Copy paste files with certain extension from several subfolders in bash-CodePudding

Sorry for being naive, but I struggle for long time.

I have a directory that looks like this

dir 
 |--folder1
 |     |--- subfolder1
 |     |--- ...
 |     |--- subfolder100
 |
 |--folder2 
      |--- subfolder1
      |--- ...
      |--- subfolder100

Each folder and subfolder contains among others files with the extension ".fq.gz"

I want to list all these files, and then copy them to my destination folder

destination=/path/to/folder/

I have tried this but it does not work for me and I have no idea why

ls -R | grep "\.fq.gz" | xargs -I {} cp {} "$destination"

the error is no such file in the directory

CodePudding user response：

The best way to explain what goes wrong is to look what is actually fed into the xargs. So,

ls -R | grep "\.fq.gz"

This will give you a list of files without their path, so

file1.fq.gz
file2.fq.gz
...

and not

folder1/subfolder3/file1.fq.gz
folder2/subfolder7/file2.fq.gz
...

And that is why it doesn't work.

THE tool for this kind of actions is of course find, as in

find dir -name '*.fq.gz' -exec cp {} "$destination" \; -print

CodePudding user response：

You could do this at once with bash's globstar option (that requires bash version 4.0 or newer), without using any external command:

shopt -s globstar
cp **/*.fq.gz "$destination"