Merging fastq files by identifiers with a shell script - bash

Question

I have to merge files with the following naming pattern :
[SampleID]_[custom_ID01]_ID[RUN_ID]_L001_R1.fastq
[SampleID]_[custom_ID02]_ID[RUN_ID]_L002_R1.fastq
[SampleID]_[custom_ID03]_ID[RUN_ID]_L003_R1.fastq
[SampleID]_[custom_ID04]_ID[RUN_ID]_L004_R1.fastq
I need to merge all files with identical [SampleID] but different "Lanes" (L001-L004).
The following script works fine when directly run in the terminal:
custom_id="000"
RUN_ID="0025"
wd="/path/to/script/" # was missing/ incorrect
# get ALL sample identifiers
touch temp1.txt
for line in $wd/*.fastq ; do
fastq_identifier=$(echo "$line" | cut -d"_" -f1);
echo $fastq_identifier >> temp1.txt
done
# get all uniqe samples identical
cat temp1.txt | uniq > temp2.txt
input_var=$(cat temp2.txt)
# concatenate all fastq (different lanes) with identical identifier
for line in $input_var; do
cat $line*fastq >> $line"_"$custom_id"_ID"$Run_ID"_L001_R1.fastq"
done
rm temp1.txt temp2.txt;
But if I create a script file (concatenate_fastq.sh) and make it executable
$ chomd +x concatenate_fastq.sh
and run it
$ ./concatenate_fastq.sh
I got the following error:
$ concatenate_fastq.sh: line 17: /*.fastq_000_ID_L001_R1.fastq: Keine Berechtigung # = Permission denied
Thx to your hints below I solved the problem by fixing
wd=/path/to/script/

Answer 1

The immediate problem seems to be that wd is unset. If you script really genuinely contains exactly the line
wd="/path/to/script/"
then I would suspect invisible control characters in the script file (using a Windows editor is a common way to shoot yourself in the foot).
More generally, your script should cope correctly when the wildcard does not match any files. A common way to do that is to shopt -s nullglob but the subsequent script would still need adaptation then.
Refactoring the script to loop only over actual matches would help avoid trouble. Perhaps something like this:
shopt -s nullglob # bashism
printf '%s\n' "$wd"/*.fastq |
cut -d_ -f1 |
uniq |
while read -r line; do
cat "$line"*fastq >> "${line}_${custom_id}_ID${Run_ID}_L001_R1.fastq"
done
You'll notice that this simplifies the script tremendously, and avoids the pesky temporary files.

Answer 2

I solved it with:
if [ $# -ne 3 ] ; then
echo -e "Usage: $0 {path_to_working_directory} {custom_ID:Z+} {run_ID:ZZZZ}\n"
exit 1
fi
cwd=$(pwd)
wd=$1
custom_id=$2
RUN_ID=$3
folder=$(basename $wd)
input_var=$(ls *fastq | cut --fields 1 -d "_" | uniq)
for line in $input_var; do
cat $line*fastq >> $line"_"$custom_id"_ID"$RUN_ID"_L001_R1.fastq"
done