Resolwe-bio

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

Added
-----
- Add support for ``Python 3.12``
- Add ``samtools-depth-single`` process
- Add gene body coverage plot from ``qorts-qc`` process to MultiQC
report
- Add retry for reads prefetch in ``import-sra-single`` and ``import-sra-paired``

Changed
-------
- Remove ``rnaseqc-qc`` 3' bias statistics from MultiQC report
- Remove ``rnaseqc-qc`` from RNA-seq workflows
- Remove ``cut_and_run.yml``
- Rename ``workflow-cutnrun-beta`` to ``workflow-cutnrun``
- Remove ``upload-sc-10x``, ``cellranger-count`` and ``cellranger-mkref``
processes


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

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

Added
-----
- Add support for ``Python 3.12``
- Add ``samtools-depth-single`` process

Fixed
-----
- Fix handling of missing post-peak QC reports in MultiQC
when MACS2 is run in broad peak mode
- Fix handling STAR alignment reports for downsampled inputs
in MultiQC


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

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

Changed
-------
- Make changes to input fields in ``workflow-cutnrun-beta``
- Reword documentation of ``macs2-callpeak``, ``macs2-batch`` and
``qc-prepeak``
- Add input option to exclude flags in ``samtools-bedcov`` process


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

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

Added
-----
- Add ``samtools-bedcov`` process
- Add ``workflow-cutnrun-beta`` workflow

Changed
-------
- Use downsampled alignment for ``rnaseqc-qc`` process in ``workflow-bbduk-star-featurecounts-qc``
and ``workflow-bbduk-star`` workflows
- Unify the use of ``resolwebio/common:4.1.1`` Docker
image version across processes
- Unify the use of ``resolwebio/base:ubuntu-22.04-14112023`` Docker
image across processes
- Add normalized count matrix output to ``differentialexpression-deseq2`` process

Fixed
-----
- Fix ``qorts-qc`` process so it can be used with hg19 annotation
and improve error handling when files are missing


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

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

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 38.x
- Change ``rnaseqc-qc`` data object label in ``workflow-bbduk-star-featurecounts-qc``,
``workflow-bbduk-star-qc`` and ``workflow-bbduk-salmon-qc`` workflows
- Add ``rnaseqc-qc`` to ``workflow-bbduk-star-featurecounts-qc``,
``workflow-bbduk-star-qc`` and ``workflow-bbduk-salmon-qc``
- Add ``qorts-qc`` to ``workflow-bbduk-star-featurecounts-qc``

Fixed
-----
- Fixed stranded input options in ``rnaseqc-qc`` process
- Change GEO metadata test file for ``geo-import`` process
and fix corresponding test function


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

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

Changed
-------
- **BACKWARD INCOMPATIBLE:** Require Resolwe 37.x
- Add ``sample_annotation`` Jinja expressions filter that accepts an annotation
path and returns its value
- Update field paths for sample annotation in ``geo-import`` process
- Update species annotation in ``alignment-star`` process

Fixed
-----
- Fix Cut&Run workflow to scale the correct input BAM file using the
spike-in scaling factor


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