Usage:
pipeline.py (--fastq <FASTQS>...) --config <config> [-o <outdir>] [--log <log>] [--control <CONTROLS>...]
Options:
-f <FASTQS>, --fastq <FASTQS>
-r <CONTROLS>, --control <CONTROLS>
-c <config>, --config <config>
--o <outdir>, --outdir <outdir>
--log <log>, -l <log>
Notes:
For the --fastq argument, provide any number of paired read files ordered like:
--fastq <Samp0_R1> <Samp0_R2> <Samp1_R1> <Samp1_R2> . . .
The --control argument should be provided in the same way.
--log is the file path to store log output in.