Gracefully handle failures when GATK creates an empty idx file during annotation
Rework initial fastq retrieval and gunzipping to work in parallel. Explicitly move this functionality to RNA-seq and ChiP-seq pipelines and remove duplicated checks. Remove outdated demultiplexing code. Fixes #281
Enable specification of samples in multiple batches: allows a single normal sample to match with multiple tumors. Attach variant calling output to tumor samples and avoid splitting tumor/normal into separate VCFs. Fixes for filtering: avoid ploidy post-filtering and GATK filtering on MuTecT output. #285