Thank you for posting your manifest file. I think you are on the right track and a small update to the manifest file will make this script work for you.
When I look at your file, I see this:
sample-id
absolute-filepath
direction
BN-1_1.fq.gz
/home/faizansaleem/Desktop/faizan/Betel-Nut_Data
forward
BN-1_2.fq.gz
/home/faizansaleem/Desktop/faizan/Betel-Nut_Data
reverse
BN-2_1.fq.gz
/home/faizansaleem/Desktop/faizan/Betel-Nut_Data
forward
BN-2_2.fq.gz
/home/faizansaleem/Desktop/faizan/Betel-Nut_Data
reverse
Note how your absolute-filepath column is always the same! That’s wont work.