Resolwe

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

Added
-----
- Add ``gatk-refine-variants`` process
- Add ensembl-vep tool to the ``resolwebio/dnaseq:6.2.0`` Docker image
- Add ``upload-vep-cache`` process
- Add ``ensembl-vep`` process
- Add ``variants-to-table`` process

Changed
-------
- **BACKWARD INCOMPATIBLE:** Update ``merge-fastq-single`` and
``merge-fastq-paired`` processes to use sample relations for merging
FASTQ files
- **BACKWARD INCOMPATIBLE:** Rewrite ``feature_counts`` process to
Python
- **BACKWARD INCOMPATIBLE:** Create a separate process
``gatk-genomicsdb-import`` for importing GVCFs into the database and
use it as an input in the parallelised ``gatk-genotype-gvcfs`` process
- Support ChIP-Seq and ATAC-Seq data sets in ``geo-import`` process
- Replace the stdout/stdin file interface in SortSam / SetNmMdAndUqTags
stage of the ``wgs-preprocess-bwa2`` with two distinct analysis steps


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

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

Added
-----
- Add BWA-mem2 to the ``resolwebio/common`` Docker image
- Add ``bwamem2-index`` process
- Add ``bwamem2`` process
- Add ``wgs-preprocess-bwa2`` process
- Add ``upload-bwamem2-index`` process


Changed
-------
- Use ``resolwebio/common:2.9.0`` Docker image version in
``resolwebio/dnaseq`` Docker image
- Optimize CPU usage in process ``gatk-haplotypecaller-gvcf``
- Make the read trimming step (trimmomatic) optional in the
``workflow-wgs-gvcf`` workflow
- Add aligned reads (BAM format) as an alternative input option in the
``wgs-preprocess`` process
- Set the requirements for number of cores from 20 to 4 and memory from
16 GB to 32 GB in ``alignment-bwa-mem`` process

Fixed
-----
- Fix an edge case in ``methylation-array-sesame`` process where calling
the ``sesame.R`` script using Plumbum was failing for some compressed
IDAT inputs due to the file encoding issues


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

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

Changed
-------
- Replace Bedtools with Samtools for BAM to FASTQ file format conversion
in ``bamtofastq-paired`` process
- Bump docker image version in ``methylation-array-sesame`` process
- Add ``qin`` and ``ignorebadquality`` options to ``bbduk-single`` and
``bbduk-paired`` processes

Fixed
-----
- Use clean file name for gene sets from differential expressions
- Fix saving estimated counts output in ``tximport_summarize.R`` script
- Add ``config.yaml`` to methylation_arrays Dockerfile
- Use raw SigSet for performing QC in the SeSAMe pipeline


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

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

Added
-----
- Add more information about output to the ``methylation-array-sesame``
pipeline documentation
- Support filtering by ``subject_information.sample_label``,
``subject_information.subject_id``, ``subject_information.batch``,
``subject_information.group``, ``disease_information.disease_type``,
``disease_information.disease_status``,
``immuno_oncology_treatment_type.io_drug``,
``immuno_oncology_treatment_type.io_treatment``,
``response_and_survival_analysis.confirmed_bor``,
``response_and_survival_analysis.pfs_event``, ``general.description``,
``general.biosample_source``, and ``general.biosample_treatment``
fields in sample descriptor on API

Changed
-------
- Improve automatic sample naming in the ``geo-import`` process

Fixed
-----
- Fix stalled sam-to-bam conversion in ``wgs-preprocess`` process
- Return column betas to ``methylation-array-sesame`` pipeline output


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

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

Changed
-------
- Remove mapping of probe_ids to ENSEMBL ids and add extra variables in
``methylation-array-sesame`` process


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

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

Added
-----
- Add ``wgs-preprocess`` process
- Add ``gatk-haplotypecaller-gvcf`` process
- Add ``workflow-wgs-gvcf`` process
- Add ``gatk-genotype-gvcfs`` process
- Add ``gatk-vqsr`` process
- Add ``bamtofastq-paired`` process
- Add ``methylation_array`` docker image
- Add ``methylation-array-sesame`` process
- Add support for Python 3.9
- Support downloading knowledge base features and mappings from S3 bucket
- Cap process memory consumption at 10GB

Changed
-------
- Bump GATK to version 4.2.0.0 in ``resolwebio/dnaseq:6.0.0`` Docker
image
- Update ``workflow-mirna``
- Add new parameters -maximumlength/-M and -no-indels in processes
``cutadapt-single`` and ``cutadatp-paired``
- Add new ``id_attribute`` to ``feature_counts`` process

Fixed
-----
- Remove some duplicated code in ``test_probe_mapping``
- Rename FastQC output bundle in Trimmomatic processes so that the
reports are correctly sorted/included in MultiQC reports
- Fix method signature for KB feature/mapping filtering


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