Resolwe-bio

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Added
-----
- Add optional calculation of variance in abundance estimates in
the process ``salmon-quant``
- Add process ``rnaseq-vc-preprocess``


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Added
-----
- 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


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

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


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

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

Added
-----
- Add process ``gatk-split-ncigar``
- Add process ``gatk-variant-filtration``
- Add process ``snpeff``
- Add workflow ``workflow-rnaseq-variantcalling``
- Add support for ``Python`` 3.10

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 30.x
- **BACKWARD INCOMPATIBLE:** Change the slug of the process
``snpeff`` to ``snpeff-legacy``
- **BACKWARD INCOMPATIBLE:** Deprecate process ``upload-orange-metadata``
in favour of processes ``upload-metadata`` and
``upload-metadata-unique``
- Add parameter ``--use-original-qualities`` to ``bqsr`` process
- Add ``fn_ignore_dirs`` options to MultiQC configuration file in
``resolwebio/common:3.0.1`` Docker image
- Add parameter ``--exclude-filtered`` to ``gatk-select-variants``
process
- Normalize processes that use ``resolwebio/dnaseq`` Docker image to
use the latest version 6.3.1 and modify tests as necessary
- Rewrite process ``vc-gatk4-hc`` to Python
- Prepare ``resolwebio/rnaseq:6.0.0`` Docker image:

- Update Python package versions for Python 3.8
- Pin R package versions
- Bump genome-tools to 1.6.2
- Add Java memory settings to processes ``bqsr`` and ``markduplicates``
- Update SnpEff version to 5.1 in ``resolwebio/snpeff:2.1.0`` Docker
image
- Add additional file output with source ids and target ids to process
``goenrichment``
- Normalize all processes that rely on ``rnaseq`` Docker image to use
the latest ``resolwebio/rnaseq:6.0.0`` Docker image version

Fixed
-----
- Fix ``--cl-config`` input option in MultiQC process. Use
``resolwebio/common:3.0.1`` Docker image with updated MultiQC
configuration file to omit parsing the unwanted ``tmp`` folder
- Fix LISTENER_CONNECTION settings to work on Mac
- Add tool Tabix to ``resolwebio/snpeff:2.1.1`` Docker image


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