Resolwe-bio

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Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 44.x
- Bump ``alignment-bowtie``'s Docker image and reorder arguments
- Move ``differentialexpression-edger`` to ``rpkgs`` Docker image and move
external scripts ``diffexp_filtering.R`` and ``expressionmerge.py``
into the process
- Change ``differentialexpression-deseq2`` process Docker image to
``resolwebio/rpkgs``
- Modify how ``rnanorm`` is called and bump Docker image version for
``feature_counts``
- Bump Docker image version for ``salmon-quant`` and modernize
``tximport_summarize.R`` script
- Modify how ``rnanorm`` is called in ``star-quantification`` process and
bump Docker image version
- Rework error handling in ``basespace-file-import``
- Change URI of ``resolwebio/biox`` Docker image in ``mappability-bcm`` and
``expression-dicty`` processes

Fixed
-----
- Fix missing external files in ``basespace-file-import`` test files and
simplify them
- Send variants from processes in batches to avoid crash when variants list is
too big
- Fix genebody coverage plot in ``multiqc`` process


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

Added
-----
- Add support for ``Python 3.13``
- Save test folder data using actions/upload-artifact
- Allow staff users to create and update ``Variant``, ``VariantCall`` and
``VariantExperiment`` objects via API endpoint

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Django 5.1 and bump version of other
dependencies
- **BACKWARD INCOMPATIBLE:** Require Resolwe 43.x
- Use ``pyproject.toml`` instead of ``setup.py``
- Calculate up to 5 principal components in ``pca`` process
- Add ``annotation`` as nested field to ``Variant`` serializer
- Add an output field in ``alignment-star``
indicating whether input reads were downsampled
- Change the metric reporting gene body coverage in MultiQC
to align with QoRTs vignette recommendations
- Add downsampled alignment as an input to MultiQC process
in ``workflow-bbduk-star-featurecounts-qc`` workflow

Fixed
-----
- Optimize ``variant-annotation`` process to handle a larger
number of variants
- Fix the disabling of BAM writer input in ``vc-gatk4-hc``


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

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

Added
-----
- Allow overriding docker image prefix via environment variable

Fixed
-----
- Normalize project name from `resolwe-bio` to `resolwe_bio` in about file
to ensure setup.py is compliant with PEP 625 standard


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

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

Added
-----
- Add filtering ``Variant`` by ``VariantExperiment`` and ``VariantCall``
- Use generic permission filters when filtering variants by related models
- Return only distinct ``VariantExperiment`` objects
- Add ``--bam-output`` input argument to ``vc-gatk4-hc``
- Add ``--max-mnp-distance`` input argument to ``vc-gatk4-hc``

Changed
-------
- Change output data object name in ``gtf-to-bed`` process,
add geneset as a required field
and hide canonical transcripts table if gene feature type is selected


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

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

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 42.x


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

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

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 41.x
- Change ``reference`` and ``alternative`` field types in ``Variant`` model


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