if then else statement will not loop properly - bash

Question

I figured how to get an if then else statement to work but it now seems to have broken. =( I cannot work out what is going wrong!
There are up to 10 directories in ./ called barcode01 - 09 and one called unclassified. This script is supposed to go into each one, prep the directory for ~/Taxonomy.R (Which requires all the fastq files to be gzipped and put into a sub-directory titled "data". It then runs the ~/Taxonomy.R script to make a metadata file for each.
Edit the tmp.txt file is created using ls > tmp.txt then echo "0" >> tmp.txt to make a sacrificial list of directories for the script to chew through then stop when it gets to 0.
#!/bin/bash
source deactivate
source activate R-Env
value=(sed -n 1p tmp.txt)
if [ "$value" = "0" ]
then
rm tmp.txt
else
cd "$(sed -n 1p tmp.txt)"
gzip *fastq
#
for i in *.gz
do
mv "$i" "${i%.*}_R1.fastq.gz";
done
#this adds the direction identifier "R1" to all the fastq.gzips
mkdir Data
mv *gz Data
~/Taxonomy3.R
cd Data
mv * ..
cd ..
rm -r Data
cd ..
sed '1d' tmp.txt > tmp2.txt
mv tmp2.txt tmp.txt
fi
Currently, it is only making the metadata file in the first barcode directory.

Answer 1

If you indent your code, things will get a lot clearer.
On the other hand, modifying your tmp.txt file this way id slow and dangerous. Better traverse its contents only reading it.
#!/bin/bash
source deactivate
source activate R-Env
for value in $(<tmp.txt)
do
cd "$value"
gzip *fastq
for i in *.gz
do
# This adds the direction identifier "R1" to all the fastq.gzips
mv "$i" "${i%.*}_R1.fastq.gz"
done
mkdir Data
mv *gz Data
~/Taxonomy3.R
mv Data/* .
rmdir Data
cd -
done
rm tmp.txt
With this reworked script you only need to create the tmp.txt file WITHOUT adding any marker at the end (in fact, you never needed it, you could have checked for empty file).
For each folder in the script, the operations you wanted are executed. I simplified some folder changing, minimizing it to the required ones for the R script to properly run. To go back, I used cd -, which goes to the previous folder, that way you can have more than one leven in your tmp.txt file.
Hope everything else is clear.