How to input multiple files from a list of files in bash script

Question

I have a list of files in bam_files.txt which looks like this:

/home/test/2cells_2_trim.bam
/home/test/6h_1_trim.bam
/home/test/2cells_1_trim.bam
/home/test/6h_2_trim.bam

I want to do something like this:

cuffnorm -o cuffnorm_out /home/software/genes.gtf test/*.bam

but while reading files from bam_files.txt and not directly from directory (as shown above).

I want to read all the files together in the same command.

Can someone please help? Thanks a lot. Appreciate your help.

Answer 1

You could read bam_files.txt into an array, then use the array as arguments to cuffnorm:

mapfile -t bam_files < bam_files.txt
cuffnorm -o cuffnorm_out /home/software/genes.gtf "${bam_files[@]}"