===================
Added
-----
- Add ``gatk-merge-vcfs`` process
Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 29.x
- **BACKWARD INCOMPATIBLE:** Update ``workflow-wgs-gvcf`` to include
BWA-MEM2-based preprocessing step. Support triggering the pipeline
using a pre-aligned BAM input file
- Add ``qin`` and ``ignorebadquality`` BBDuk options to workflows
``workflow-bbduk-salmon-qc-single``,
``workflow-bbduk-salmon-qc-paired``,
``workflow-bbduk-star-featurecounts-qc-single``,
``workflow-bbduk-star-featurecounts-qc-paired``,
``workflow-bbduk-star-fc-quant-single``,
``workflow-bbduk-star-fc-quant-paired``,
``workflow-bbduk-star-htseq``,
``workflow-bbduk-star-htseq-paired``
- Replace ReSDK interface with Python API calls when accesing the
gene KB in processes ``salmon-quant``, ``alleyoop-collapse``,
``slam-count`` and ``mapped-microarray-expression``
- Use downsampled alignment for running QoRTs in 3' mRNA-Seq workflows
``workflow-bbduk-star-fc-quant-single``,
``workflow-bbduk-star-fc-quant-paired``,
``workflow-cutadapt-star-fc-quant-single``,
``workflow-cutadapt-star-fc-quant-wo-depletion-single``
- Replace ``ANONYMOUS_USER_ID`` with ``ANONYMOUS_USER_NAME`` in
settings.py
- Add java memory settings in ``gatk-genomicsdb-import``
Fixed
-----
- Fix data name and advanced options in ``variants-to-table`` process
===================