bcbio/bcbio-nextgen: v1.1.9

Fix for get VEP cache. Support Picard's new syntax for ReorderSam (REFERENCE -> SEQUENCE_DICTIONARY). Remove mitochondrial reads from ChIP/ATAC-seq calling. Add documentation describing ATAC-seq outputs. Add ENCODE library complexity metrics for ATAC/ChIP-seq to MultiQC report (see https://www.encodeproject.org/data-standards/terms/#library for a description of the metrics) Add STAR sample-specific 2-pass. This helps assign a moderate number of reads per genes. Thanks to @naumenko-sa for the intial implementation and push to get this going. Index transcriptomes only once for pseudo/quasi aligner tools. This fixes race conditions that can happen. Add --buildversion option, for tracking which version of a gene build was used. This is used during bcbio_setup_genome.py. Suggested formats are source_version, so Ensembl_94, EnsemblMetazoa_25, FlyBase_26, etc. Sort MACS2 bedgraph files before compressing. Thanks to @LMannarino for the suggestion. Check for the reserved field sample in RNA-seq metadata and quit with a useful error message. Thanks to @marypiper for suggesting this. Split ATAC-seq BAM files into nucleosome-free and mono/di/tri nucleosome files, so we can call peaks on them separately. Call peaks on NF/MN/DN/TN regions separately for each caller during ATAC-seq. Allow viral contamination to be assasyed on non tumor/normal samples. Ensure EBV coverage is calculated when run on genomes with it included as a contig