Resolwe

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Changed
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- **BACKWARD INCOMPATIBLE:** Require Resolwe 42.x


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Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 41.x
- Change ``reference`` and ``alternative`` field types in ``Variant`` model


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Added
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- Allow filtering ``Sample`` by ``Variant``
- Allow filtering variant annotations by variant id
- Add filters to ``Variant`` and ``VariantCall`` objects
- Add ``known_fusions`` file input to ``arriba`` process and
``gene-fusion-calling-arriba`` workflow

Changed
-------
- Change ``variant-annotation`` process
to skip downstream/upstream and intergenic variants
- Change clinical diagnosis and annotation fields type to text
- When filtering variants do not return duplicated objects
- Optimize resource usage in processes ``bbduk-single``, ``bbduk-paired``,
``upload-fastq-single``, ``upload-fastq-paired``,
``files-to-fastq-single`` and ``files-to-fastq-paired``
- Update the ``pca`` process with the functionality from the
deprecated ``pca-beta`` process
- Bump resources requirements for ``arriba`` process

Fixed
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- Change max char length of REF and ALT fields
for variant model to 150
- Fix failing requests in the ``geo-import`` process by using eutils for
fetching data from SRA
- Fix rendering of ``star_index`` input field in
``gene-fusion-calling-arriba`` workflow


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Added
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- Add processes ``gtf-to-bed``, ``samtools-mpileup-single``
``arriba``, ``gene-fusion-calling-arriba``
- Add additional parameters for ``calculate-bigwig`` process
- Add filter by sample to variant objects

Changed
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- Change variant model annotation field max length to 500 and
clinical diagnosis field max lenght to 1000. Set dbsnp and
clinvar fields to max lenght of 150
- Change the default value of the ``--ChimOutType`` parameter in the
``alignment-star`` and ``workflow-bbduk-star-qc`` to ``WithinBAM HardClip``

Fixed
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- Fix ``--numberOfProcessors`` input in ``calculate-bigwig`` process
- Fix ``alignment-star`` process to correctly handle the ``--chimOutType``
parameter


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Added
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- Add additional parameters for chimeric alignments to ``star.py``
and ``bbduk_star.py``
- Expose ``Variant`` and ``VariantCall`` models in python processes

Changed
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- **BACKWARD INCOMPATIBLE:** Remove obsolete processes and releated scripts:
``cuffmerge``, ``chipseq-peakscore``, ``chipseq-genescore``, ``etc-bcm``,
``mergeetc``, ``upload-etc``, ``upload-bam-secondary``,
``upload-bam-scseq-indexed``, ``create-geneset-venn``,
``upload-proteomics-sample``, ``upload-proteomics-sample-set``,
``upload-header-sam``, ``upload-multiplexed-single``,
``upload-multiplexed-paired``, ``bam-split``, ``prepare-geo-chipseq``,
``prepare-geo-rnaseq``, ``seqtk-rev-complement-single``,
``seqtk-rev-complement-paired``, ``differentialexpression-shrna``,
``shrna-quant`` and ``workflow-trim-align-quant``.
- Use default value ``False`` for ``skip_missing_interpreters`` in tox.ini file

Fixed
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- Improve the robustness of ``geo-import`` process by
repeatedly trying to fetch the metadata from the SRA


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Changed
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- **BACKWARD INCOMPATIBLE:** Implement peak calling step and
add QC reporting to the Cut & Run workflow
- Bump requirements versions
- Report additional QC information in the variant table output
of RNA-seq variant calling pipeline

Fixed
-----
- Extend the selection of supported fields in VariantCall serializer
- Fix the ``mutations-table`` process so that only a single variant instance
is reported for each variant in ``variants`` application. The process now
also correcly handles the ``depth`` field reporting.
- Fix that the number of used threads is correctly coerced to integer in
``xengsort-index``
- Fixed data object naming in ``pca-beta`` process


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