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Added
-----
- Add AF filter to amplicon report
- Add number of samples to the output of expression aggregator
- Add ``ChIP-Rx``, ``ChIPmentation`` and ``eClIP`` experiment types to
``reads`` descriptor schema
- Add ``pandas`` Python package to ``resolwebio/latex`` Docker image
- Add primerclip, samtools, picard-tools and bwa to ``resolwebio/dnaseq``
Docker image
- Add ``cufflinks``, ``RNASeqT`` R library, ``pyarrow`` and ``sklearn`` Python
packages to ``resolwebio/rnaseq`` Docker image
- Add ``wigToBigWig`` tool to ``resolwebio/chipseq`` Docker image
Changed
-------
- **BACKWARD INCOMPATIBLE:** Drop Python 2 support, require Python 3.4 or 3.5
- **BACKWARD INCOMPATIBLE:** Make species part of the feature primary key
- **BACKWARD INCOMPATIBLE:** Substitute Python 2 with Python 3 in
``resolwebio/rnaseq`` Docker image. The processes to be updated to this
version of the Docker image should also have their Python scripts updated to
Python 3.
- Require Resolwe 5.x
- Set maximum RAM requirement in ``bbduk`` process
- Move *Assay type* input parameter in RNA-Seq descriptor schema from advanced
options to regular options
- Use ``resolwebio/rnaseq`` Docker image in Cutadapt processes
- Use additional adapter trimming option in ``cutadapt-custom-single/paired``
processes
- Show antibody information in ``reads`` descriptor for ``ChIP-Seq``,
``ChIPmentation``, ``ChIP-Rx``, ``eClIP``, ``MNase-Seq``, ``MeDIP-Seq``,
``RIP-Seq`` and ``ChIA-PET`` experiment types
- Use ``resolwebio/dnaseq`` Docker image in ``align-bwa-trim`` process
- Refactor ``resolwebio/chipseq`` Docker image
- Use Resolwe's Test Runner for running tests and add ability to only run a
partial test suite based on what proceses have Changed
- Configure Jenkins to only run a partial test suite when testing a pull
request
- Make tests use the live Resolwe API host instead of external server
Fixed
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- Fix merging multiple expressions in DESeq process
- Fix ``resolwebio/rnaseq`` Docker image's README
- Handle multiple ALT values in amplicon report
- Fix BAM file input in ``rsem`` process
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