Bash scripting FastQC for multiple fastq files in multiple directories I am completely new to bioinformatics so I'm looking to learn how to do this.

I have multiple directories with fastq files: E.g; 10 Directories with each time series, each with Treatment and control directories, each with rep1 rep2 rep3.

For example: T9/Infected/Rep1/*.fastq.gz.

I'm looking to create a loop to run fastQC on each fastq file instead of having to submit a separate job for each directory.

Then to either output the fastQC data to a single directory or if possible a directory corresponding to each rep - e.g. rep1 results go into a folder called rep1 and so on.
multiqc kind of glazes over some important information, like the exact adapters and duplicated sequences in a library. If you plan to spend big $$ for sequencing a library it is better to look at both the multiqc report and the actual fastqc html report to get a better idea of any error modes. 

Going off of @Kubator's answer, I noticed that there was no command to run fastqc.

Here's a simple one-liner to run fastqc in parallel on all of your fastq files. The -j 25 uses 25 threads. Change 25 to however many threads you want/have for max speed.

#Run fastqc on everything in parallel.
&gt; find ../reads/ -name '*.fastq.gz' | awk '{printf("fastqc \"%s\"\n", $0)}' | parallel -j 25 --verbose
# copies all the fastqc files to directory ./    
&gt; find ../reads/ -name '*fastqc.*' | xargs -I '{}' mv '{}' ./


These files might be output by multiqc, anyway!

edit - now the command is safe for whitespace in file names. Please, no newlines in filenames though!