Prioritize Google Batch API exit codes with fallback to .exitcode file#6498
Merged
pditommaso merged 3 commits intomasterfrom Oct 21, 2025
Merged
Prioritize Google Batch API exit codes with fallback to .exitcode file#6498pditommaso merged 3 commits intomasterfrom
pditommaso merged 3 commits intomasterfrom
Conversation
✅ Deploy Preview for nextflow-docs-staging ready!
To edit notification comments on pull requests, go to your Netlify project configuration. |
Signed-off-by: jorgee <jorge.ejarque@seqera.io>
Signed-off-by: jorgee <jorge.ejarque@seqera.io>
Signed-off-by: jorgee <jorge.ejarque@seqera.io>
17ef676 to
ce7eb22
Compare
pditommaso
approved these changes
Oct 21, 2025
This was referenced Jan 29, 2026
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Fixes #6481
This PR improves exit code handling for Google Batch tasks by prioritizing the exit code from the Google Batch API over the
.exitcodefile, with graceful fallback when API data is unavailable.Changes
.exitcodefile when API doesn't provide exit code dataRationale
The Google Batch API provides more reliable exit codes than the
.exitcodefile, especially when tasks fail early (e.g., Fusion mount failures with exit code 175). In these cases, the.exitcodefile may not be written, causing Nextflow to reportInteger.MAX_VALUE(displayed as-). By checking the API first, we ensure accurate exit code reporting consistent with AWS Batch and Azure Batch executors.