Changes spades default mode from rna to meta

[yesimon]

The rnaSpades mode is heavily focused on mRNA transcriptome assembly and is very aggressive at splicing assemblies into short transcripts. The —meta mode would be more suitable for our DNA/RNA assembly even though it is optimized for DNA metagenomes.

One barrier is that meta spades only accepts a single paired end library and doesn’t accept unpaired reads for now. Although not too common, we should handle this by warning after Trimmomatic if a significant number of reads become orphaned.

[notestaff]

A branch adding metaspades is https://github.com/broadinstitute/viral-ngs/tree/is-add-metaspades