You could use quite the syntax you want, but for the first line. If you write
SAMPLE=
Then variable SAMPLE is set to the empty string. But if you write
SAMPLE=$(
Then the interpreter looks for the closing parenthesis to end the statement. That is, you can write:
SAMPLES=$( #comment for f in $(find . -name *fastq.gz) ; #comment do # comment basename $f | #comment cut -c 1-4 done | #comment sort | uniq)
(BTW, you can nest $()
to avoid the older backquote syntax.)