Ensembl/ensembl-hive

Use cd ... || exit in case cd fails.

Problematic code:

cd generated_files
rm -r *.c

func(){
  cd foo
  do_something
}

Correct code:

cd generated_files || exit
rm -r *.c

# For functions, you may want to use return:
func(){
  cd foo || return
  do_something
}

Rationale:

cd can fail for a variety of reasons: misspelled paths, missing directories, missing permissions, broken symlinks and more.

If/when it does, the script will keep going and do all its operations in the wrong directory. This can be messy, especially if the operations involve creating or deleting a lot of files.

To avoid this, make sure you handle the cases when cd fails. Ways to do this include

• cd foo || exit as suggested to just abort immediately
• if cd foo; then echo "Ok"; else echo "Fail"; fi for custom handling
• <(cd foo && cmd) as an alternative to <(cd foo || exit; cmd) in <(..), $(..) or ( )

Exceptions:

ShellCheck does not give this warning when cd is on the left of a || or &&, or the condition of a if, while or until loop. Having a set -e command anywhere in the script will disable this message, even though it won't necessarily prevent the issue.

If you are accounting for cd failures in a way shellcheck doesn't realize, you can disable this message with a [[directive]].

Notice

Original content from the ShellCheck https://github.com/koalaman/shellcheck/wiki.