Resolwe-bio

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

Added
-----
- Add ``workflow-subsample-bwa-aln-single`` and
``workflow-subsample-bwa-aln-paired`` workflows

Changed
-------
- **BACKWARD INCOMPATIBLE:** Use Salmon 1.2.1 in ``salmon-quant`` and
``salmon-index`` processes
- Salmon quant 1.2.1 is not backwards compatible with indices generated
with Salmon index prior to version 1.0.0, thus Salmon tool is updated
to version 1.2.1 in processes that utilize Salmon to detect library
strandedness type.
- Expose additional limit options in ``alignment-star`` process
- Bump SRA toolkit to 2.10.0 in ``resolwebio/common:1.5.0`` Docker image
- Use SRA tookit 2.10.0 in ``import-sra``, ``import-sra-single`` and
``import-sra-paired`` processes
- Format floats to 2 decimal places in custom ChIP-seq pre/post-peak
MultiQC reports


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

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

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


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