Added script to automate multiple calls to extract_barcodes.py for cases...

... are large number of input fastq files (paired or unpaired data).
I think you should drop this parameter, and instead walk the ``input_dir`` to find fastq files. The easy way to do this would be:

all_files = glob('%s/*fastq' % input_dir) + glob('%s/*/*fastq' % input_dir)

The more flexible way would be to use [``os.walk``](https://docs.python.org/2/library/os.html#os.walk).