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Merged
merged 1 commit into from
May 13, 2025

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@fntlnz fntlnz commented May 13, 2025

When a process is 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 running RNASeq
are including the exit code in their retry strategy.

related to nf-core/tools#3564

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
  • If necessary, also make a PR on the nf-core/rnaseq branch on the 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).

@fntlnz fntlnz changed the title exit code for unrecoverable snapshots errors Make jobs automatically resubmit for exit code 175 May 13, 2025
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.0.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

When a process is 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 running RNASeq
are including the exit code in their retry strategy.
@fntlnz fntlnz force-pushed the snapshot-exit-code branch from 9140dd4 to c83289f Compare May 13, 2025 14:05
@SPPearce SPPearce enabled auto-merge May 13, 2025 14:20
@SPPearce SPPearce merged commit 15c160f into nf-core:dev May 13, 2025
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3 participants