Resolwe

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Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 38.x
- Change ``rnaseqc-qc`` data object label in ``workflow-bbduk-star-featurecounts-qc``,
``workflow-bbduk-star-qc`` and ``workflow-bbduk-salmon-qc`` workflows
- Add ``rnaseqc-qc`` to ``workflow-bbduk-star-featurecounts-qc``,
``workflow-bbduk-star-qc`` and ``workflow-bbduk-salmon-qc``
- Add ``qorts-qc`` to ``workflow-bbduk-star-featurecounts-qc``

Fixed
-----
- Fixed stranded input options in ``rnaseqc-qc`` process
- Change GEO metadata test file for ``geo-import`` process
and fix corresponding test function


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

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

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 37.x
- Add ``sample_annotation`` Jinja expressions filter that accepts an annotation
path and returns its value
- Update field paths for sample annotation in ``geo-import`` process
- Update species annotation in ``alignment-star`` process

Fixed
-----
- Fix Cut&Run workflow to scale the correct input BAM file using the
spike-in scaling factor


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

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

Fixed
-----
- Report gene body coverage by ``rnaseqc-qc`` and assigned reads
by ``star-quantification`` for all samples in MultiQC


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

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

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``


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

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

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


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