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Hopefully by now you have had enough experience installing packages via conda that it is second nature to think of going to https://anaconda.org/ searching for multiqc, finding  https://anaconda.org/bioconda/multiqc, and seeing that it recommends a command of conda install -c bioconda multiqc suggesting you can use this command and not worry about anything else. Instead, if you go to the multiqc homepage you might (or might probably not, disappointingly,  it is not very visible disappointingly) that next to their conda installation instruction is a small warning icon which takes you to a page about setting up bioconda channels as a prerequisite to installing multiqc. Friday's class will go into detail about managing channels like this and it is not suggested that you follow the commands on that page. 

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mkdir fastqc_output
cp /corral-repl/utexas/BioITeam/gva_course/GVA2022GVA.launcher.slurm fastqc.slurm
nano multiqcfastqc.slurm

Again while in nano you will edit most of the same lines you edited in the in the breseq tutorial. Note that most of these lines have additional text to the right of the line. This commented text is present to help remind you what goes on each line, leaving it alone will not hurt anything, removing it may make it more difficult for you to remember what the purpose of the line is

The changes to lines 22 and 23 are optional but will give you an idea of what types of email you could expect from TACC if you choose to use these options. Just be sure to pay attention to these 2 lines starting with a single # symbol after editing them.

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fastqc -t 6848 -o fastqc_output/ *.gz

Using both the * wildcard, and 68 48 threads, analysis of many samples are initiated at the same time making the output somewhat difficult to read, but significantly increasing the speed at which the samples get analyzed.

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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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