nextNEOpi_v1.2

Changes:

• support BAM files as input data
• switch Singularity container repository from quay.io to https://depot.galaxyproject.org/singularity
• command line parameter to disable OptiType --disable_OptiType
• auto detection of PE/SE sequencing data
• deal with symlinked directories when using singularity
• do not auto bind mount the user home into singularity containers
• avoid race condition during ensembl VEP cache and plugin installation
• bug fixes
• updates: CNVkit 0.99, pVACseq 2.0.4
• code cleanup