Yes, this is one of the benefits of using virtual machines. You can have a virtual machine with each version of the software enabling version lock-down and ease of validation.
However, there is no way to migrate data from one version to the other. So, if you are keeping older data after updating to a new version of the software you will need to keep the older version in order to access it, or you will need to re-process the FASTQ files with the new version of the software.
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