Passing lines from the text file of a list of files to or as arguments

Using a while read loop:

while read -r file1 file2 trash; do
  something with "$file1" and "$file2"
done < /path/to/input_file

This will read your input file line by line, setting file1 and file2 with the first and second columns respectively. trash is probably unnecessary but I like to include it to handle things you may encounter such as:

file1.fastq.gz file2.fastq.gz foo

If your file contained a line like the above and you did not include the trash variable (or one similar), your file2 variable would be set to: file2.fastq.gz foo

xargs is another way, if your file format is exactly as you say: two whitespace-separated fields per line (noting the ... ellipsis).

< input xargs -n2 ./script-here

... will read the file named input line-by-line and pass two arguments to ./script-here.

You can rearrange the redirection:

xargs -n2 ./script-here < input

... if it makes better intuitive sense to you.