Eliminate BBMap from pipeline

[willbradshaw]

Especially in recent runs, using BBMap to identify viral false-positives arising from contamination seems to significantly increase the runtime and computational cost of the pipeline. We should be able to replace it, either with another aligner or by modifying the configuration of Bowtie2 (which is used for the same purpose but seems to detect a different set of false positives). However, this will require careful QC to check that we're not introducing new false positives into the final pipeline output.