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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?

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