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 |
| 3.0 | 2023-04-28 | Aozan 3.0 release |
| 3.0.1 | 2023-05-24 | Aozan 3.0.1 release |
| 3.0.2 | 2023-07-07 | Aozan 3.0.2 release |
| 3.1 | 2024-04-25 | Aozan 3.1 release |
| 3.1.1 | 2024-07-17 | Aozan 3.1.1 release |
Release 0.1 – 2011-12-08
| Type | Changes | By |
|---|---|---|
 |
Initial version. | jourdren |
Release 0.2 – 2011-12-09
| Type | Changes | By |
|---|---|---|
 |
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 a hiseq.deny file that contains all the run ids to not process. | jourdren |
 |
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 |
|
Remove temporary files (design, hiseq_log_ directory). | jourdren |
|
Fix issue when zip design files. | jourdren |
Release 0.4 – 2011-12-09
| Type | Changes | By |
|---|---|---|
|
Fix issue with pid checking of already running aozan process. | jourdren |
Release 0.5 – 2011-12-12
| Type | Changes | By |
|---|---|---|
|
Aozan has now a log file name aozan.log. | jourdren |
|
Trace exception in log file. | jourdren |
|
Issue with pid of currently running instance of Aozan. | jourdren |
|
Now get the good Basecall_Stats_FLOWCELLID path even for RTA 1.10.36. | jourdren |
|
Now show in log the new disk usage and disk free at the end of sync step and demux step. | jourdren |
|
Demux space estimation. | jourdren |
Release 0.6 – 2011-12-16
| Type | Changes | By |
|---|---|---|
|
Fix mail message when a run is discovered. | jourdren |
|
Don't show Aozan welcome message when there is nothing to do. | jourdren |
|
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 typo in mail message when the end of run is discovered. | jourdren |
|
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 |
|
In demux step, add Casava design warnings to log and to the success mail send to users. | jourdren |
|
The default number of threads is now the number of available processors/cores. | jourdren |
Release 0.8 – 2012-05-16
| Type | Changes | By |
|---|---|---|
|
Add support for Casava 1.8.2. | jourdren |
|
Add Quality control report step. | jourdren |
Release 0.9 – 2012-06-20
| Type | Changes | By |
|---|---|---|
|
When an exception is thrown, send a mail with the exception message and traceback. | jourdren |
|
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 |
|
In Casava design checking now only allow strings using ascii charset. | jourdren |
|
Aozan qc test do not fail if data to test does not exist. | jourdren |
|
FastQC don't throw exception if no read read. | jourdren |
|
No write the qc raw data before the xml qc report. | jourdren |
|
If an unexcepted exception is thrown in qc step, now send a mail. | jourdren |
Release 0.10 – 2012-10-08
| Type | Changes | By |
|---|---|---|
|
Jython is now bundled in Aozan. | jourdren |
Release 1.0 – 2013-04-26
| Type | Changes | By |
|---|---|---|
|
The quality control step now contains a optional module for assessing sample contamination using a re-implementation of FastQ Screen. | perrin |
|
Add quality control restoration points to avoid relaunch all the analysis if a fatal error occurs before the end. | perrin |
|
Now estimate the space needed for the current run and check if enough free space in directory for next step is available. | perrin |
|
Add a common logger for java and python code. | perrin |
Release 1.1 – 2013-09-02
| Type | Changes | By |
|---|---|---|
|
Add a new module for contamination detection that use partial FASTQ files to reduce computation time without lost of information. | perrin |
|
Add a collector for reading TileOutMetrics.bin InterOp binary files. | perrin |
|
Add a collector for reading ErrorOutMetrics.bin InterOp binary files. | perrin |
|
Add a collector for reading ExtractionOutMetrics.bin InterOp binary files. | perrin |
|
The contamination detection report is now available in two formats: HTML and CSV. | perrin |
|
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 a debug mode in configuration Aozan file. | perrin |
Release 1.1.1 – 2013-09-20
| Type | Changes | By |
|---|---|---|
|
Aozan now use FastQC 0.10.1. | perrin |
|
Now show values for Undetermined instead of NA. | perrin |
Release 1.1.2 – 2013-09-24
| Type | Changes | By |
|---|---|---|
|
Fix missing closing tags in XSL files. | perrin |
Release 1.1.3 – 2013-10-14
| Type | Changes | By |
|---|---|---|
|
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 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 |
|
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 |
|
In the CASAVA/bcl2fastq samplesheet validator, add a tab to check genome sample. | perrin |
|
Add an HiSeq data continuous synchronization mode. | jourdren |
|
Formatter file rules for eclipse or other IDE can be download on code.google.com Aozan site. | perrin |
Release 1.2.1 – 2014-01-17
| Type | Changes | By |
|---|---|---|
|
Homogeization of the configuration settings names. Now use the new Settings class to retrieve a configuration value. | perrin |
|
In the test on demultiplexing data 'percentinlanesample', add a score that depends of the sample count in the lane. | perrin |
|
Update Guava library version dependency from 14.0.1 to 15.1. | perrin |
Release 1.2.2 – 2014-01-28
| Type | Changes | By |
|---|---|---|
|
The mapping for contamination detection was launched in mono-thread mode. | perrin |
Release 1.2.3 – 2014-03-11
| Type | Changes | By |
|---|---|---|
|
The alias genome names file used by FastQScreen is updated and no more rewritten. | perrin |
|
Now check main parameters from configuration before starting Aozan. | perrin |
|
Launching steps when synchronization step is skipped without entry in infinite loop. The useful directory and archives for next steps are been created. | perrin |
|
The QC report is now generated only if one 'qc.test' is enabled. Useful collectors are automatically called. | perrin |
|
The 'From' field header in emails sent by Aozan was not set. | jourdren |
Release 1.2.4 – 2014-03-14
| Type | Changes | By |
|---|---|---|
|
When check main paths in configuration, the paths are no more converted to lower case. | jourdren |
|
Add setting for bcl2fastq/casava compression format (.bz2, .gz, none, bzip2, gz, gzip). | jourdren |
|
Remove blast database prefix configuration setting. | perrin |
Release 1.2.5 – 2014-04-04
| Type | Changes | By |
|---|---|---|
|
Now check aozan configuration file at the beginning. Sends an email if fails. | perrin |
Release 1.2.6 – 2014-05-06
| Type | Changes | By |
|---|---|---|
|
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 |
|---|---|---|
|
Aozan now requires Java 7 and use samtools/picard 1.92 as dependency. | perrin |
|
Update email sending code. Now the email date is already set. | perrin |
|
Compute phasing and prephasing values with RTA v1.18. Ignore null tiles metric values in Interop file. | perrin |
|
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 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 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 global tests to the QC step. This new type of test comes with some global tests. | jourdren |
|
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 two parameters in the Aozan configuration to run FastQC and contaminants detection on undetermined FASTQ files. | sperrin |
|
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 |
|
Aozan now use blastn from ncbi-blast+ in addition of blastall. | sperrin |
|
Aozan use now FastQC 0.11.2 which has been enhanced like previous Aozan version (bad tiles modules, blastn in Overrepresented sequences modules). | sperrin |
|
Aozan can now use the bowtie 2 mapper in FastqScreen step. The default mapper used in Aozan still bowtie 1. | sperrin |
|
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 |
|
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 two samples tests on recovery cluster modules to get percent on raw and passing filter recovery clusters. | sperrin |
|
Aozan now use Maven 3 for building binaries and website. | sperrin |
|
Global test UndeterminedClustersPercentGlobalTest, now ignore not indexed lane. | sperrin |
|
QC global report, now button project filter by lane. | sperrin |
|
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 |
|---|---|---|
|
Global test UndeterminedClustersPercentGlobalTest, fix compute percent. | sperrin |
Release 1.4 – 2015-03-05
| Type | Changes | By |
|---|---|---|
|
Add lock file for each run at each step in context with several instance of Aozan running. | jourdren |
|
Add detection contamination project report in HTML, compile data from samples. | sperrin |
|
Fix read collector on InterOp, now it can treat run with multindexes or run without index. | sperrin |
|
Archive on run, now is create after the detection run step instead of synchronization step. | sperrin |
|
Aozan now use Eoulsan 2.0-alpha5 as dependency. | sperrin |
|
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 action to create of lock file on each step. | jourdren |
|
Example on final quality control report, add table on project. | sperrin |
|
Change default logger level, replace INFO by CONF. | sperrin |
|
In detection contamination project report, add lane number with sample name (case technical replicates), can be manage project with several genome. | sperrin |
|
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 |
|
The official Aozan Git repository is now GitHub instead of Google code. | jourdren |
Release 1.4.2 – 2015-04-14
| Type | Changes | By |
|---|---|---|
|
New dependency for errorprone static code analysis tool execution each time mvn compile is called. | jourdren |
|
Update detection contaminant project report. | sperrin |
|
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 |
|---|---|---|
|
New dependency on FastQC version 0.11.3, publish 25/03/2015. | sperrin |
|
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 |
|---|---|---|
|
Now Aozan can manager HiSeq and NextSeq sequencer at the same time. | sperrin |
|
Now Aozan can manager futhermore bcl2fastq2 and new version on sample sheet file. | sperrin |
|
Now Aozan can run the demultiplexing step with Docker images on bcl2fastq 1 or 2. | sperrin |
|
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 |
|---|---|---|
|
Replace the implementation of the SampleSheet classes by a new one. | jourdren |
|
Many refactoring in Java and Python code. | jourdren |
|
Many small fixes. | jourdren |
Release 2.0-rc3 – 2015-10-29
| Type | Changes | By |
|---|---|---|
|
In estimate_space_needed.py, Python hiseq module was not loaded. | jourdren |
|
Fix changes.xml XML. | jourdren |
Release 2.0-rc4 – 2015-10-29
| Type | Changes | By |
|---|---|---|
|
In estimate_space_needed.py, Python hiseq_run module was not loaded (not hiseq module !!!). | jourdren |
Release 2.0-rc5 – 2015-10-31
| Type | Changes | By |
|---|---|---|
|
Do not search for undetermined fastq files in lanes where there is only one sample without index. | jourdren |
|
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 |
|
Update Illumina FASTQ header parser to allow headers with index that are not a nucleotide sequence. | jourdren |
|
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 FASTQ filename creation from samplesheet for bcl2fastq 2 output. | jourdren |
|
Fix NullPointerException when no genome reference is defined for sample.. | jourdren |
|
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 |
|---|---|---|
|
In the Sample class, rename getProject() to getSampleProject() and isProjectField() to isSampleProjectField(). | jourdren |
|
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 |
|---|---|---|
|
The detection of the samplesheet V1 header is now case insensible and existing '_' characters are removed for the detection. | jourdren |
|
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 |
|---|---|---|
|
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 |
|---|---|---|
|
When several qc analysis must be done, the configuration of the first qc when used for the other qc analysis. | jourdren |
|
In FastQC blasts of overrepresented sequences, due to concurency issue, multiple blast instances could be executed at the same time. | jourdren |
|
Fix tar warning message on stderr in the demux step. | jourdren |
|
Many Java code refactoring and dead code removing. | jourdren |
|
Rename packages fr.ens.transcriptome.aozan.* to fr.ens.biologie.genomique.aozan.* as the new website of the ENS genomic platform is https://genomique.biologie.ens.fr. Update the URL of the website to http://outils.genomique.biologie.ens.fr/aozan. | jourdren |
|
The encoding of the website is now UTF-8. | jourdren |
|
Many small code and javadoc fixes after running IDEA inspect tool. | jourdren |
Release 2.0-rc11 – 2016-01-27
| Type | Changes | By |
|---|---|---|
|
Do not send an email if the first base report does not yet exist for RTA 1 output. | jourdren |
|
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 |
|---|---|---|
|
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 |
|---|---|---|
|
The QC step now support dual indexing. | jourdren |
|
Aozan now use Eoulsan 2.0-beta3 and htsjdk 1.118. | jourdren |
|
The new Aozan website URL is http://outils.genomic.biologie.ens.fr/aozan and the new Genomic platform website is https://genomique.biologie.ens.fr. | jourdren |
Release 2.0-rc14 – 2016-07-04
| Type | Changes | By |
|---|---|---|
|
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 |
|
The file with all QC data is now renamed from data-RUN_ID.txt to RUN_ID.data. | jourdren |
|
Remove bcl2fastq 1.x support. | jourdren |
|
Replace all occurences of "casava" by "bcl2fastq". | jourdren |
|
Remplace all occurences of "design" by "samplesheet". | jourdren |
|
In QC, rename all data entries starting with "design." by "samplesheet.". | jourdren |
|
Add a prefix for data of all ReadCollector entries. | jourdren |
|
Remove "HiSeq" and "NextSeq" strings from all Aozan messages, use instead the family name of the sequencer and its serial number. | jourdren |
|
Force use LANG=C environment variable in aozan.sh. | jourdren |
|
The emails are now sent in UTF8. | jourdren |
|
In OverrepresentedSequencesBlast, several blast are now performed at each execution of blast. | jourdren |
|
Reorganize GenomeAliases class code. | jourdren |
Release 2.0-rc15 – 2016-07-11
| Type | Changes | By |
|---|---|---|
|
FastQC 0.11.5 is now embedded in Aozan. | jourdren |
|
The 'qc.conf.threads' configuration settings value now works for Fastq-screen. | jourdren |
|
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 |
|
The subject message of the email sent when a new run is detected now contains the correct number of the run cycles. | jourdren |
|
The choice of the FASTQ file compression level is now (re)working. | jourdren |
|
The additional arguments of bcl2fastq were not correctly handled. | jourdren |
|
The FastqScreen now works when the FASTQ files are empty. | jourdren |
|
The genome aliases for FastqScreen were not correctly loaded. | jourdren |
|
Fix exception in FastQC when few reads are processed. | jourdren |
|
Fix exception in undetermined collector when few reads are processed. | jourdren |
Release 2.0-rc16 – 2016-07-14
| Type | Changes | By |
|---|---|---|
|
Add 2 new tests to show Q30 of the run lanes and of all the run. | firmo |
|
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 |
|---|---|---|
|
Reorganize key names in RunData to use an id for each sample/pooledsample/project instead of their name. | jourdren |
|
All the tests configuration keys are now prefixed with its type (lane, sample, project, global and samplestats). | jourdren |
|
All the files in the report directory have now the 755 permissions. | jourdren |
|
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 |
|
The samplesheet in the FASTQ output directory is now always named "SampleSheet.csv". | jourdren |
|
The Phasing and Prephasing calculations from Aozan are now similar to Illumina calculations. | firmo |
|
Aozan JUnit tests have now migrated from JUnit 3 to JUnit 4.11 . | firmo |
|
Can now set prioritized runs using the "runs.priority" file. | firmo |
|
Can now deny runs from performing an Aozan test using the "*.deny" file. | firmo |
|
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 |
|
new test giving sum of pooled samples used. | firmo |
|
Fully renamed tests, doc and classes associated with qc-tests. | firmo |
|
Samplesheet files can now also be in XLSX format. | firmo |
|
Rename Sample stats section to Pooled samples. | jourdren |
|
Rename many "qc.conf.*" keys. | jourdren |
|
Update the "writing a plugin" section of the documentation with the latest version of the API of Aozan. | jourdren |
|
Update and reorganize the configuration example. | jourdren |
Release 2.0-rc18 – 2016-08-25
| Type | Changes | By |
|---|---|---|
|
Entries in done files were written with the 2 byte of the Byte order mark. | jourdren |
|
Fix some typos in email messages. | jourdren |
|
When a configuration key related to a path key did not exist, an exception was thrown when checking the path existance. | jourdren |
|
The default compression level value was not set for the right configuration key. | jourdren |
|
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 |
|
The samplesheet in XLSX format are now also saved in the zip archive. | jourdren |
|
Fix non-existing variable Python error when archiving samplesheet. | jourdren |
|
In demux step, the temporary samplesheet file used by bcl2fastq was removed twice. | jourdren |
|
At startup of aozan.aozan_main(), now check if the configuration file exists.. | jourdren |
|
Added recompression step. | firmo |
Release 2.0-rc19 – 2016-10-03
| Type | Changes | By |
|---|---|---|
|
Fix issue when using old configuration keys in upper case. | jourdren |
|
Fix issue when parsing intervals for QC tests in configuration file. | jourdren |
|
Fix missing collector dependencies of some QC tests. | jourdren |
|
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 missing collector dependencies of some QC tests. | jourdren |
|
Fix issue with sample in upper case in the demultiplexing collector in QC. | jourdren |
|
Fixed errors when samples in the samplesheet were unsorted. | firmo |
|
Fixed some typo in aozan error messages. | firmo |
|
Fixed errors when converting samplesheet to CSV leave empty column. | firmo |
|
Fix Aozan can now handle FASTQ files that are in a sample subdirectory generated by Bcl2fastq. | jourdren |
|
When the value of a setting entry in the configuration was empty, an error was thrown. | jourdren |
|
The version of bcl2fastq was read from the right log file in QC step. | jourdren |
|
Parameter files for failed runs are now also archived. | firmo |
|
Docker can now be used to launch Blast in the Overrepresented sequences module of FastQC. | jourdren |
|
Add a script that allows to create an Aozan demo configuration file and downloads all required files. | jourdren |
|
Now checks if system is linux type. | firmo |
|
Now checks if programs are availables in PATH before execution. | firmo |
|
Can now provide samplesheets xls where field contains ',' character. | firmo |
|
When bcl2fastq execution fails, send error log attached in mail. | firmo |
|
Now supports bcl2fastq 2.18. | firmo |
|
Update the QC demo example. | jourdren |
|
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 some Java 8 compilation errors. | jourdren |
|
The sample id in the FASTQ filenames was not corretly sometimes guessed. | jourdren |
|
For large FASTQ files, the FastQC report was not generated. | jourdren |
|
Fix error when parsing an empty PID file. | jourdren |
|
When the "qc.conf.threads" configuration property is not set, now use all available cores to launch FastQ Screen. | jourdren |
|
The key results generated by ConversionStatsCollector with bcl2fastq 2.16 was not the same as with bcl2fastq 2.18. | jourdren |
|
The default amount of memory allocated by Aozan is now 4096 instead of 2048MiB. | jourdren |
|
Update documentation. | jourdren |
Release 2.0 – 2017-02-14
| Type | Changes | By |
|---|---|---|
|
Spaces, simple and double quotes can now be used in paths to the Aozan input and output files. | jourdren |
|
Fix NullPointerException when process undetermined samples in RecoverableRawClusterPercentSampleTest. | jourdren |
|
StartTTLS, SSL, and login/password can now be used to configure the connection to the SMTP server to send emails. | jourdren |
|
The FastQC and Fastq Screen reports have now the same prefix as the FASTQ files. | jourdren |
|
Add two new configuration property to unzip and/or remove FastQC Zip report file. | jourdren |
|
Aozan now use Eoulsan 2.0-beta4 as dependency. | jourdren |
|
Aozan now supports Illumina HiSeq 3/4000 and HiSeq X. | jourdren |
Release 2.1 – 2017-11-08
| Type | Changes | By |
|---|---|---|
|
Aozan now thrown an error if an empty string is used for the number mismatches in the settings. | jourdren |
|
Fix unknown variable error while creating error message while demultiplexing. | jourdren |
|
Fix issue of Fastq Screen when mapping very small FASTQ files. | jourdren |
|
Aozan now works with MiSeq flowcell ids. | jourdren |
|
In some cases, Aozan did not guest the correct sample number for FASTQ filenames generated by bcl2fastq. | jourdren |
|
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 |
|
When replacing index shortcuts in samplesheet by real sequences, index1 was processed instead of index2. | jourdren |
|
When launching FastQScreen on very small FASTQ file, Aozan stalled. | jourdren |
|
Add a new demux.archive.samplesheets option in Aozan configuration file to avoid samplesheets archiving. | jourdren |
|
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 |
|---|---|---|
|
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 |
|---|---|---|
|
In paired-end mode, the links in the main report to FastQC reports were null. | jourdren |
|
Fix NullPointerException in Fastq Screen collector when no sample reference was defined in the samplesheet. | jourdren |
|
Fix error when accessing to genome alias names and the Fastq Screen collector was not enabled. | jourdren |
|
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 the order of the Fastq Screen genome tests in the report. | jourdren |
|
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 |
|---|---|---|
|
The entry for FastQ Screen report path for read 2 in paired-end mode was not exists. | jourdren |
|
The genome alias file was not updated when an unknown genome name was added. | jourdren |
Release 3.0 – 2023-04-28
| Type | Changes | By |
|---|---|---|
|
Rewrite all the Python code in Java. | jourdren |
|
Add support of NextSeq 1000/2000. | jourdren |
|
Add support of BCL convert in addition to Bcl2fastq. | jourdren |
|
Aozan can execute actions. If no action name is defined on command line, Aozan 3.x will work as Aozan 2.x. | jourdren |
|
A new configuration setting allow to trim reads to a maximal length when launching Fastq Screen collector. | jourdren |
|
Add new tests: OccupancyPercentGlobalTest and GenomeNamesSampleTest. | jourdren |
|
Add PrimaryAnalysisMetricsCollector and a new global test for loading concentration percent. | jourdren |
|
Now depends on the kenetre libraries instead of Eoulsan. Some Aozan code (e.g. InterOP files parsing) has been moved to Kenetre. | jourdren |
|
Aozan now requires Java 11 at runtime and for compilation. | jourdren |
|
Replace "Genomic Paris Centre" by "GenomiqueENS" as the IBENS genomics core facility has changed its name. | jourdren |
|
Aozan now requires Apache POI 4.1.2 instead of 3.12. | jourdren |
|
If execute MultiQC in Docker mode, now use the MultiQC 1.12 Docker image by default. | jourdren |
|
Update DemultiplexStatsCollector to handle both Demultiplex_Stats.csv and Quality_Metrics.csv file with BCL-Convert >=3.9. | jourdren |
|
In IlluminaSamplesheetRunConfigurationProvider, now replace underscores in sample ids by dashes. This option is enabled by default. The "samplesheet.allow.underscores.in.sample.ids" allow to disable it. | jourdren |
|
Now before launching BCL convert, move forbidden fields of the BCLConvert_Data section of the samplesheet in an other section. In Aozan2QC step, if this other section exists, merge the section in the original section. | jourdren |
|
Aozan 2 QC Now use FastQC 11.9. | jourdren |
|
In Fastq Screen TSV output file, the name of the last column was missing. Update column names in this file to names used in the latest versions of Fastq screen. | jourdren |
|
In OverrepresentedSequencesBlast class, fix issue that enable blast even if blast command is not available. | jourdren |
|
In OverrepresentedSequencesBlast, now use a the SAX API instead of the DOM API to parse blast XML result file. When a large XML output file is produced, an OutOfMemoryError error could occurs. | jourdren |
Release 3.0.1 – 2023-05-24
| Type | Changes | By |
|---|---|---|
|
Fix SMTP configuration with StartTTLS, SSL and login/password. | jourdren |
Release 3.0.2 – 2023-07-07
| Type | Changes | By |
|---|---|---|
|
Fix issue for demultiplexing without using Docker. | jourdren |
Release 3.1 – 2024-04-25
| Type | Changes | By |
|---|---|---|
|
Blast can be disabled for the "Overrepresented sequences" of the FastQC report if an "Aozan" section with a "disable.blast" is set to true in the samplesheet of the run. | jourdren |
|
Add a new configuration option named "qc.report.tests.to.remove.in.basic.report" that allow to create an additional HTML report but without some tests of the main report. | jourdren |
|
Add a new configuration parameter "samplesheet.allow.sample.ids.max.length" that allow to disable maximal sample ID length at 20 characters. | jourdren |
|
User can now define template emails for the emails sent at the end of a step. | jourdren |
|
Add a new option in legacy mode named "aozan.log.start.stop" that log the startup and the shutdown of Aozan. This option is disabled by default. | jourdren |
|
Exec and list action are now hidden util there are not stable. | jourdren |
|
Aozan now use Kenetre 0.25 has dependency. | jourdren |
|
When using BCL Convert in Docker mode, set default version to 4.2.7. | jourdren |
|
Since NextSeq Software 1.7.0 in PrimaryAnalysisMetrics.csv file, the "Average %Q30" metric has been renamed to "≥ Q30". Aozan has been updated to handle this. | jourdren |
|
Now allow samplesheets with name like samplesheet_SERIALNUMBER_0086.xls or samplesheet_SERIALNUMBER_86.xls. | jourdren |
|
Some MiSeq outputs were not handled by Aozan. | jourdren |
|
The configuration "mail.header" and "mail.footer" parameter were not handled in legacy mode. | jourdren |
|
In Illumina samplesheets, discard blank fields in data sections. | jourdren |
|
Existing BOM character at the beginning of Illumina samplesheets in CVS format are now handled. | jourdren |
|
Fix MiSeq run discovery. | jourdren |
Release 3.1.1 – 2024-07-17
| Type | Changes | By |
|---|---|---|
|
Aozan now use Kenetre 0.27 has dependency. | jourdren |
|
"samplesheet.allow.underscores.in.sample.ids" and "samplesheet.allow.sample.ids.max.length" configuration parameters were not correctly handled. | jourdren |
|
Fix discovery of runs generated by RTA 4. | jourdren |
|
In IlluminaSampleSheetConverter remove the "Sample_Project" column from sample sheet has it is no more allowed by NextSeq Control Software. | jourdren |