Resolwe

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

Added
-----

Changed
-------
- Extend the MultiQC report so that the Sample summary table is created
for the compatible Data objects
- Bump CPU and memory requirements for the ``alignment-bowtie2`` process
- Move upload test files of differential expression to its own folder

Fixed
-----
- Fix typo in ``scheduling_class`` variable in several Python processes
- Handle cases of improper tags passed to ``read_group`` argument of
the ``bqsr`` process
- When processing differential expression files, a validation is
performed for numeric columns


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

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

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


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

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

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


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

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

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


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

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

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


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