Deprecated: Function get_magic_quotes_gpc() is deprecated in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 99

Deprecated: The each() function is deprecated. This message will be suppressed on further calls in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 619

Warning: Cannot modify header information - headers already sent by (output started at /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php:99) in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 1169

Warning: Cannot modify header information - headers already sent by (output started at /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php:99) in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 1176

Warning: Cannot modify header information - headers already sent by (output started at /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php:99) in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 1176

Warning: Cannot modify header information - headers already sent by (output started at /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php:99) in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 1176

Warning: Cannot modify header information - headers already sent by (output started at /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php:99) in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 1176

Warning: Cannot modify header information - headers already sent by (output started at /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php:99) in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 1176

Warning: Cannot modify header information - headers already sent by (output started at /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php:99) in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 1176

Warning: Cannot modify header information - headers already sent by (output started at /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php:99) in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 1176

Warning: Cannot modify header information - headers already sent by (output started at /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php:99) in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 1176

Warning: Cannot modify header information - headers already sent by (output started at /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php:99) in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 1176

Warning: Cannot modify header information - headers already sent by (output started at /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php:99) in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 1176

Warning: Cannot modify header information - headers already sent by (output started at /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php:99) in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 1176

Warning: Cannot modify header information - headers already sent by (output started at /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php:99) in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 1176

Warning: Cannot modify header information - headers already sent by (output started at /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php:99) in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 1176

Warning: Cannot modify header information - headers already sent by (output started at /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php:99) in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 1176

Warning: Cannot modify header information - headers already sent by (output started at /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php:99) in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 1176

Warning: Cannot modify header information - headers already sent by (output started at /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php:99) in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 1176

Warning: Cannot modify header information - headers already sent by (output started at /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php:99) in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 1176

Warning: Cannot modify header information - headers already sent by (output started at /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php:99) in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 1176

Warning: Cannot modify header information - headers already sent by (output started at /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php:99) in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 1176

Warning: Cannot modify header information - headers already sent by (output started at /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php:99) in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 1176

Warning: Cannot modify header information - headers already sent by (output started at /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php:99) in /hermes/walnacweb04/walnacweb04ab/b2791/pow.jasaeld/htdocs/De1337/nothing/index.php on line 1176
8000 Avoid deleting files ignored by git during `pipelines sync` by tgelafr-pfzr · Pull Request #3847 · nf-core/tools · GitHub
Nothing Special   »   [go: up one dir, main page]

Skip to content

Conversation

tgelafr-pfzr
Copy link
@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.


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!

tgelafr-pfzr and others added 2 commits October 22, 2025 09:47
* 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 <romert01@pfizer.com>
@codecov
Copy link
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).

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@tgelafr-pfzr tgelafr-pfzr linked an issue Oct 22, 2025 that may be closed by this pull request
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

nf-core sync silently deletes ignored files

2 participants

0