Creating a pre-processing pipeline for GATK
I'm just learning to create Q scripts right now.
Currently I'm using CommandLineFunction to create the calls for bcl2fastq, bwa, samtools, and picard.
Right now I'm stuck trying to find a way to pass a system path to my script as an argument.
I'm trying to run "cd /path/to/rundirectory/" followed by "bcl2fastq".
How do I pass the path to the run directory to the "cd" command?