bash script split file names

Question

I have the following bash script:

#!/bin/bash

for r in $(find . -name "*.fastq");
do

  cat <<EOF
  #qsub <<EOF
#!/bin/bash -l

#PBS -N $r

EOF

done

Unfortunately, all filename get split:

> sh  cFiltering_pbs.sh 
  #qsub <<EOF
#!/bin/bash -l

#PBS -N ./76A

  #qsub <<EOF
#!/bin/bash -l

#PBS -N Paired.fastq

  #qsub <<EOF
#!/bin/bash -l

#PBS -N ./104A

  #qsub <<EOF
#!/bin/bash -l

#PBS -N Paired.fastq

Here is the find output:

find . -name "*.fastq"
./76A Paired.fastq
./104A Paired.fastq

What did I miss?

yes, they're all in the same directory. I solved it with this https://unix.stackexchange.com/a/9499/34872 — user977828, Jan 17 '19 at 23:26
see: Why does my shell script choke on whitespace or other special characters? and Recursively iterate through files in a directory and also http://mywiki.wooledge.org/WordSplitting — ilkkachu, Jan 17 '19 at 23:37

score 2 · Answer 1 · answered Jan 17 '19 at 23:36

Instead of using find you can simply loop through the files themselves. Notice that I have double-quoted "$r"; you need to do that to keep the space in the filenames intact and unparsed by the shell.

for r in *.fastq
do
    # Stuff using "$r"...
    :
done

bash script split file names

1 Answers1