Resolwe-bio

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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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Added
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- Add automatic headers extractor to ``bam-split`` process
- Add HTML amplicon plot in ``coveragebed`` process
- Add raw RSEM tool output to `rsem` process output
- Add support for transcript-level differential expression
in ``deseq2`` process

Changed
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- **BACKWARD INCOMPATIBLE:** Bump Django requirement to version 1.11.x
- **BACKWARD INCOMPATIBLE:** Make ``BioProcessTestCase`` non-transactional
- Require Resolwe 4.x
- Add the advanced options checkbox to the ``rna-seq`` descriptor schema
- Remove static amplicon plot from ``coveragebed`` and ``amplicon-report``
processes
- Update Dockerfile for ``resolwebio/latex`` with newer syntax and add some
additional Python packages


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Added
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- Add ``resolwebio/base`` Docker image based on Ubuntu 17.04
- Add ``resolwebio/dnaseq`` Docker image
- Add ``DESeq2`` tool to ``resolwebio/rnaseq`` docker image
- Add input filename regex validator for ``upload-master-file`` process

Changed
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- Remove obsolete mongokey escape functionality
- Report novel splice-site junctions in HISAT2
- Use the latest stable versions of the following bioinformatics
tools in ``resolwebio/rnaseq`` docker image: Cutadapt 1.14,
FastQC 0.11.5, HTSeq 0.9.1, and SAMtools 1.5


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Added
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- Add Mus musculus to all BCM workflows' schemas
- Add ``bam-split`` process with supporting processes
``upload-bam-primary``, ``upload-bam-secondary`` and
``upload-header-sam``

Changed
-------
- Enable Chemut workflow and process tests

Fixed
-----
- Fix chemut ``intervals`` input option


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Added
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- New base and legacy Docker images for processes, which support non-root
execution as implemented by Resolwe

Changed
-------
- **BACKWARD INCOMPATIBLE:** Modify all processes to explicitly use the new Docker images
- **BACKWARD INCOMPATIBLE:** Remove ``clustering-hierarchical-genes-etc`` process
- Require Resolwe 3.x


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Added
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- Add ``index-fasta-nucl`` and ``rsem`` process
- Add custom Cutadapt - STAR - RSEM workflow


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