Resolwe-bio

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

Added
-----
- Add filtered BAM output to ``macs2-callpeak`` process
- Add an option to use filtered BAM files from ``macs2-callpeak`` to
``rose2``, ``workflow-macs-rose``, and ``macs2-rose2-batch``
- Add ChIPQC to the ``resolwebio/chipseq:4.1.0`` Docker image
- Add ``chipqc`` process

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 22.x
- **BACKWARD INCOMPATIBLE:** Remove processes ``alignment-subread`` and
``subread-index``
- **BACKWARD INCOMPATIBLE:** Remove process ``upload-genome``. Refactor
processes and workflows that required ``data:genome:fasta`` type of
object on the input to work with ``data:seq:nucleotide`` or dedicated
aligner index files instead.
- Change ``macs2-batch`` and ``macs2-rose2-batch`` to use tagAlign
files by default
- Bump Salmon to version 1.2.1 in ``resolwebio/rnaseq:4.10.0`` Docker
image. Fix build issues affecting ``jpeg`` and ``png`` R packages.
- Support ``chipqc`` process outputs in MultiQC
- Support ``chipqc`` in ``workflow-macs-rose``, ``workflow-macs2``,
``macs2-batch`` and ``macs2-rose2-batch`` processes
- Bump memory requirements for process ``upload-fasta-nucl`` to 8 GB

Fixed
-------
- Fix Data name in ``bowtie-index``, ``bowtie2-index``, ``bwa-index``,
``hisat2-index`` and ``walt-index``
- Fix filtering of empty VCF files in ``lofreq`` process


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

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

Added
-----
- Add ``workflow-wgs-paired`` workflow
- Add processes: ``bowtie-index``, ``bowtie2-index``, ``bwa-index``,
``hisat2-index``, ``subread-index`` and ``walt-index``.
- Add ``Dictyostelium purpureum`` species choice to ``sample``
descriptor schema

Changed
-------
- **BACKWARD INCOMPATIBLE:** Refactor ``upload-fasta-nucl`` process:
``species`` and ``build`` input information on FASTA file upload are
now mandatory, while ``source`` input has been removed.
- **BACKWARD INCOMPATIBLE:** Change the ``alignment-star-index`` process
type to ``data:index:star``. The process now accepts only
``upload-fasta-nucl`` objects on input.
- Add trimming with Trimmomatic in ``workflow-wgbs-single`` and
``workflow-wgbs-paired`` workflows
- Make intervals an optional input in ``bqsr`` process
- Make intervals an optional input in ``vc-gatk4-hc`` process
- Bump memory requirements in ``walt`` process to 32 GB

Fixed
-------
- Fix data type of adapters input field in ``alignment-summary`` process
- Fix handling of multiple adapters in ``alignment-summary`` process


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

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

Added
-----
- Add ``merge-fastq-single`` and ``merge-fastq-paired`` processes that
merge multiple ``data:reads:fastq`` data objects into a single
``data:reads:fastq`` data object (and consequently a single sample)
- Add ``bs-conversion-rate`` process
- Add support for Python 3.8

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 21.x
- **BACKWARD INCOMPATIBLE:** Split ``workflow-wgbs`` into
``workflow-wgbs-single`` and ``workflow-wgbs-paired`` workflows
- Extend the ``workflow-wgbs-single`` and ``workflow-wgbs-paired`` with
the ``markduplicates``, ``insert-size`` and ``bs-conversion-rate``
QC processes
- Support detection and separation of control spike-in-derived reads
from endogenous sequencing reads in ``walt`` process
- Replace duplicate-remover in ``walt`` to unify both (.mr and .bam)
output alignment files
- Support ``markduplicates`` and ``bs-conversion-rate`` process outputs
in ``multiqc`` reports
- Enable multiple SRR numbers as inputs in processes ``import-sra``,
``import-sra-single``, and ``import-sra-paired``
- Bump memory requirements in ``rrbs-metrics`` process
- Improve process test input data for the ``alignment-star`` process
- Bump Bedtools to v2.29.2 in ``resolwebio/common:1.3.2`` Docker image

Fixed
-----
- Fix Jbrowse track creation in ``upload-genome`` process. When
gzip input was used in ``prepare-refseqs.pl``, not all sequence chunks
were created for some inputs.
- Fix ``macs2-callpeak`` process to work with paired-end reads when
not using tagAlign files
- Fix ``bed_file_corrections_genome_browsers.py`` script to handle cases
where the input file is empty


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

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

Added
-----
- Add ``alignment-summary`` process
- Add ``insert-size`` process
- Add ``wgs-metrics`` process
- Add ``rrbs-metrics`` process
- Add ``workflow-macs2`` workflow

Changed
-------
- **BACKWARD INCOMPATIBLE:** Use featureCounts instead of Stringtie in
the ``workflow-corall-single`` and ``workflow-corall-paired``
workflows
- **BACKWARD INCOMPATIBLE:** Remove ``stringtie`` and
``upload-metabolic-pathway`` processes
- **BACKWARD INCOMPATIBLE:** Refactor ``walt`` process to support
Picard quality metrics and update ``methcounts`` process and to match
the new outputs
- **BACKWARD INCOMPATIBLE:** Support MultiQC report in ``wgbs`` workflow
- Remove Stringtie tool from ``resolwebio/rnaseq`` Docker image
- Remove ``resolwe/base:ubuntu-14.04`` and ``resolwe/base:ubuntu-17.10``
Docker images
- Use pigz for output file compression in ``bbduk-single`` and
``bbduk-paired`` processes
- Use ``resolwebio/rnaseq:4.9.0`` Docker image in processes
``bbduk-single``, ``bbduk-paired``, ``trimmomatic-single``,
``trimmomatic-paired``, ``alignment-bowtie``, ``alignment-bowtie2``,
``alignment-hisat2``, ``alignment-subread``, ``cuffmerge``, ``pca``,
``cuffdiff``, ``differentialexpression-edger``, ``cufflinks``,
``cuffnorm``, ``cuffquant``, ``expression-aggregator``,
``htseq-count``, ``htseq-count-raw``, ``index-fasta-nucl``, ``rsem``,
``upload-bam``, ``upload-bam-indexed``, ``upload-bam-secondary``,
``upload-expression``, ``upload-expression-cuffnorm``,
``upload-expression-star``, ``upload-genome``,
``upload-gaf``, ``upload-obo``, ``upload-fasta-nucl``,
``regtools-junctions-annotate``, ``cutadapt-custom-single``,
``cutadapt-custom-paired``, ``bam-split``, ``gff-to-gtf``,
``spikein-qc``, ``differentialexpression-shrna``, ``feature_counts``,
``salmon-index``, ``salmon-quant``, ``library-strandedness``,
``qorts-qc``, ``alignment-star``, ``alignment-star-index``,
``cutadapt-3prime-single``, ``cutadapt-single``, ``cutadapt-paired``,
``differentialexpression-deseq2``, ``cutadapt-corall-single``,
``cutadapt-corall-paired``, ``umi-tools-dedup`` and ``shrna-quant``.
- Use ``resolwebio/common:1.3.1`` Docker image in processes
``amplicon-table``, ``mergeexpressions``, ``upload-bedpe``,
``upload-bam-scseq-indexed``, ``upload-diffexp``, ``upload-etc``,
``upload-sc-10x``, ``upload-multiplexed-single``,
``upload-multiplexed-paired``, ``archive-samples``,
``samtools-idxstats``, ``seqtk-sample-single``,
``seqtk-sample-paired``, ``basespace-file-import``,
``clustering-hierarchical-samples``,
``clustering-hierarchical-genes``, ``import-sra``,
``import-sra-single``, ``import-sra-paired``.
- Compute TPM values and map gene_ids to gene symbols in
``alleyoop-collapse`` process output
- Rewrite ``multiqc`` process to Python
- Save ``lib_format_counts.json`` in a separate output field in the
``salmon-quant`` process
- Use ``resolwebio/common:1.3.1`` as a base Docker image for the
``resolwebio/wgbs:1.2.0`` Docker image
- Support MultiQC reports in ChIP-seq workflows

Fixed
-----
- Fix Mapping search for ``source_id`` / ``target_id``
- Fix handling of input file names in processes: ``cellranger-count``,
``cutadapt-3prime-single``, ``cutadapt-corall-single``,
``cutadapt-corall-paired``, ``salmon-quant``, ``umi-tools-dedup``,
``upload-sc-10x`` and ``upload-bam-scseq-indexed``
- Fix handling of chimeric alignments in ``alignment-star``


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

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

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


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