Resolwe

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Fixed
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- Fix ``macs2-callpeak`` process version


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Added
-------
- Add ``upload-proteomics-sample`` and ``upload-proteomics-sample-set``
processes for uploading custom tables holding proteomics data

Fixed
-------
- Changed ``scale-bigwig`` output file field label to ``bigwig file``
- Bump memory requirements in processes ``import-sra``,
``import-sra-single`` and ``import-sra-paired`` to 8GB


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Added
-------
- Add peakcalling to removed duplicates step in species' line of the
``workflow-cutnrun`` workflow

Fixed
-------
- Add BigWig timeout and bin size parameters to ``markduplicates``,
``alignmentsieve`` and ``workflow-cutnrun``. Add bin size parameter
to ``alignment-bowtie2``.


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

Added
-------
- Added parameters ``--normalizeUsing`` and ``--smoothLength`` to
script ``bamtobigwig.sh`` to be used in ``bamCoverage`` program
- Added parameters ``--no-unal`` and ``--no-overlap`` to process
``alignment-bowtie``
- Add ``alignmentsieve`` process
- Add Trim Galore tool to ``resolwebio/rnaseq:4.12.0``
- Add ``trimgalore-paired`` process
- Add ``bedtools-bamtobed`` and ``scale-bigwig`` processes
- Added BigWig timeout input parameter to ``alignment-bowtie2`` process
- Add workflow ``workflow-cutnrun``
- Add ``clustering-hierarchical-etc`` process
- Add ``find-similar`` process

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 25.x
- **BACKWARD INCOMPATIBLE:** Rewrite ``differentialexpression-deseq2``
to Python
- Add format parameter to ``macs2-callpeak``
- Rewrite ``differentialexpression-edger`` to Python
- Rewrite ``cuffdiff`` to Python
- Alignment processes ``alignment-bowtie``, ``alignment-bowtie2``,
``alignment-star``, ``alignment-bwa-mem``, ``alignment-bwa-sw``,
``alignment-bwa-aln``, ``alignment-hisat2`` and ``walt`` now issue a
warning instead of an error when sample and genome species mismatch
- Support automated upload of gene sets in proceses ``cuffdiff``,
``differentialexpression-deseq2`` and ``differentialexpression-edger``
- Support the analysis of S. cerevisiea samples in ``macs2-callpeak``
process


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

Added
-------
- Add ``resolwebio/sra-tools`` Docker image
- Add ``resolwebio/orange`` Docker image
- Add ``upload-orange-metadata`` process

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 24.x
- **BACKWARD INCOMPATIBLE:** Include feature full names in full-text
search
- Support automatic species annotation in alignment processes:
``alignment-bowtie``, ``alignment-bowtie2``, ``alignment-bwa-mem``,
``alignment-bwa-sw``, ``alignment-bwa-aln``, ``alignment-hisat2``,
``alignment-star``, ``walt``
- Pin ``XML`` R package to ensure compatibility with R 3.6.3 in
``resolwebio/chipseq:4.1.3`` Docker image
- Use ``resolwebio/sra-tools:1.0.0`` Docker image in processes
``import-sra``, ``import-sra-single`` and ``import-sra-paired``
- Optionally use sra-tools ``prefetch`` command when downloading and
converting SRA files to FASTQ format

Fixed
-----
- Bump Docker image version in ``chipqc`` process to fix enrichment
heatmap plot


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

Added
-------
- Prepare ``resolwebio/rnaseq:4.11.0`` Docker image:
Add rnanorm (1.3.0) RNA-seq normalization package. Use
``resolwebio/common:1.6.0`` Docker image as a base image. Pin ``XML``
R package to fix the image build issues. Install BBMap package from
Google Drive.

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 23.x.
- **BACKWARD INCOMPATIBLE:** Use rnanorm Python package for TPM/CPM
normalization of RNA-seq data in featureCounts and HTSeq-count tools
- Support Nanostring sample reports in MultiQC
- Support Nanostring analysis results in
``differentialexpression-deseq2`` process

Fixed
-----
- Order results on autocomplete API endpoint in knowledge-base by
relevance
- Support filtering by type on knowledge base Feature API
- Attach ``rose2`` Data object to the input sample


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