bash - Build file path & expand wildcard from variables -

input_dir="~/path/to/dir/" file_ext=".fastq.gz" input_path="${input_dir}*${file_ext}"  echo "$input_path" # returns: ~/path/to/dir/*.fastq.gz  f in "$input_path" ; echo "$f" ; done  # returns: ~/path/to/dir/*.fastq.gz 

i expecting list of files extension .fastq.gz.

unfortunately, can't store glob pattern without losing information elements , aren't intended quoted. thus, 2 separate variables need used prefix , suffix at glob expansion time, glob expanded unquoted between them:

input_dir=~/path/to/dir/ # ~ must not in quotes; use $home if want quote file_ext=".fastq.gz" f in "${input_dir}"/*"${file_ext}";   echo "found $f" done 

note pattern -- "$prefix"/*"$suffix" -- both expansions within quotes; prevents expanded portions being subject string-splitting or glob expansion.

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if want store directive controlling how files identified in shell variable, consider array storing find arguments:

# array variable, 1 entry per argument find_args=( ~/path/to/dir -maxdepth 1 -name '*.fastq.gz' )  while ifs= read -r -d '' filename;   printf 'found %q\n' "$filename" done < <(find "${find_args[@]}" -print0) 

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another option perform expansion on, , store result in array variable, iterating on contents of variable in for loop:

input_dir=~/path/to/dir file_ext=.fastq.gz input_files=( "$input_dir"/*"$file_ext" )  f in "${input_files[@]}";   printf 'found %q\n' "$f" done 

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by way -- aware if glob expression matches no files, glob default evaluate expression itself. may wise check whether $f actually exists, handle case, or enable nullglob shell option (which disables behavior) @ top of script.

thus:

 shopt -s nullglob # prevents non-matching glob evaluating 

...or...

for f in "$input_dir"/*"$file_ext";   # lack of quotes acceptable here because [[ ]] suppresses string-splitting , globbing   [[ -e $f || -l $f ]] || { printf '%s\n' "$f not found" >&2; continue; }   printf 'found %q\n' "$f" done