Resolwe-bio

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Added
-----
- Add ``alleyoop-rates`` process
- Add ``alleyoop-utr-rates`` process
- Add ``alleyoop-summary`` process
- Add ``alleyoop-snpeval`` process
- Add ``alleyoop-collapse`` process
- Add ``slam-count`` process
- Add ``workflow-slamdunk-paired`` workflow

Changed
-------
- **BACKWARD INCOMPATIBLE:** Refactor ``slamdunk-all-paired`` process
to support genome browser visualization and add additional output
fields
- Append sample and genome reference information to the summary output
file in the ``filtering-chemut`` process
- Bigwig output field in ``bamclipper``, ``bqsr`` and ``markduplicates``
processes is no longer required
- Support Slamdunk/Alleyoop processes in MultiQC
- Enable sorting of files in ``alignment-star`` process using Samtools
- Support merging of multi-lane sequencing data into a single (pair) of
FASTQ files in the ``upload-fastq-single``, ``upload-fastq-paired``,
``files-to-fastq-single`` and ``files-to-fastq-paired`` processes


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

Added
-----
- Add ``resolwebio/slamdunk`` Docker image
- Add Tabix (1.7-2) to ``resolwebio/bamliquidator:1.2.0`` Docker image
- Add ``seqtk-rev-complement-single`` and
``seqtk-rev-complement-paired`` process
- Add ``slamdunk-all-paired`` process

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 20.x
- Make BaseSpace file download more robust
- Bump ``rose2`` to 1.1.0, ``bamliquidator`` to 1.3.8, and use
``resolwebio/base:ubuntu-18.04`` Docker image as a base image in
``resolwebio/bamliquidator:1.1.0`` Docker image
- Use ``resolwebio/bamliquidator:1.2.0`` in ``rose2`` process
- Bump CPU, memory and Docker image (``resolwebio/rnaseq:4.9.0``)
requirements in ``alignment-bwa-mem``, ``alignment-bwa-sw`` and
``alignment-bwa-aln`` processes
- Use multi-threading option in Samtools commands in
``alignment-bwa-mem``, ``alignment-bwa-sw`` and ``alignment-bwa-aln``
processes


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Changed
-------
- Renamed ``workflow-trim-align-quant`` workflow to make the name more
informative


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

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

Added
-----
- Add ``Macaca mulatta`` species choice to the ``sample`` descriptor
schema
- Add ``workflow-cutadapt-star-fc-quant-wo-depletion-single`` process

Changed
-------
- Test files improved for ``workflow-wes``, ``bamclipper``,
``markduplicates`` and ``bqsr``
- Fix typo in ``differentialexpression-shrna`` process docstring

Fixed
-----
- Fix transcript-to-gene_id mapping for Salmon expressions in
``differentialexpression-deseq2`` process. Transcript versions are
now ignored when matching IDs using the transcript-to-gene_id mapping
table.
- Fix ``workflow-cutadapt-star-fc-quant-single`` process description


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

Changed
-------
- Update order of QC reports in MultiQC configuration file. The updated
configuration file is part of the ``resolwebio/common:1.3.1``
Docker image.
- Bump Jbrowse to version 1.16.6 in ``resolwebio/rnaseq:4.9.0`` Docker
image
- Use JBrowse ``generate-names.pl`` script to index GTF/GFF3 features
upon annotation file upload
- Support Salmon reports in MultiQC and expose ``dirs_depth`` parameter
- Expose transcript-level expression file in the ``salmon-quant``
process

Added
-----
- Add ``workflow-bbduk-salmon-qc-single`` and
``workflow-bbduk-salmon-qc-paired`` workflows

Fixed
-----
- Give process ``upload-bedpe`` access to network


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

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

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 19.x
- **BACKWARD INCOMPATIBLE:** Unify ``cutadapt-single`` and
``cutadapt-paired`` process inputs and refactor to use Cutadapt v2.4
- Expose BetaPrior parameter in ``differentialexpression-deseq2``
process
- Install R from CRAN-maintained repositories in Docker images build
from the ``resolwebio/base:ubuntu-18.04`` base image
- Prepare ``resolwebio/common:1.3.0`` Docker image:

- Install R v3.6.1
- Bump Resdk to v10.1.0
- Install gawk package
- Fix Docker image build issues
- Use ``resolwebio/common:1.3.0`` as a base image for
``resolwebio/rnaseq:4.8.0``
- Update StringTie to v2.0.0 in ``resolwebio/rnaseq:4.8.0``
- Support StringTie analysis results in DESeq2 tool

Added
-----
- Add ``cutadapt-3prime-single`` process
- Add ``workflow-cutadapt-star-fc-quant-single`` process
- Add argument ``skip`` to ``bamclipper`` which enables skipping of
the said process
- Add ``cutadapt-corall-single`` and ``cutadapt-corall-paired``
processes for pre-processing of reads obtained using Corall Total
RNA-seq library prep kit
- Add ``umi-tools-dedup`` process
- Add ``stringtie`` process
- Add ``workflow-corall-single`` and ``workflow-corall-paired``
workflows optimized for Corall Total RNA-seq library prep kit data

Fixed
-----
- Fix warning message in hierarchical clustering of genes. Incorrect
gene names were reported in the warning message about removed
genes. Computation of hierarchical clustering was correct.


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