Resolwe-bio

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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``.


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

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

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


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

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

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


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

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

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


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

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

Added
-------
- Add Sample QC information fields to the ``sample`` descriptor schema

Changed
-------
- **BACKWARD INCOMPATIBLE:** Disable editing capabilities of Knowledge
Base API endpoints
- Bump Samtools to version 1.10 in ``resolwebio/common:1.6.0`` Docker
image
- Migrate search for Knowledge Base enpoints from Elasticsearch to
PostgreSQL
- Use ``resolwebio/common:1.6.0`` for the ``resolwebio/wgbs:1.3.0``
Docker image
- Support samtools markdup report in ``walt`` process when removing
duplicates
- Support samtools markdup report from ``walt`` in MultiQC
- Support samtools markdup report in ``workflow-wgbs-single`` and in
``workflow-wgbs-paired`` workflows
- Bump memory requirements to 32GB in processes: ``feature_counts``,
``coveragebed``, ``library-strandedness``, ``qorts-qc``,
``salmon-quant`` and ``vc-realign-recalibrate``
- Rename ``workflow-slamdunk-paired`` process

Fixed
-------
- Fix read length estimation in ``chipqc``


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

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

Added
-----
- Add ``workflow-subsample-bwa-aln-single`` and
``workflow-subsample-bwa-aln-paired`` workflows

Changed
-------
- **BACKWARD INCOMPATIBLE:** Use Salmon 1.2.1 in ``salmon-quant`` and
``salmon-index`` processes
- Salmon quant 1.2.1 is not backwards compatible with indices generated
with Salmon index prior to version 1.0.0, thus Salmon tool is updated
to version 1.2.1 in processes that utilize Salmon to detect library
strandedness type.
- Expose additional limit options in ``alignment-star`` process
- Bump SRA toolkit to 2.10.0 in ``resolwebio/common:1.5.0`` Docker image
- Use SRA tookit 2.10.0 in ``import-sra``, ``import-sra-single`` and
``import-sra-paired`` processes
- Format floats to 2 decimal places in custom ChIP-seq pre/post-peak
MultiQC reports


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