Eliminate ExtractIlluminaBarcodes call by default prior to IlluminaBaseCallsToSam

[tomkinsc]

If the relatively recent parameter, MATCH_BARCODES_INLINE, is set to true in the call to IlluminaBaseCallsToSam, barcode matching will be done in the course of demultiplexing, eliminating the need to call ExtractIlluminaBarcodes before demultiplexing.

Eliminating the call to ExtractIlluminaBarcodes should reduce demux turnaround time at the expense of losing the full list of counts for observed barcodes written by IlluminaBaseCallsToSam to the file specified in the commonBarcodes argument.

Since the commonBarcodes is subsequently used as input to illumina.py guess_barcodes, if MATCH_BARCODES_INLINE is used, the call to illumina.py guess_barcodes will need to be skipped or omitted.

We may want to include a boolean toggling between a faster mode with MATCH_BARCODES_INLINE=true but no illumina.py guess_barcodes output, and the current state where ExtractIlluminaBarcodes is called before IlluminaBaseCallsToSam, and illumina.py guess_barcodes is called after.

[dpark01]

What if we separate barcode guessing (a useful thing to do) to a separate wdl task that gets called in parallel in relevant workflows? Remove ExtractIlluminaBarcodes and guess_barcodes from illumina_demux.