Resolwe

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Added
-----
- Add Euclidean distance metric in ``find-similar`` and
``clustering-hierarchical-etc`` processes

Changed
-------
- Change ``star-quantification`` process to include number of assigned reads
in the summary report
- Change ``MultiQC`` report to include assigned reads from ``star-quantification``
process
- Change ``workflow-bbduk-star-qc`` workflow to include assigned reads
by ``star-quantification`` in ``MultiQC`` report
- Bump storage requirements in processes ``alignment-bwa-sw`` and
``alignment-bwa-aln``


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

Added
-----
- Add support for ``Python 3.11``

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 36.x
- **BACKWARD INCOMPATIBLE:** Require Django 4.2
- Rename ``filter_sense_rate`` to ``filter_rnaseqc_metrics`` in ``filter.py``
and add additional fields for filtering
- Changed the ordering of exons in ``format_ucsc`` function of ``rnaseq-qc`` process
and add collapse_only option for stranded protocols
- Change test files and modify test function for ``rnaseqc-qc`` process
- Bump ``postgresql`` and ``redis`` containers version
- Rename ``workflow-rnaseq-variantcalling`` from ``RNA-seq Variant Calling``
to ``RNA-seq Variant Calling Workflow``
- Support optional triggering of MultiQC in ``workflow-rnaseq-variantcalling``
- Add ``mask`` option to processes ``gatk-variant-filtration`` and
``gatk-variant-filtration-single`` and enable this option in
``workflow-rnaseq-variantcalling``


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

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

Added
-----
- Add command ``filter_features`` to the listener that caches the returned
``Feature`` objects to speed up the queries
- Add ``rnaseqc-qc`` process including a function for parsing UCSC annotations
and modify ``multiqc`` to accomodate its results

Changed
-------
- Change test files for ``multiqc``
- Modify ``filter`` command on the ``Feature`` class to use cache
- Explicitly set process resources in processes ``alignment-bowtie`` and
``alignment-bowtie2``
- Improve warnings in ``geo-import`` process for series without raw data

Fixed
-----
- Fix SRA parameters to pass zero values in ``geo-import`` workflow


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

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

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 35.x
- Support the use of BAM file as an input in the workflow
``workflow-rnaseq-variantcalling``
- Adjust assigned CPU core count requirements for processes
- Always use ``Docker`` default seccomp profile

Fixed
-----
- Fix ``min_read_len`` parameter to pass zero values in
``import-sra-single``, ``import-sra-paired``, ``import-sra``
- Prevent ``bbduk-single`` and ``bbduk-paired`` processes from stopping
when the number of lanes exceeds the number of available cores
- Fix BBDuk settings in the workflow ``workflow-rnaseq-variantcalling``


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

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

Added
-----
- Add option to filter by genotype fields in processes
``gatk-variant-filtration`` and ``gatk-variant-filtration-single``
- Add option for 2-pass mode to workflow ``workflow-bbduk-star-qc``

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 34.x
- Bump the STAR version in processes ``alignment-star`` and
``alignment-star-index``. Deprecate test processes
``alignment-star-new``, ``alignment-star-index-new`` and
``workflow-bbduk-star-qc-new``
- Support filtering by genotype fields in the process
``mutations-table`` and change the default options for variant
filtration in the workflow ``workflow-rnaseq-variantcalling``
- Optimize resource usage for ``SchedulingClass.INTERACTIVE``
processes

Fixed
-----
- Add output field ``feature_type`` to the process
``star-quantification``


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

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

Added
-----
- Add option to compute gene counts in ``alignment-star`` process
- Add processes ``alignment-star-new`` and
``alignment-star-index-new`` that use STAR version
2.7.10b
- Add process ``star-quantification``
- Add workflows ``workflow-bbduk-star-qc`` and
``workflow-bbduk-star-qc-new``

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 33.x
- **BACKWARD INCOMPATIBLE:** Drop support for ``Python <= 3.9``
- **BACKWARD INCOMPATIBLE:** Remove default ordering from Feature API
endpoint
- Update ordering weights for full-text search on Feature API endpoint


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