Resolwe

===================

Added
-----
- Added ``variants`` application

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 40.x
- **BACKWARD INCOMPATIBLE:** Use the updated xengsort version
in processes ``xengsort-index`` and ``xengsort-classify``
- **BACKWARD INCOMPATIBLE:** Remove support for ``Python 3.10``
- Extend the ``mutations-table`` process with the support for writing
the variant information to the ``variants`` application
- Use ``simple_unaccent`` configuration when generating search vectors

Fixed
-----
- Fix handling of multiple instances of STAR aligner input in the
``multiqc`` process


===================

===================

Added
-----
- The (pre)release is built and pushed to the ``PyPI``
automatically when tag is pushed to the repository
- Add ``pca-beta`` process

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 39.x
- Rewrite ``expression-aggregator`` process to Python and make it
compatible with the new annotation model
- Use GRCh38.109 genome annotation version in snpEff processes
- Remove sample annotation functionality from ``geo-import`` process


===================

===================

Added
-----
- Add support for ``Python 3.12``
- Add ``samtools-depth-single`` process
- Add gene body coverage plot from ``qorts-qc`` process to MultiQC
report
- Add retry for reads prefetch in ``import-sra-single`` and ``import-sra-paired``

Changed
-------
- Remove ``rnaseqc-qc`` 3' bias statistics from MultiQC report
- Remove ``rnaseqc-qc`` from RNA-seq workflows
- Remove ``cut_and_run.yml``
- Rename ``workflow-cutnrun-beta`` to ``workflow-cutnrun``
- Remove ``upload-sc-10x``, ``cellranger-count`` and ``cellranger-mkref``
processes


===================

===================

Added
-----
- Add support for ``Python 3.12``
- Add ``samtools-depth-single`` process

Fixed
-----
- Fix handling of missing post-peak QC reports in MultiQC
when MACS2 is run in broad peak mode
- Fix handling STAR alignment reports for downsampled inputs
in MultiQC


===================

===================

Changed
-------
- Make changes to input fields in ``workflow-cutnrun-beta``
- Reword documentation of ``macs2-callpeak``, ``macs2-batch`` and
``qc-prepeak``
- Add input option to exclude flags in ``samtools-bedcov`` process


===================

===================

Added
-----
- Add ``samtools-bedcov`` process
- Add ``workflow-cutnrun-beta`` workflow

Changed
-------
- Use downsampled alignment for ``rnaseqc-qc`` process in ``workflow-bbduk-star-featurecounts-qc``
and ``workflow-bbduk-star`` workflows
- Unify the use of ``resolwebio/common:4.1.1`` Docker
image version across processes
- Unify the use of ``resolwebio/base:ubuntu-22.04-14112023`` Docker
image across processes
- Add normalized count matrix output to ``differentialexpression-deseq2`` process

Fixed
-----
- Fix ``qorts-qc`` process so it can be used with hg19 annotation
and improve error handling when files are missing


===================