Resolwe-bio

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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


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

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

Added
-----
- Add per-lane processing for processes ``alignment-star``,
``feature_counts``, ``bbduk-single``, ``bbduk-paired`` and
workflow ``workflow-bbduk-star-featurecounts-qc``
- Add option of interval padding to process ``vc-gatk4-hc``
- Add process ``snpeff-single``

Changed
-------
- **BACKWARD INCOMPATIBLE:** Remove comparison to reference in
process ``mutations-table``
- **BACKWARD INCOMPATIBLE:** Update workflow
``workflow-rnaseq-variantcalling``:

- merge with functionality from deprecated workflow
``workflow-rnaseq-variantcalling-beta``
- add processes ``snpeff-single`` and ``mutations-table``
- remove process ``gatk-select-variants-single``
- Remove group nesting for QC fields in ``general`` descriptor
schema
- Add memory limit to parallel GATK SplitNCigarReads step in
process ``rnaseq-vc-preprocess``
- Update process categories
- Remove ``Show advanced options`` checkbox from all
processes and workflows

Fixed
-----
- Enable ordering on knowledge-base endpoints
- Fix the check for genome builds of inputs in process ``snpeff``


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

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

Added
-----
- Add ``REDIS_CONNECTION_STRING`` setting needed by the ``Resolwe``
- Add process ``samtools-view``
- Add process ``samtools-coverage``

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 32.x
- Support GEO series with EBI samples in ``geo-import`` process

Fixed
-----
- Output all detected input variants in ``mutations-table`` process
- Change ``__`` separators in field names to ``_`` in ``general``
descriptor schema
- Change choice values of the field ``biomarkers_pdl1_tps_cat`` in
``general`` descriptor schema

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

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

Fixed
-----
- Rename field ``general_information`` to ``general`` in ``general``
descriptor schema


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

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

Changed
-------
- Flatten General descriptor schema

Fixed
-----
- Bump version of ``rnaseq-vc-preprocess`` process
- Fix sample naming in ``multiqc`` process to avoid leaving out data in
the MultiQC report


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