Resolwe

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Added
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- Add ``general`` descriptor schema

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 31.x
- Use all three fragment length estimates before failing due to negative
the estimate in ``macs2-callpeak`` process

Fixed
-----
- Fix ChIPQC plot rendering in ``multiqc`` process for samples
containing file extensions in their name
- Update SRA url for fetching experiment metadata in ``geo-import``
process


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

Added
-----
- Add ``xengsort-index`` and ``xengsort-classify`` proceses

Changed
-------
- **BACKWARD INCOMPATIBLE:** Generalize the ``scale-bigwig`` process
and rename it to ``calculate-bigwig``
- Use ``resolwebio/wgbs:3.0.0`` in ``walt``, ``methcounts``, ``hmr`` and
``bs-conversion-rate`` processes
- Use ``resolwebio/chipseq:6.0.0`` in ``macs2-callpeak``, ``macs14``,
``qc-prepeak``, ``chipseq-peakscore``, ``chipseq-genescore`` and
``upload-bed`` processes
- Change ``merge-fastq-single`` and ``merge-fastq-paired`` process type
- Use ``resolwebio/chipseq:6.1.0`` in ``chipqc`` process
- Use ``resolwebio/methylation_arrays:1.1.0`` in the
``methylation-array-sesame`` process
- Improve error reporting for invalid fragment length estimates and fix
memory issues with MarkDuplicates in ``macs2-callpeak`` process
- Remove ``make_report.py`` script from resolwe-bio

Fixed
-----
- Fix sporadically failing tests of ``macs2-callpeak`` by removing
pipes in Plumbum commands
- Fix variants_filtered output in ``filtering-chemut`` process
- Fix typo in ``alignment-star`` process
- Remove unused tools bigwig_chroms_to_ucsc.py and check_bam_source.py


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

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

Added
-----

Changed
-------
- **BACKWARD INCOMPATIBLE:** Update GATK to GATK4 in process ``vc-chemut``
and update the workflow ``workflow-chemut``
- Rewrite the process ``filtering-chemut`` to Python
- Remove slamseq processes ``alleyoop-collapse``, ``alleyoop-rates``,
``alleyoop-snpeval``, ``alleyoop-summary``, ``alleyoop-utr-rates``,
``slam-count``, ``slamdunk-all-paired`` the workflow
``workflow-slamdunk-paired`` and related code in ``multiqc``
- Use ``resolwebio/common:3.1.0`` in ``upload-metadata-unique`` and
``upload-metadata`` processes
- Use the parent Data object name for the data name of processes and
workflows previously named after the sample name of the input file
- Remove Docker files from project
- Remove BigWig outputs created with ``bamtobigwig.sh`` script in
processes ``walt``, ``alignment-bowtie``, ``alignment-bowtie2``,
``alignment-bwa-mem``, ``alignment-bwa-sw``, ``alignment-bwa-aln``,
``alignment-bwa-mem2``, ``alignment-hisat2``, ``upload-bam``,
``upload-bam-indexed``, ``upload-bam-secondary``, ``alignmentsieve``,
``bamclipper``, ``bqsr``, ``markduplicates``, ``bam-split``,
``umi-tools-dedup`` and workflow ``workflow-cutnrun``

Fixed
-----
- Update the process ``mutations-table`` so that it handles empty input
VCF files


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

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

Added
-----
- Add processes ``gatk-variant-filtration-single`` and
``gatk-select-variants-single``
- Add ExtendedCollectionFilter filter to allow filtering collections by samples
containing given species, tissue type, outcome or treatment type
- Add process ``reference-space`` and ``upload-ml-expression``
- Rewrite ``macs2-callpeak`` process to Python
- Add process ``mutations-table``

Changed
-------
- Specify tmp dir for GATK processes
- Attach workflow data objects to Samples
- Remove ``workflow-accel`` pipeline and related process:
``align-bwa-trim``, ``coveragebed``, ``picard-pcrmetrics``,
``upload-picard-pcrmetrics``, ``upload-picard-pcrmetrics``,
``vc-realign-recalibrate``, ``vc-gatk-hc``, ``lofreq``,
``snpeff-legacy``, ``amplicon-report``, ``amplicon-table``,
``upload-master-file``, ``amplicon-archive-multi-report``,
``upload-snpeff``
- Rewrite processes to Python and add ``geneset`` DescriptorSchema to
Data made by processes:

- ``upload-geneset``
- ``create-geneset``
- ``create-geneset-venn``

Fixed
-----
- Attach GATK VariantFiltration and SelectVariants output to the
Sample object in ``workflow-rnaseq-variantcalling`` pipeline
- Set ``Persistence`` property to ``TEMP`` for processes
``find-similar`` and ``clustering-hierarchical-etc``
- Fix input schema in pipeline ``workflow-rnaseq-variantcalling``
- Fail gracefully when no relation labels are found in
``merge-fastq-single`` and ``merge-fastq-paired`` processes


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

Changed
-------
- **BACKWARD INCOMPATIBLE:** Drop support for ``Python 3.11``
- Support dynamic calculation of processes' resource requirements.
- Add ``process_exception`` method to auditlog middleware
- Add ``deleted`` field to ``AnnotationValues`` model
- Remove not used method ``remove_delete_markers`` from the ``AnnotationValue``
model
- Allow using ``DictRelatedField`` on models without version
- Remove deprecated endpoint ``upload_config_deprecated``


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

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

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require ``Django 5.1.x`` and bump version of
dependencies
- Support objects without permissions in ``DictRelatedField``
- Due to poorly written and unmaintained code, the ``VersionField``
functionality has been integrated into ``Resolwe``. This integration is based
on the code from repository https://github.com/mcldev/django-versionfield .

Fixed
-----
- Fix error when deleting observer subscription

Added
-----
- Add support for ``Python 3.13``


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