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A good shell script should also be relatively easy to call. That's why, for example, we have this script takes only a short name of the desired reference and uses it to select the correct path, and only requires the name of the R1 fastq for paired-end reads, using that path to determine the name of the R2 fastq file. While we won't go into the details of that defaulting in this discussion, and these specific choices may not be appropriate for your environment, you might want to look at those parts of the code script for ideas on how to accomplish similar goals.
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