Finished modifications for better bowtie2 multi-target support, also higher specificity bowtie2 mapping after first iteration
small mod to fix bowtie2-index crashes, issue #33
Fixed a bug where bowtie2 would be called (and crash) even if no contigs were written out.
added a keepassemblies param that controls deletion of assemblies, testing alternative to bowtie2 k=1
Must check that file exists before checking size.
Small fix to finisher in an attempt at addressing a race condition with a slow file system.
Merge branch 'bowtie2-multitargets' into develop