Resolwe

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Added
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- Allow overriding docker image prefix via environment variable

Changed
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Fixed
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- Normalize project name from `resolwe-bio` to `resolwe_bio` in about file
to ensure setup.py is compliant with PEP 625 standard


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Added
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- Add filtering ``Variant`` by ``VariantExperiment`` and ``VariantCall``
- Use generic permission filters when filtering variants by related models
- Return only distinct ``VariantExperiment`` objects
- Add ``--bam-output`` input argument to ``vc-gatk4-hc``
- Add ``--max-mnp-distance`` input argument to ``vc-gatk4-hc``

Changed
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- Change output data object name in ``gtf-to-bed`` process,
add geneset as a required field
and hide canonical transcripts table if gene feature type is selected


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


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Changed
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- **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
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- 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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