Pipeline improvements 201906

List of new improvements:

• Optimized Ehive pipeline for resource usage and job counts
• New Epigenome QC pipeline with PPQT and Deeptools plots
• New RNA-Seq QC pipeline (with experimental batch effect checking)
• Cellranger for single cell and single nuclei samples
• Scanpy report with 3D UMAP plot for single cell and single nuclei samples
• Bcl2Fastq mask-short-adapter-reads param reset for short read cycles
• Updated doc template
• Using conda yaml file for travis-ci
• Indexing cram output before iRODS upload
• Minor changes added to the metadata db schema
• Fixed security issues for sqlalchemy and jinja versions
• Added a histogram plot in analysis QC page for alignment stats