Make jobs automatically resubmit for exit code 175#3564
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mirpedrol merged 3 commits intonf-core:devfrom May 21, 2025
Merged
Make jobs automatically resubmit for exit code 175#3564mirpedrol merged 3 commits intonf-core:devfrom
mirpedrol merged 3 commits intonf-core:devfrom
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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.
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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).
mirpedrol
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Should we add a comment indicating that 175 is for Fusion?
Otherwise LGTM, thanks!
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Thanks @mirpedrol done via 41550cc |
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@mirpedrol is this ready to get merged? I don't have permissions :D |
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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 :) |
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Thank you @mirpedrol ! |
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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
CHANGELOG.mdis updateddocsis updated