Update download_raw_data.sh script to ensure consistent directory structure

[erictleung]

Currently, the data is downloaded to /data/raw/, but within this, the data is heavily nested.

Update script to automatically create the directory structure from practical use instead of manually moving the data from the nested structure.

Template directory structure

MiSeqRun_XXX
   - Processed
   - RawData
       - files.../
       - lane*-fastq.gz

Don't move undetermined sequences found in the file base call.