Provide resiliency to Galaxy API errors when uploading bcbio-nextgen results
Avoid adding *-orig files when merging from subparts instead of incorporating new file name
Fix split/recombine variant calling with BAM post-alignment preparation steps. Correctly pass multiple regional BAMs. Generally clean up process to use align BAMs and multiple keys instead of re-using work_bam. Thanks to Severine Catreux
Initial work to support CRAM input to pipelines. Not yet finished
Futher fixes for parallelizing by regions with post-alignment BAM preparation: handle single samples correctly and correctly handle special cases in structural variant calling and upload. Thanks to Severine Catreux
Return proper name of rRNA interval list file.
Look up rRNA in GTF file instead of using BWA and mapping

This was not functional, it always returned NA. This method
should work for the genome files we support so there is no need
to do anything more complicated.