Fix bug in override of coordination directory - Githubissues

DataBiosphere / toil

A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.

http://toil.ucsc-cgl.org/.

Apache License 2.0

901 stars 240 forks source link

Fix bug in override of coordination directory #5153

Open gmloose opened 1 week ago

gmloose commented 1 week ago

The override of the coordination directory that a user could make was not applied correctly. Instead of setting self.coordination_dir the variable self.workDir would be modified. This has been fixed.

Changelog Entry

To be copied to the draft changelog by merger:

PR submitter writes their recommendation for a changelog entry here

Reviewer Checklist

[ ] Make sure it is coming from issues/XXXX-fix-the-thing in the Toil repo, or from an external repo.
- [ ] If it is coming from an external repo, make sure to pull it in for CI with:
```
contrib/admin/test-pr otheruser theirbranchname issues/XXXX-fix-the-thing
```
- [ ] If there is no associated issue, create one.
- [ ] Read through the code changes. Make sure that it doesn't have:
- [ ] Addition of trailing whitespace.
- [ ] New variable or member names in camelCase that want to be in snake_case.
- [ ] New functions without type hints.
- [ ] New functions or classes without informative docstrings.
- [ ] Changes to semantics not reflected in the relevant docstrings.
- [ ] New or changed command line options for Toil workflows that are not reflected in docs/running/{cliOptions,cwl,wdl}.rst
- [ ] New features without tests.
- [ ] Comment on the lines of code where problems exist with a review comment. You can shift-click the line numbers in the diff to select multiple lines.
- [ ] Finish the review with an overall description of your opinion.

Merger Checklist

[ ] Make sure the PR passes tests.
[ ] Make sure the PR has been reviewed since its last modification. If not, review it.
[ ] Merge with the Github "Squash and merge" feature.
- [ ] If there are multiple authors' commits, add Co-authored-by to give credit to all contributing authors.
[ ] Copy its recommended changelog entry to the Draft Changelog.
[ ] Append the issue number in parentheses to the changelog entry.

adamnovak commented 5 days ago

I'm not going to bother waiting for a re-test on this, I'm just going to merge it.

adamnovak commented 5 days ago

Actually we haven't ever had this pass full CI, so we probably should wait for that at least once.