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 unix.stackexchange.com/a/9499/34872 — user977828
– user977828, Commented Jan 17, 2019 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 mywiki.wooledge.org/WordSplitting — ilkkachu
– ilkkachu, Commented Jan 17, 2019 at 23:37

Chris Davies · Accepted Answer · 2019-01-17 23:36:01Z

2

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

answered Jan 17, 2019 at 23:36

Chris Davies

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