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@tgelafr-pfzr tgelafr-pfzr commented Oct 22, 2025

Avoid deleting files ignored by git during pipelines sync.

Follow up on this issue: #2146, but avoids committing previously ignored files after switching to the TEMPLATE branch by keeping record of them before checkout.


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  • 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!

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codecov bot commented Oct 22, 2025

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 77.31%. Comparing base (6d6c996) to head (7104b03).

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@tgelafr-pfzr tgelafr-pfzr linked an issue Oct 22, 2025 that may be closed by this pull request
tgelafr-pfzr and others added 3 commits October 31, 2025 15:29
* functioning modifications and running tests

* helper functions for git file retrieval

* typos

* easier to read git add syntax

* small simplification

* Updated docstrings

* helper method for tests

* Refactoring for clarity

---------

Co-authored-by: Tatiana Gelaf Romer <[email protected]>
@tgelafr-pfzr tgelafr-pfzr force-pushed the bug/2146-gitignore-pipelines-sync branch from 7104b03 to 9aa835b Compare October 31, 2025 19:30
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nf-core sync silently deletes ignored files

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