Of course we are assuming that there is a pattern in the file names that you can exploit to group files. If not, either you have to do it manually or you need a look up table to link files to groups.

These are some useful string manipulations and expansions for bash, besides the * wildcard:

myfiles[135].fastq.gz will match myfiles1.fastq.gz, myfiles3.fastq.gz, and myfiles1.fastq.gz (but not, say myfiles2.fastq.gz or myfiles11.fastq.gz).

myfiles{1..10}.fastq.gz will try to match myfiles1.fastq.gz myfiles2.fastq.gz myfiles3.fastq.gz ... myfiles10.fastq.gz

${fq%%.*} will remove everything after the first . in string $fq while ${fq%.*} will remove everything after the last ..

And lots more here for example http://www.tldp.org/LDP/abs/html/string-manipulation.html

But for more sophisticated manipulations it might be better to use python or similar.

XCGD2_R2.FB-P7-Rd2-LC.*_trimLCwithMCF.fastq should match all those files with different numbers. You can check this in that directory with running ls XCGD2_R2.FB-P7-Rd2-LC.*_trimLCwithMCF.fastq and see if all files are listed.

The * is a wildcard meaning "anything of any size" and is expanded by your shell.

Or did I misunderstand what you want to get?