Help description for --moveOutputs is backward

[tikk3r]

I am a little confused about the --moveOutputs option for Toil. In the help it is described as

  --moveOutputs BOOL    When using a filesystem based job store, output files
                        are by default moved to the output directory, and a
                        symlink to the moved exported file is created at the
                        initial location. Setting this option to True instead
                        copies the files into the output directory. Applies to
                        filesystem-based job stores only. default=False

from the argument's name I would expect move behaviour to trigger if this parameter is set to True, but from the description it sounds like it triggers move behaviour if set to False and seems to imply it will automatically do so if it detects a certain type of jobstore.

Searching through the code for moveOutputs/moveExports I can't really find anything beyond this however, which also seems to only move if set to True.

toil/src/toil/jobStores/fileJobStore.py

Lines 379 to 382 in 7be5b65

	if self.moveExports:
	self._move_and_linkback(srcPath, destPath, executable=executable)
	else:
	atomic_copy(srcPath, destPath, executable=executable)

What would be the correct usage of this option?

┆Issue is synchronized with this Jira Story
┆Issue Number: TOIL-1810

[adamnovak]

I think the description text is backwards, possibly because I think we used to have a pair of --X and --no-X options here. If you use --moveOutputs=True, output files will get moved out of the job store and linked back if possible (which is when everything is on a filesystem). If you use --moveOutputs=False, that won't happen. The default is False, so nothing will be moved.

[tikk3r]

Thanks for clarifying!