Resolwe

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Added
-----
- Add bioservices python package to the ``resolwebio/common:2.8.0``
Docker image
- Add ``upload-idat`` process
- Add ``upload-microarray-expression`` and
``mapped-microarray-expression`` processes
- Add ``map-microarray-probes`` process

Changed
-------
- **BACKWARD INCOMPATIBLE:** Support microarray expressions upload in
``geo-import`` process
- Trigger an error for microarray data in differential expression
processes ``differentialexpression-edger`` and
``differentialexpression-deseq2``


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Added
-----
- Add GEOparse to the ``resolwebio/common:2.7.0`` Docker image
- Add fastq file validation in ``import-sra-single`` and
``import-sra-paired`` processes
- Add ``geo-import`` process

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 28.x
- Use ``resolwebio/base:ubuntu-20.04`` Docker image for building
``resolwebio/sra-tools`` Docker image. Include ``dnaio`` Python
library in ``resolwebio/sra-tools``.

Fixed
-----
- Fix handling of non-sample data inputs in ``multiqc`` process


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Added
-----
- Fail if wrong filtering arguments are used in KB Feature / Mapping
search endpoints

Changed
-------
- Use Amazon ECR when building ``resolwebio/base`` Docker images
- Use pinned version of the ``resolwebio/base`` Docker image for
building ``resolwebio/common`` Docker image. Update versions of
bioinformatic tools installed in the ``resolwebio/common`` image.
- Use only tagged versions of ``resolwebio/base`` Docker images in
processes
- Save gene-level estimated counts to the ``rc`` output field in the
``salmon-quant`` process

Fixed
-----
- Fix file import in processes ``upload-multiplexed-single`` and
``upload-multiplexed-paired``
- Fix ``import-sra-single`` and ``import-sra-paired`` to correctly
determine Illumina 1.5 and 1.3 quality encoding


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Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 27.x
- Move docker images from Docker Hub to Amazon ECR


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Added
-----
- Add OncXerna specific clinical descriptor schema ``oncxerna_clinical``

Changed
-------
- **BACKWARD INCOMPATIBLE:** Support new protocol in Resolwe 26.x


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

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

Added
-------
- Add initial general clinical descriptor schema ``general_clinical``
- Add ``id`` field to ``Feature`` and ``Mapping`` serializers
- Add ``resolwebio/base:ubuntu-20.04`` Docker image

Changed
-------
- Update the url for the Orange table example template in
``upload-orange-metadata``


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