Tags give the ability to mark specific points in history as being important
  • 2.6.1   Fixed minor bug related to a variable declaration
  • 2.6.0   PyQua upgraded to python 3
  • 2.5.3   Fixed bug related to fastqc data file
  • 2.4.4
    Release 2.4.4

    All

    • Added Singularity recipe file to the repository
    • Fixed issues with run_folder vs runfolder. Now it's run_folder everywhere

    QualityReport

    • Added \batchmode to the latex template so when there is an error during the compilation, the process does not stay stuck
  • 2.4.2   bugfixes
    Release 2.4.2

    QualityReport

    • Added PyQua Logo in the main quality report page
    • Fixed path handling for bedtools in get_bed_size_function
    • Fixed path handling for tools in bioinfo_analysis quality report
    • Fixed coverage boxplot graphic name
  • 2.4.0   New quality check with file sizes
    Release 2.4.0

    QualityAnalysis

    • Corrected an issue with fastq file handling leading to incorrect output log location.
    • Improved tool path handling so when the user define a path in the setting the last '/' is not mandatory.
    • Added fastqsize sub-command to fastQ command : it computes the size of the fastq files. The aim is to identify interrupted or incomplete analyses.
    • Added samsize sub-command to samQ command : it computes the size of the bam/sam files. The aim is to identify interrupted or incomplete analyses.
    • Added vcfsize sub-command to vcfQ command : it computes the size of the vcf files. The aim is to identify interrupted or incomplete analyses.
    • Added annsize sub-command to the new annQ command : it computes the size of the ann files. The aim is to identify interrupted or incomplete analyses.

    QualityControl

    • Corrected an issue with the custom bed format which broke if you have more than the expected column number. Used columns are now deduced with the number of columns minus 3 and 2.
    • Corrected a bug where the genome version is not appearing in the quality report.
    • Added fastqsize quality control to get fastqsize quality analysis data.
    • Added samsize quality control to get samsize quality analysis data.
    • Added vcfsize quality control to get vcfsize quality analysis data.
    • Added annsize quality control to get annsize quality analysis data.

    QualityReport

    • Added try except statement to help users debugging tool path issues when checking for tool versions.
    • Institution name is now configurable through in the custom latex template that the user may give.
    • Added a section in the sequencing_run report for the fastqsize quality analysis.
    • Added a section in the analysis report for the samsize quality analysis.
    • Added a section in the analysis report for the vcfsize quality analysis.
    • Added a section in the analysis report for the annsize quality analysis.
  • 2.3.11-stable
    587a4716 · Version 2.3.11 ·
    Release 2.3.11-stable

    All

    • Fixed issue in QualityReport when no demultiplexing quality analysis is available
    • Fixed wrong splitting sequence in QualityControl/low_depth_regions that was based on a local artifact
    • Fixed regex to get sample names in fastqstat based on filenames. This should not break as easily as it was and if it fails, it will return 'unknown' as a sample name
  • 2.3.10-stable
    Release 2.3.10-stable

    All

    • Tool pathes are now instanciated globally in the package right after the check of the input setting file, so that we can used them everywhere in the code without passing the setting_file to each function.

    QualityAnalysis

    • When a command is launched with a samtools view command pipe, the number of threads used by the command is divided by two to compensate.
    • Added samtools depth parameter -aa to have the depth on all bed positions
    • Added samtools depth parameter -d 100000 to avoid the default depth cutting above 8000 (default in samtools)
    • Made a change in the launch of Picard CollectInsertSizeMetrics so it only use one thread at a time to avoid I/O saturation. Pretty bad computing performance though but otherwise it takes hours to complete because picard instances are crippling each other. Nothing much to do.

    QualityControl

    • Changed bed size computing method not to count twice same positions with overlapping intervals
    • Added a check where the bed size and the number of positions outputed with samtools depth is compared. If they are not the same, the programm exit with an error message
    • Added a threshold parameter on low_depth_regions quality control so the user can have his custom rule of what is a 'low depth region'

    QualityReport

    • Some changes in the low depth region part to be compatible with the new threshold parameter
  • 2.3.5-stable   Validé à Rouen
    ad71443e · Licence ·
    Release 2.3.5-stable

    All

    • Added tool path handling, it's not the purpose of the tool but still needed when working with multiple teams using different versions of the same tool