aozan configuration file at the beginning. Sends an email if fails. perrin

Release 1.2.6 – 2014-05-06

Type Changes By
Fix Now check if FASTQ files are not empty before creating partial FASTQ files used by FastqScreen for contamination detection. perrin

Release 1.2.7 – 2014-09-01

Type Changes By
Update Aozan now requires Java 7 and use samtools/picard 1.92 as dependency. perrin
Fix Update email sending code. Now the email date is already set. perrin
Update Compute phasing and prephasing values with RTA v1.18. Ignore null tiles metric values in Interop file. perrin
Add Add a new web page to explain how to create a plugin for Aozan. perrin

Release 1.2.8 – 2014-09-11

Type Changes By
Fix Fix compute phasing and prephasing values from tiles metric Interop file. Multiply by 100 values to get the same values as before v1.2.7. perrin
Fix Fix indentation in html report. Fix display error for lines > 1000 characters when processed by some mail server. perrin

Release 1.3 – 2014-10-16

Type Changes By
Add Add global tests to the QC step. This new type of test comes with some global tests. jourdren
Add Aozan now provide a QC module that analyzes indices of reads in the undetermined FASTQ files. For each indices, this module suggest the sample(s) and the number of reads that can be recovered using a demultiplexing step with one more mismatch that the number of mismatches has been used. This module create two reports: one per indexed lanes and one per indexed samples, both in CVS and HTML format. jourdren
Add Add two parameters in the Aozan configuration to run FastQC and contaminants detection on undetermined FASTQ files. sperrin
Add Add a new "include" directive in Aozan configuration file. With this enhancement it will be easier to use Aozan in a multi-servers context using the same core configuration file by all Aozan instances. sperrin
Update Aozan now use blastn from ncbi-blast+ in addition of blastall. sperrin
Update Aozan use now FastQC 0.11.2 which has been enhanced like previous Aozan version (bad tiles modules, blastn in Overrepresented sequences modules). sperrin
Update Aozan can now use the bowtie 2 mapper in FastqScreen step. The default mapper used in Aozan still bowtie 1. sperrin
Update Update the control quality report with a table for global tests. Add button to filter by project name displayed samples in the QC report. sperrin
Add Aozan now use Eoulsan 2.0-alpha1 as dependency. A bug in this new Eoulsan version forces us to add amazonaws library as Aozan dependancy. This amazonaws dependency will be remove once Aozan will use a fixed version of Eoulsan. sperrin

Release 1.3.1 – 2014-12-12

Type Changes By
Add Add two samples tests on recovery cluster modules to get percent on raw and passing filter recovery clusters. sperrin
Add Aozan now use Maven 3 for building binaries and website. sperrin
Fix Global test UndeterminedClustersPercentGlobalTest, now ignore not indexed lane. sperrin
Update QC global report, now button project filter by lane. sperrin
Update Update dependancies in pom.xml : 1) now use Eoulsan-2.0-alpha3, 2) remove dependency to aws-java-sdk only usefully with Eoulsan version 2.0-alpha1 sperrin

Release 1.3.2 – 2014-12-30

Type Changes By
Fix Global test UndeterminedClustersPercentGlobalTest, fix compute percent. sperrin

Release 1.4 – 2015-03-05

Type Changes By
Add Add lock file for each run at each step in context with several instance of Aozan running. jourdren
Add Add detection contamination project report in HTML, compile data from samples. sperrin
Fix Fix read collector on InterOp, now it can treat run with multindexes or run without index. sperrin
Update Archive on run, now is create after the detection run step instead of synchronization step. sperrin
Add Aozan now use Eoulsan 2.0-alpha5 as dependency. sperrin
Add Add project tests to the QC step. This new type of test comes with some project tests. sperrin

Release 1.4.1 – 2015-03-19

Type Changes By
Fix Fix action to create of lock file on each step. jourdren
Update Example on final quality control report, add table on project. sperrin
Add Change default logger level, replace INFO by CONF. sperrin
Update In detection contamination project report, add lane number with sample name (case technical replicates), can be manage project with several genome. sperrin
Fix Now ProjectStatsCollector don't require UndeterminedIndexesCollector and FastqScreenCollector. Only if they are required for QC step, it can use data to compute related statistics. sperrin
Update The official Aozan Git repository is now GitHub instead of Google code. jourdren

Release 1.4.2 – 2015-04-14

Type Changes By
Add New dependency for errorprone static code analysis tool execution each time mvn compile is called. jourdren
Update Update detection contaminant project report. sperrin
Fix With PE run, now all statistical data in quality control report are display, no more NA. sperrin

Release 1.5 – 2015-04-29

Type Changes By
Add New dependency on FastQC version 0.11.3, publish 25/03/2015. sperrin
Fix The ProjectStatCollector can now collect data on recovery on undetermined reads when a lane is no indexed, the control quality report displays NA for this lane. sperrin

Release 2.0-rc1 – 2015-10-01

Type Changes By
Add Now Aozan can manager HiSeq and NextSeq sequencer at the same time. sperrin
Add Now Aozan can manager futhermore bcl2fastq2 and new version on sample sheet file. sperrin
Add Now Aozan can run the demultiplexing step with Docker images on bcl2fastq 1 or 2. sperrin
Add The final quality control report includes a sample statistic table to compile data on technical replica if the run contains only one project name. sperrin

Release 2.0-rc2 – 2015-10-29

Type Changes By
Update Replace the implementation of the SampleSheet classes by a new one. jourdren
Fix Many refactoring in Java and Python code. jourdren
Fix Many small fixes. jourdren

Release 2.0-rc3 – 2015-10-29

Type Changes By
Fix In, Python hiseq module was not loaded. jourdren
Fix Fix changes.xml XML. jourdren

Release 2.0-rc4 – 2015-10-29

Type Changes By
Fix In, Python hiseq_run module was not loaded (not hiseq module !!!). jourdren

Release 2.0-rc5 – 2015-10-31

Type Changes By
Fix Do not search for undetermined fastq files in lanes where there is only one sample without index. jourdren
Fix Bcl2fastq 2 output is bugged: Read number attritute in ConversionStats.xml is random for the first read when no index is set in the lane. jourdren
Fix Update Illumina FASTQ header parser to allow headers with index that are not a nucleotide sequence. jourdren
Fix Several fixes to avoid craches when no undetermined FASTQ exists when collect data or process tests in the QC step. jourdren

Release 2.0-rc6 – 2015-11-01

Type Changes By
Fix Fix FASTQ filename creation from samplesheet for bcl2fastq 2 output. jourdren
Fix Fix NullPointerException when no genome reference is defined for sample.. jourdren
Fix For clusting recovering, do not process undetermined Illumina sequences without index nucleotide sequence in FASTQ header. jourdren

Release 2.0-rc7 – 2015-11-03

Type Changes By
Update In the Sample class, rename getProject() to getSampleProject() and isProjectField() to isSampleProjectField(). jourdren
Update For debugging, save a snapshot of the run data information after the end of each collector. jourdren

Release 2.0-rc8 – 2015-11-17

Type Changes By
Update The detection of the samplesheet V1 header is now case insensible and existing '_' characters are removed for the detection. jourdren
Fix Now don't check RTA version of the run to avoid reading the runParameter.xml file when it has not been created while synchronizing runs. jourdren

Release 2.0-rc9 – 2015-11-18

Type Changes By
Update Remove synchronization of runs that had just finished after the end of each step. This feature is now unnecessary with the partial synchronization feature. jourdren

Release 2.0-rc10 – 2016-01-06

Type Changes By
Fix When several qc analysis must be done, the configuration of the first qc when used for the other qc analysis. jourdren
Fix In FastQC blasts of overrepresented sequences, due to concurency issue, multiple blast instances could be executed at the same time. jourdren
Fix Fix tar warning message on stderr in the demux step. jourdren
Update Many Java code refactoring and dead code removing. jourdren
Update Rename packages fr.ens.transcriptome.aozan.* to fr.ens.biologie.genomique.aozan.* as the new website of the ENS genomic platform is Update the URL of the website to jourdren
Update The encoding of the website is now UTF-8. jourdren
Update Many small code and javadoc fixes after running IDEA inspect tool. jourdren

Release 2.0-rc11 – 2016-01-27

Type Changes By
Fix Do not send an email if the first base report does not yet exist for RTA 1 output. jourdren
Fix In the meanqualityscorepfsamplestats and samplestatspercentq30basepf tests, a NullPointerException was thrown if a sample does not exists in all the lane of the run. jourdren

Release 2.0-rc12 – 2016-02-01

Type Changes By
Fix In the percentsampleinproject and samplestatsfsqmapped tests, a NullPointerException was thrown if a sample does not exists in all the lane of the run. jourdren

Release 2.0-rc13 – 2016-04-05

Type Changes By
Fix The QC step now support dual indexing. jourdren
Update Aozan now use Eoulsan 2.0-beta3 and htsjdk 1.118. jourdren
Update The new Aozan website URL is and the new Genomic platform website is jourdren

Release 2.0-rc14 – 2016-07-04

Type Changes By
Update The user can now define the number of mismatches of barcode for bcl2fastq in the samplesheet using the "MismatchCount" value of the "Settings" section. jourdren
Update The file with all QC data is now renamed from data-RUN_ID.txt to jourdren
Update Remove bcl2fastq 1.x support. jourdren
Update Replace all occurences of "casava" by "bcl2fastq". jourdren
Update Remplace all occurences of "design" by "samplesheet". jourdren
Update In QC, rename all data entries starting with "design." by "samplesheet.". jourdren
Update Add a prefix for data of all ReadCollector entries. jourdren
Update Remove "HiSeq" and "NextSeq" strings from all Aozan messages, use instead the family name of the sequencer and its serial number. jourdren
Update Force use LANG=C environment variable in jourdren
Update The emails are now sent in UTF8. jourdren
Update In OverrepresentedSequencesBlast, several blast are now performed at each execution of blast. jourdren
Update Reorganize GenomeAliases class code. jourdren

Release 2.0-rc15 – 2016-07-11

Type Changes By
Update FastQC 0.11.5 is now embedded in Aozan. jourdren
Fix The 'qc.conf.threads' configuration settings value now works for Fastq-screen. jourdren
Fix The Eoulsan configuration needed by FastqScreen is now only set when FastqScreen is enabled. If a setting is required by FastqScreen is not set, an error message is now thrown. jourdren
Fix The subject message of the email sent when a new run is detected now contains the correct number of the run cycles. jourdren
Fix The choice of the FASTQ file compression level is now (re)working. jourdren
Fix The additional arguments of bcl2fastq were not correctly handled. jourdren
Fix The FastqScreen now works when the FASTQ files are empty. jourdren
Fix The genome aliases for FastqScreen were not correctly loaded. jourdren
Fix Fix exception in FastQC when few reads are processed. jourdren
Fix Fix exception in undetermined collector when few reads are processed. jourdren

Release 2.0-rc16 – 2016-07-14

Type Changes By
Add Add 2 new tests to show Q30 of the run lanes and of all the run. firmo
Fix In FastQC report for overrepresented sequences, the blast message was a Java reference instead of the real blast result message. jourdren

Release 2.0-rc17 – 2016-08-23

Type Changes By
Update Reorganize key names in RunData to use an id for each sample/pooledsample/project instead of their name. jourdren
Update All the tests configuration keys are now prefixed with its type (lane, sample, project, global and samplestats). jourdren
Fix All the files in the report directory have now the 755 permissions. jourdren
Update When the samplesheet is not generated by an external tool, Aozan can now use the SampleSheet.csv file as samplesheet if no other samplesheet is provided by the user. jourdren
Update The samplesheet in the FASTQ output directory is now always named "SampleSheet.csv". jourdren
Fix The Phasing and Prephasing calculations from Aozan are now similar to Illumina calculations. firmo
Update Aozan JUnit tests have now migrated from JUnit 3 to JUnit 4.11 . firmo
Add Can now set prioritized runs using the "runs.priority" file. firmo
Add Can now deny runs from performing an Aozan test using the "*.deny" file. firmo
Update The "*.done" files telling which run succesfully finished a step are now locked and protected from multiple process trying to modify these files simultaneously. firmo
Add new test giving sum of pooled samples used. firmo
Update Fully renamed tests, doc and classes associated with qc-tests. firmo
Add Samplesheet files can now also be in XLSX format. firmo
Update Rename Sample stats section to Pooled samples. jourdren
Update Rename many "qc.conf.*" keys. jourdren
Update Update the "writing a plugin" section of the documentation with the latest version of the API of Aozan. jourdren
Update Update and reorganize the configuration example. jourdren

Release 2.0-rc18 – 2016-08-25

Type Changes By
Fix Entries in done files were written with the 2 byte of the Byte order mark. jourdren
Fix Fix some typos in email messages. jourdren
Fix When a configuration key related to a path key did not exist, an exception was thrown when checking the path existance. jourdren
Fix The default compression level value was not set for the right configuration key. jourdren
Fix In detection_end_run.discover_terminated_runs(), do not raise an exception when create_run_summary_reports() failed because an error message has been already sent.. jourdren
Fix The samplesheet in XLSX format are now also saved in the zip archive. jourdren
Fix Fix non-existing variable Python error when archiving samplesheet. jourdren
Fix In demux step, the temporary samplesheet file used by bcl2fastq was removed twice. jourdren
Update At startup of aozan.aozan_main(), now check if the configuration file exists.. jourdren
Add Added recompression step. firmo

Release 2.0-rc19 – 2016-10-03

Type Changes By
Fix Fix issue when using old configuration keys in upper case. jourdren
Fix Fix issue when parsing intervals for QC tests in configuration file. jourdren
Fix Fix missing collector dependencies of some QC tests. jourdren
Fix Aozan can now handle FASTQ files for QC when samples of a project are in a dedicated subdirectory directory of the project directory. jourdren
Fix Fix missing collector dependencies of some QC tests. jourdren
Fix Fix issue with sample in upper case in the demultiplexing collector in QC. jourdren
Fix Fixed errors when samples in the samplesheet were unsorted. firmo
Fix Fixed some typo in aozan error messages. firmo
Fix Fixed errors when converting samplesheet to CSV leave empty column. firmo
Fix Fix Aozan can now handle FASTQ files that are in a sample subdirectory generated by Bcl2fastq. jourdren
Fix When the value of a setting entry in the configuration was empty, an error was thrown. jourdren
Fix The version of bcl2fastq was read from the right log file in QC step. jourdren
Add Parameter files for failed runs are now also archived. firmo
Update Docker can now be used to launch Blast in the Overrepresented sequences module of FastQC. jourdren
Add Add a script that allows to create an Aozan demo configuration file and downloads all required files. jourdren
Add Now checks if system is linux type. firmo
Add Now checks if programs are availables in PATH before execution. firmo
Update Can now provide samplesheets xls where field contains ',' character. firmo
Update When bcl2fastq execution fails, send error log attached in mail. firmo
Update Now supports bcl2fastq 2.18. firmo
Update Update the QC demo example. jourdren
Update The change of the rights of output files to read only can now be disabled using the "read.only.output.files" configuration property. jourdren

Release 2.0-rc20 – 2016-10-28

Type Changes By
Fix Fix some Java 8 compilation errors. jourdren
Fix The sample id in the FASTQ filenames was not corretly sometimes guessed. jourdren
Fix For large FASTQ files, the FastQC report was not generated. jourdren
Fix Fix error when parsing an empty PID file. jourdren
Fix When the "qc.conf.threads" configuration property is not set, now use all available cores to launch FastQ Screen. jourdren
Fix The key results generated by ConversionStatsCollector with bcl2fastq 2.16 was not the same as with bcl2fastq 2.18. jourdren
Update The default amount of memory allocated by Aozan is now 4096 instead of 2048MiB. jourdren
Update Update documentation. jourdren

Release 2.0 – 2017-02-14

Type Changes By
Fix Spaces, simple and double quotes can now be used in paths to the Aozan input and output files. jourdren
Fix Fix NullPointerException when process undetermined samples in RecoverableRawClusterPercentSampleTest. jourdren
Update StartTTLS, SSL, and login/password can now be used to configure the connection to the SMTP server to send emails. jourdren
Update The FastQC and Fastq Screen reports have now the same prefix as the FASTQ files. jourdren
Add Add two new configuration property to unzip and/or remove FastQC Zip report file. jourdren
Update Aozan now use Eoulsan 2.0-beta4 as dependency. jourdren
Add Aozan now supports Illumina HiSeq 3/4000 and HiSeq X. jourdren

Release 2.1 – 2017-11-08

Type Changes By
Fix Aozan now thrown an error if an empty string is used for the number mismatches in the settings. jourdren
Fix Fix unknown variable error while creating error message while demultiplexing. jourdren
Fix Fix issue of Fastq Screen when mapping very small FASTQ files. jourdren
Fix Aozan now works with MiSeq flowcell ids. jourdren
Fix In some cases, Aozan did not guest the correct sample number for FASTQ filenames generated by bcl2fastq. jourdren
Fix In FastQScreen mapped percentage test, the sample genome reference name was used as key instead the real genome reference name obtained using the genome alias. jourdren
Fix When replacing index shortcuts in samplesheet by real sequences, index1 was processed instead of index2. jourdren
Fix When launching FastQScreen on very small FASTQ file, Aozan stalled. jourdren
Add Add a new demux.archive.samplesheets option in Aozan configuration file to avoid samplesheets archiving. jourdren
Add Now throw a warning when a index 2 field exists and not index 1 field in samplesheet. jourdren

Release 2.1.1 – 2017-11-23

Type Changes By
Fix When a genome alias was used as reference genome for FastQScreen, the mapping of the reads was not performed. jourdren

Release 2.2 – 2017-12-10

Type Changes By
Fix In paired-end mode, the links in the main report to FastQC reports were null. jourdren
Fix Fix NullPointerException in Fastq Screen collector when no sample reference was defined in the samplesheet. jourdren
Fix Fix error when accessing to genome alias names and the Fastq Screen collector was not enabled. jourdren
Fix The gathering of cluster recovering counts in EntityStat is now not made if dual indexing is enabled because the recovery cluster collector does not work with dual indexing. jourdren
Fix Fix the order of the Fastq Screen genome tests in the report. jourdren
Add Add a MultiQC collector and project test. MultiQC will use Bcl2fastq stats, FastQC and Fastq Screen data. jourdren

Release 2.2.1 – 2017-12-21

Type Changes By
Fix The entry for FastQ Screen report path for read 2 in paired-end mode was not exists. jourdren
Fix The genome alias file was not updated when an unknown genome name was added. jourdren