+
Skip to content

Make jobs automatically resubmit for exit code 175 #3564

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 3 commits into from
May 21, 2025

Conversation

fntlnz
Copy link
Contributor

@fntlnz fntlnz commented May 13, 2025

When a pipeline's whole Linux process tree is in the process of being snapshotted via Fusion Snapshots and encounters an unrecoverable error the Fusion Snapshots runtime emits a specific exit code (175) to signal that to Nextflow.

This PR makes sure that users creating pipelines out of the template are including the exit code in their retry strategy.

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

When a pipeline process is in the process of being snapshotted via Fusion Snapshots
and encounters an unrecoverable error the Fusion Snapshots runtime emits
a specific exit code (175) to signal that to Nextflow.

This PR makes sure that users creating pipelines out of the template
are including the exit code in their retry strategy.
@fntlnz fntlnz force-pushed the snapshot-exit-code branch from 92dd020 to be9d768 Compare May 13, 2025 13:11
@maxulysse maxulysse requested a review from mirpedrol May 13, 2025 13:17
Copy link

codecov bot commented May 13, 2025

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 76.35%. Comparing base (dd6c4bf) to head (5e25e56).
Report is 4 commits behind head on dev.

☔ 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.

maxulysse added a commit to nf-core/sarek that referenced this pull request May 13, 2025
maxulysse added a commit to nf-core/sarek that referenced this pull request May 13, 2025
cf nf-core/tools#3564

<!--
# nf-core/sarek pull request

Many thanks for contributing to nf-core/sarek!

Please fill in the appropriate checklist below (delete whatever is not
relevant).
These are the most common things requested on pull requests (PRs).

Remember that PRs should be made against the dev branch, unless you're
preparing a pipeline release.

Learn more about contributing:
[CONTRIBUTING.md](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
-->

## PR checklist

- [ ] This comment contains a description of changes (with reason).
- [ ] If you've fixed a bug or added code that should be tested, add
tests!
- [ ] If you've added a new tool - have you followed the pipeline
conventions in the [contribution
docs](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the
[nf-core/test-datasets](https://github.com/nf-core/test-datasets)
repository.
- [ ] Make sure your code lints (`nf-core pipelines lint`).
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker
--outdir <OUTDIR>`).
- [ ] Check for unexpected warnings in debug mode (`nextflow run .
-profile debug,test,docker --outdir <OUTDIR>`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
- [ ] Output Documentation in `docs/output.md` is updated.
- [ ] `CHANGELOG.md` is updated.
- [ ] `README.md` is updated (including new tool citations and
authors/contributors).
Copy link
Member

@mirpedrol mirpedrol left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Should we add a comment indicating that 175 is for Fusion?
Otherwise LGTM, thanks!

@fntlnz
Copy link
Contributor Author

fntlnz commented May 14, 2025

Thanks @mirpedrol done via 41550cc

@fntlnz
Copy link
Contributor Author

fntlnz commented May 21, 2025

@mirpedrol is this ready to get merged? I don't have permissions :D

@mirpedrol
Copy link
Member

I sent you an invitation to join the nf-core organisation so that you can have permissions to merge. Let's wait for the tests to run and then we can merge :)

@mirpedrol mirpedrol merged commit b28be77 into nf-core:dev May 21, 2025
97 checks passed
@fntlnz
Copy link
Contributor Author

fntlnz commented May 21, 2025

Thank you @mirpedrol !

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.

2 participants
点击 这是indexloc提供的php浏览器服务,不要输入任何密码和下载