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Fix Issues/3729: Cleanup nextflow files / directories after pipeline download#3750

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JulianFlesch merged 8 commits into
nf-core:devfrom
JulianFlesch:issues/3729-download-cleanup
Oct 8, 2025
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Fix Issues/3729: Cleanup nextflow files / directories after pipeline download#3750
JulianFlesch merged 8 commits into
nf-core:devfrom
JulianFlesch:issues/3729-download-cleanup

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@JulianFlesch

@JulianFlesch JulianFlesch commented Sep 9, 2025 •
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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

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

@JulianFlesch JulianFlesch requested a review from a team September 9, 2025 09:08
@JulianFlesch JulianFlesch self-assigned this Sep 9, 2025
@JulianFlesch JulianFlesch added enhancement download nf-core download labels Sep 9, 2025
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codecov Bot commented Sep 9, 2025 •
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Codecov Report

❌ Patch coverage is 90.90909% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 77.36%. Comparing base (c5af93a) to head (e397d50).
⚠️ Report is 9 commits behind head on dev.

Files with missing lines Patch % Lines
nf_core/pipelines/download/download.py 91.66% 1 Missing ⚠️
nf_core/pipelines/download/utils.py 90.00% 1 Missing ⚠️

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@JulianFlesch JulianFlesch moved this from Todo to In Review in nf-core infrastructure projects Sep 9, 2025
mashehu
mashehu reviewed Sep 29, 2025
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Comment thread nf_core/pipelines/download/utils.py Outdated
mashehu
mashehu reviewed Sep 29, 2025
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Comment thread nf_core/pipelines/download/utils.py Outdated
tmp.cleanup()
except: # noqa: E722
os.chdir(original_dir)
tmp.cleanup()

@mashehu mashehu Sep 29, 2025

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I don't think the cleanup is needed, because tempfile should take care of that already

@JulianFlesch JulianFlesch Oct 7, 2025

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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.

@mashehu mashehu Oct 7, 2025

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but then you don't need tmp.cleanup(), it will be removed anyway.

@JulianFlesch JulianFlesch Oct 7, 2025

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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!

@JulianFlesch JulianFlesch added this to the 3.4.0 milestone Oct 7, 2025
@github-project-automation github-project-automation Bot moved this from In Review to In Progress in nf-core infrastructure projects Oct 7, 2025
@JulianFlesch JulianFlesch merged commit 7a02ae6 into nf-core:dev Oct 8, 2025
199 of 202 checks passed
@github-project-automation github-project-automation Bot moved this from In Progress to Done in nf-core infrastructure projects Oct 8, 2025
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@mashehu mashehu mashehu approved these changes

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@JulianFlesch JulianFlesch

Labels

download nf-core download enhancement

Projects

nf-core infrastructure projects
Status: Done

Milestone

3.4.0

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3 participants

@JulianFlesch @mashehu @ewels