Resolwe-bio

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Fixed
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- Fix ``cuffnorm`` process to correctly use sample names as labels in output
files and expand ``cuffnorm`` tests


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Changed
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- Update description text of ``cutadapt-star-htseq`` descriptor schema to
better describe the difference between gene/transcript-type analyses
- Speed-up management command for inserting mappings


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Added
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- Add R, tabix, and CheMut R library to ``resolwebio/dnaseq`` Docker image
- Add ``SRA Toolkit`` to ``resolwebio/rnaseq`` Docker image

Changed
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- Require Resolwe 6.x
- Extend pathway map with species and source field
- Move template and logo for multi-sample report into ``resolwebio/latex``
Docker image
- Refactor ``amplicon-report`` process to contain all relevant inputs for
``amplicon-archive-multi-report``
- Refactor ``amplicon-archive-multi-report``
- Use ``resolwebio/dnaseq:1.2.0`` Docker image in ``filtering_chemut`` process

Fixed
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- Enable DEBUG setting in tests using Django's ``LiveServerTestCase``
- Wait for ElasticSeach to index the data in ``KBBioProcessTestCase``
- Remove unused parameters in TopHat (2.0.13) process and Chip-seq workflow


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Added
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- Add ``amplicon-archive-multi-report`` process
- Add ``upload-metabolic-pathway`` process
- Add memory-optimized primerclip as a separate ``align-bwa-trim2`` process
- Add ``workflow-accel-2`` workflow

Changed
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- Improve ``PCA`` process performance
- Use ``resolwebio/chipseq:1.1.0`` Docker image in ``macs14`` process
- Change formatting of ``EFF[*].AA`` column in ``snpeff`` process
- Save unmapped reads in ``aligment-hisat2`` process
- Turn off test profiling

Fixed
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- Fix pre-sorting in ``upload-master-file`` process
- Revert ``align-bwa-trim`` process to use non-memory-optimized primerclip
- Fix file processing in ``cutadapt-custom-paired`` process


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Added
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- 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
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- **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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Fixed
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- Update Features and Mappings ElasticSearch indices building to be compatible
with Resolwe 4.0


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