Resolwe-bio

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

Changed
-------
- Bump Cutadapt to v2.4 and use ``resolwebio/common:1.2.0`` as a base
image in ``resolwebio/rnaseq:4.6.0``

Added
-----
- Add pigz package to ``resolwebio/common:1.2.0`` Docker image
- Add StringTie and UMI-tools to ``resolwebio/rnaseq:4.7.0`` Docker
image

Fixed
-----
- Fix ``spikeins-qc`` process to correctly handle the case where all
expressions are without spikeins
- Fix an error in ``macs2-callpeak`` process that prevented correct
reporting of build/species mismatch between inputs
- Support UCSC annotations in ``feature_counts`` process by assigning
empty string gene_ids to the "unknown" gene


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

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

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 18.x
- Bump the number of allocated CPU cores to 20 in ``alignment-bwa-mem``
process
- Bump memory requirements in ``seqtk-sample-single`` and
``seqtk-sample-paired`` processes
- Bump Salmon to v0.14.0 in ``resolwebio/rnaseq:4.5.0`` Docker image
- Expose additional inputs in ``salmon-index`` process
- Use ``resolwebio/rnaseq:4.5.0`` Docker image in processes that call
Salmon tool (``library-strandedness``, ``feature_counts`` and
``qorts-qc``)
- Implement dropdown menu for ``upload-bedpe`` process
- Add validation stringency parameter to ``bqsr`` process and propagate
it to the ``workflow-wes`` as well
- Add LENIENT value to validation stringency parameter of the
``markduplicates`` process
- Improve performance of RPKUM normalization in ``featureCounts`` process

Added
-----
- Add ``salmon-quant`` process

Fixed
-----
- Fix genome upload process to correctly handle filenames with dots
- Fix merging of expressions in ``archive-samples`` process. Previously
some genes were missing in the merged expression files. The genes that
were present had expression values correctly assigned. The process was
optimized for performance and now supports parallelization.


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

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

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 17.x
- **BACKWARD INCOMPATIBLE:** Use Elasticsearch version 6.x
- **BACKWARD INCOMPATIBLE:** Bump Django requirement to version 2.2
- **BACKWARD INCOMPATIBLE:** Remove obsolete RNA-seq workflows
``workflow-bbduk-star-featurecounts-single``,
``workflow-bbduk-star-featurecounts-paired``,
``workflow-cutadapt-star-featurecounts-single`` and
``workflow-cutadapt-star-featurecounts-paired``
- **BACKWARD INCOMPATIBLE:** Remove obsolete descriptor schemas:
``rna-seq-bbduk-star-featurecounts``, ``quantseq``,
``rna-seq-cutadapt-star-featurecounts`` and
``kapa-rna-seq-bbduk-star-featurecounts``
- **BACKWARD INCOMPATIBLE:** In ``upload-fasta-nucl`` process, store
compressed and uncompressed FASTA files in ``fastagz`` and ``fasta``
ouput fields, respectively
- Allow setting the Java memory usage flags for the QoRTs tool in
``resolwebio/common:1.1.3`` Docker image
- Use ``resolwebio/common:1.1.3`` Docker image as a base image for
``resolwebio/rnaseq:4.4.2``
- Bump GATK4 version to 4.1.2.0 in ``resolwebio/dnaseq:4.2.0``
- Use MultiQC configuration file and prepend directory name to sample
names by default in ``multiqc`` process
- Bump ``resolwebio/common`` to 1.1.3 in ``resolwebio/dnaseq:4.2.0``
- Process ``vc-gatk4-hc`` now also accepts BED files through parameter
``intervals_bed``

Added
-----
- Support Python 3.7
- Add Tabix (1.7-2) to ``resolwebio/wgbs`` docker image
- Add JBrowse index output to ``hmr`` process
- Add ``bamclipper`` tool and ``parallel`` package to ``resolwebio/dnaseq:4.2.0`` image
- Support ``hg19_mm10`` hybrid genome in ``bam-split`` process
- Support mappability-based normalization (RPKUM) in featureCounts
- Add BEDPE upload process
- Add ``bamclipper`` process
- Add ``markduplicates`` process
- Add ``bqsr`` (BaseQualityScoreRecalibrator) process
- Add whole exome sequencing (WES) pipeline

Fixed
-----
- Fix building problems of ``resolwebio/dnaseq`` docker
- Fix handling of no-adapters input in workflows
``workflow-bbduk-star-featurecounts-qc-single`` and
``workflow-bbduk-star-featurecounts-qc-paired``


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

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

Fixed
-----
- Use ``resolwebio/rnaseq:4.4.2`` Docker image that enforces the memory limit
and bump memory requirements for ``qorts-qc`` process
- Bump memory requirements for ``multiqc`` process


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

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

Changed
-------
- Use Genialis fork of MultiQC 1.8.0b in ``resolwebio/common:1.1.2``
- Support Samtools idxstats and QoRTs QC reports in ``multiqc`` process
- Support ``samtools-idxstats`` QC step in workflows:

- ``workflow-bbduk-star-featurecounts-qc-single``
- ``workflow-bbduk-star-featurecounts-qc-paired``
- ``workflow-bbduk-star-fc-quant-single``
- ``workflow-bbduk-star-fc-quant-paired``
- Simplify ``cellranger-count`` outputs folder structure
- Bump STAR aligner to version 2.7.0f in ``resolwebio/rnaseq:4.4.1``
Docker image
- Use ``resolwebio/rnaseq:4.4.1`` in ``alignment-star`` and
``alignment-star-index`` processes
- Save filtered count-matrix output file produced by DESeq2 differential
expression process

Added
-----
- Add ``samtools-idxstats`` process
- Improve ``cellranger-count`` and ``cellranger-mkref`` logging
- Add FastQC report to ``upload-sc-10x`` process

Fixed
-----
- Fix ``archive-samples`` to work with ``data:chipseq:callpeak:macs2``
data objects when downloading only peaks without QC reports
- Fix parsing gene set files with empty lines to avoid saving gene sets
with empty string elements


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

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

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 16.x
- **BACKWARD INCOMPATIBLE:** Rename and improve descriptions of
processes specific to CATS RNA-seq kits. Remove related
``cutadapt-star-htseq`` descriptor schema.
- **BACKWARD INCOMPATIBLE:** Remove ``workflow-accel-gatk4`` pipeline.
Remove ``amplicon-panel``, ``amplicon-panel-advanced`` and
``amplicon-master-file`` descriptor schemas.
- **BACKWARD INCOMPATIBLE:** Remove obsolete processes and descriptor
schemas: ``rna-seq-quantseq``, ``bcm-workflow-rnaseq``,
``bcm-workflow-chipseq``, ``bcm-workflow-wgbs``, ``dicty-align-reads``,
``dicty-etc``, ``affy`` and ``workflow-chip-seq``
- Expose additional parameters of ``bowtie2`` process
- Support strandedness auto detection in ``qorts-qc`` process

Added
-----
- Add shRNAde (v1.0) R package to the ``resolwebio/rnaseq:4.4.0`` Docker image
- Add ``resolwebio/scseq`` Docker image
- Add shRNA differential expression process. This is a two-step process which
trims, aligns and quantifies short hairpin RNA species. These are then used
in a differential expression.
- Add ``sc-seq`` processes:

- ``cellranger-mkref``
- ``cellranger-count``
- ``upload-sc-10x``
- ``upload-bam-scseq-indexed``

Fixed
-----
- Bump memory requirements in ``seqtk-sample-single`` and
``seqtk-sample-paired`` processes
- Fix ``cellranger-count`` html report
- Mark spliced-alignments with XS flags in ``workflow-rnaseq-cuffquant``
- Fix whitespace handling in ``cuffnorm`` process


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