Revised count filepath creation to match idiom of rest of pipeline.  Fixed missing file.path on probe rank file output.
Revised count filepath creation to match idiom of rest of pipeline.  Fixed missing file.path on probe rank file output.

ucsd-ccbb/mali-dual-crispr-pipeline,ucsd-ccbb/mali-dual-crispr-pipeline,ucsd-ccbb/mali-dual-crispr-pipeline