Skip to content

Fix bugs with workflow output and lineage#6254

Merged
bentsherman merged 4 commits intomasterfrom
fix-workflow-output-lineage
Jul 7, 2025
Merged

Fix bugs with workflow output and lineage#6254
bentsherman merged 4 commits intomasterfrom
fix-workflow-output-lineage

Conversation

@bentsherman
Copy link
Member

@bentsherman bentsherman commented Jul 4, 2025 •
edited
Loading

This PR fixes two bugs related to workflow outputs and lineage:

  1. Nested maps in published outputs were not properly normalized for the lineage / index file.
  2. Publishing a workflow output with a typical structure (list of maps containing files) causes a stack overflow error

@jorgee I have added a unit test demonstrating the stack overflow error with the LinEncoder. Can you recommend a fix?

TODO:

  • fix stack overflow error
  • document how non-task output files are handled

@bentsherman
Fix bugs with workflow output and lineage
38f1289 
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
@bentsherman bentsherman requested a review from jorgee July 4, 2025 17:52
@netlify
Copy link

netlify bot commented Jul 4, 2025 •
edited
Loading

✅ Deploy Preview for nextflow-docs-staging ready!

Name Link
🔨 Latest commit 6f0093a
🔍 Latest deploy log https://app.netlify.com/projects/nextflow-docs-staging/deploys/686bdbc93da89a00086c6e46
😎 Deploy Preview https://deploy-preview-6254--nextflow-docs-staging.netlify.app
📱 Preview on mobile
Toggle QR Code...

QR Code

Use your smartphone camera to open QR code link.

To edit notification comments on pull requests, go to your Netlify project configuration.

@jorgee
Fix encoding paths
97aa851 
Signed-off-by: jorgee <jorge.ejarque@seqera.io>
@jorgee
Copy link
Contributor

jorgee commented Jul 7, 2025 •
edited
Loading

The encoding of the Path class with GSON was creating a infinity loop creating the stackoverflow. I have added a GSON TypeAdapter to manage Path writes and reads to/from JSON as strings and seems to fix the issue.

@bentsherman
Copy link
Member Author

bentsherman commented Jul 7, 2025

@jorge thanks, can you approve it for your side? then I will add some docs and merge

@bentsherman bentsherman marked this pull request as ready for review July 7, 2025 14:37
@bentsherman bentsherman requested review from a team as code owners July 7, 2025 14:37
@bentsherman bentsherman merged commit 21a6470 into master Jul 7, 2025
23 checks passed
@bentsherman bentsherman deleted the fix-workflow-output-lineage branch July 7, 2025 14:45
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@jorgee jorgee jorgee approved these changes

Assignees

No one assigned

Labels

backport/25.04

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

2 participants

@bentsherman @jorgee