Fix Issues/3729: Cleanup nextflow files / directories after pipeline download #3750
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nf_core/pipelines/download/utils.py
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| tmp.cleanup() | ||
| except: # noqa: E722 | ||
| os.chdir(original_dir) | ||
| tmp.cleanup() |
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I don't think the cleanup is needed, because tempfile should take care of that already
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Yes :) The use of Tempdir is what was added in this PR. This solves the cleaning up in a nice way.
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but then you don't need tmp.cleanup(), it will be removed anyway.
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Ah right, sorry 🤦 I also was looking in the wrong function for a second, thinking we reference tmp outside the with context ...
Changed!
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Closes #3729
Adds a new context manager for creating and stepping into a temporary directory handles cleanup and stepping back upon errors. Wraps this around the call to
nextflow inspect.PR checklist
CHANGELOG.mdis updateddocsis updated