Resolwe

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

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


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

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

Added
-----
- Add ``dicty-time-series`` time series descriptor schema

Changed
-------
- Add options to calculate variance in abundance estimates in
the workflow ``workflow-bbduk-salmon-qc``
- Support geneset as input to process ``mutations-table``
- Bump memory requirement to 64 GB and limit memory of
parallel SplitNCigarReads step in process
``rnaseq-vc-preprocess``
- Revert ``workflow-rnaseq-variantcalling`` to run individual data
preprocess steps


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

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

Added
-----
- Add optional calculation of variance in abundance estimates in
the process ``salmon-quant``
- Add process ``rnaseq-vc-preprocess``


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