I am trying to download a bunch of files and rename them as I go. the download portion works correctly, but i can't get it to rename the files. This is the script I'm using:
COUNTER=0
for (( i = 696; i <= 773; i++ ))
do
fastq-dump --split-3 --accession SRR546$i
mv SRR546"$i"_1 ./"$COUNTER"mVD_SRR546$i_1
mv SRR546"$i"_2 ./"$COUNTER"mVD_SRR546$i_2
gzip *.fastq
COUNTER=$[COUNTER + 1]
done
This will correctly download the file SRR546696, SRR546697 etc. but does nothing to rename them.
I also tried using:
rename 's/SRR/"$COUNTER"mVD_SRR/' *.fastq
but this also did nothing.