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In this case (much as is the case with FastQC) while there are are a reasonable number of options that can be used, none are truly needed for evaluating fastq files. The only requirement is that you specify where the FastQC output that you want to generate a single report for is located. In the example above you changed into the directory containing those results and then specified multiqc should look in you current directory for the files. It would have been comparable to stay in the existing directory, and instead use a command of "multiqc fastqc_output". 

Your final product is an html file named: multiqc_report.html

Evaluate MultiQC report

As the multiqc_report.html file is a html file, you will need to transfer it back to your laptop to view it. Hopefully, by now you have learned how to do this without needing the scp tutorial open to help you. If not, consider getting my attention on zoom so i can try to help clear up any confusion you may be having.

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