Resolwe

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

Added
-----
- Add processes ``gtf-to-bed``, ``samtools-mpileup-single``
``arriba``, ``gene-fusion-calling-arriba``
- Add additional parameters for ``calculate-bigwig`` process
- Add filter by sample to variant objects

Changed
-------
- Change variant model annotation field max length to 500 and
clinical diagnosis field max lenght to 1000. Set dbsnp and
clinvar fields to max lenght of 150
- Change the default value of the ``--ChimOutType`` parameter in the
``alignment-star`` and ``workflow-bbduk-star-qc`` to ``WithinBAM HardClip``

Fixed
-----
- Fix ``--numberOfProcessors`` input in ``calculate-bigwig`` process
- Fix ``alignment-star`` process to correctly handle the ``--chimOutType``
parameter


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

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

Added
-----
- Add additional parameters for chimeric alignments to ``star.py``
and ``bbduk_star.py``
- Expose ``Variant`` and ``VariantCall`` models in python processes

Changed
-------
- **BACKWARD INCOMPATIBLE:** Remove obsolete processes and releated scripts:
``cuffmerge``, ``chipseq-peakscore``, ``chipseq-genescore``, ``etc-bcm``,
``mergeetc``, ``upload-etc``, ``upload-bam-secondary``,
``upload-bam-scseq-indexed``, ``create-geneset-venn``,
``upload-proteomics-sample``, ``upload-proteomics-sample-set``,
``upload-header-sam``, ``upload-multiplexed-single``,
``upload-multiplexed-paired``, ``bam-split``, ``prepare-geo-chipseq``,
``prepare-geo-rnaseq``, ``seqtk-rev-complement-single``,
``seqtk-rev-complement-paired``, ``differentialexpression-shrna``,
``shrna-quant`` and ``workflow-trim-align-quant``.
- Use default value ``False`` for ``skip_missing_interpreters`` in tox.ini file

Fixed
-----
- Improve the robustness of ``geo-import`` process by
repeatedly trying to fetch the metadata from the SRA


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

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

Changed
-------
- **BACKWARD INCOMPATIBLE:** Implement peak calling step and
add QC reporting to the Cut & Run workflow
- Bump requirements versions
- Report additional QC information in the variant table output
of RNA-seq variant calling pipeline

Fixed
-----
- Extend the selection of supported fields in VariantCall serializer
- Fix the ``mutations-table`` process so that only a single variant instance
is reported for each variant in ``variants`` application. The process now
also correcly handles the ``depth`` field reporting.
- Fix that the number of used threads is correctly coerced to integer in
``xengsort-index``
- Fixed data object naming in ``pca-beta`` process


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

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

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


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