Fix Jackson OffsetDateTime serialization for Nextflow 24.10+ (#321)

[drernie]

Summary

• Register JavaTimeModule and disable WRITE_DATES_AS_TIMESTAMPS on the ObjectMapper used by writeMapToPackage, so java.time.OffsetDateTime (returned by Nextflow 24.10+ WorkflowMetadata.toMap() for start/complete) serializes as ISO-8601 strings.
• Add jackson-datatype-jsr310:2.19.0 dependency to match the existing jackson-databind version.
• Restore working test input package (nf-core-gallery was deleted; switched to udp-spec/nf-quilt/source).
• Bump version to 0.9.2.

Why

Without the module registered, toJson threw Java 8 date/time type java.time.OffsetDateTime not supported by default. The exception was caught in writeMapToPackage, so the pipeline appeared to finish — but nf-quilt/config.json, params.json, and workflow.json were never written, producing packages with degraded metadata.

Closes #321

Test plan

• Pipeline run produces all three JSONs in the published package — verified at s3://udp-spec/nf-quilt/dest-0.9.2/nf-quilt/{config,params,workflow}.json
• start/complete in workflow.json are ISO-8601 strings (e.g. 2026-04-29T08:09:29.334938-07:00), not epoch decimals
• Existing test suite passes — all 10 CI jobs green (Linux/macOS/Windows × JDK 17/19/21) against pinned NXF_VER=24.10.3

🤖 Generated with Claude Code

Greptile Summary

This PR fixes a Jackson serialization failure for java.time.OffsetDateTime values returned by Nextflow 24.10+ workflow metadata, which silently prevented config.json, params.json, and workflow.json from being written to published packages. The fix registers JavaTimeModule and disables WRITE_DATES_AS_TIMESTAMPS on the static ObjectMapper, adds the matching jackson-datatype-jsr310:2.19.0 dependency, adds a targeted regression test, updates the test input package reference, and bumps the version to 0.9.2.

Confidence Score: 5/5

Safe to merge — the fix is correct, well-tested, and self-contained with no side effects on existing serialization behaviour.

All changes are focused and correct: JavaTimeModule + disabling WRITE_DATES_AS_TIMESTAMPS is the standard Jackson pattern for ISO-8601 OffsetDateTime output; the dependency version matches jackson-databind; a regression test covers both the positive and negative cases; the previous thread's concern about WRITE_DATES_AS_TIMESTAMPS was already addressed in the current HEAD.

No files require special attention.

Important Files Changed

Filename	Overview
plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy	Registers JavaTimeModule and disables WRITE_DATES_AS_TIMESTAMPS on the static ObjectMapper to fix OffsetDateTime serialization; changes are correct and thread-safe.
build.gradle	Adds jackson-datatype-jsr310:2.19.0 to match existing jackson-databind version; correct dependency for JavaTimeModule.
plugins/nf-quilt/src/test/nextflow/quilt/QuiltProductTest.groovy	Adds a regression test for OffsetDateTime ISO-8601 serialization; checks both the positive (ISO string present) and negative (no numeric epoch for start key) cases.
main.nf	Replaces deleted nf-core-gallery reference with udp-spec/nf-quilt/source package; removes unused params.hash variable.
wf/main.gallery.nf	Deleted since it referenced the no-longer-available nf-core-gallery bucket.
plugins/nf-quilt/src/resources/META-INF/MANIFEST.MF	Bumps Plugin-Version from 0.9.1 to 0.9.2; consistent with changelog and README-DEV updates.

Sequence Diagram

sequenceDiagram
    participant NF as Nextflow 24.10+
    participant QP as QuiltProduct
    participant OM as ObjectMapper
    participant JTM as JavaTimeModule
    participant PKG as QuiltPackage

    NF->>QP: WorkflowMetadata.toMap()<br/>(start/complete as OffsetDateTime)
    QP->>OM: toJson(map)
    OM->>JTM: serialize(OffsetDateTime)
    JTM-->>OM: "2026-04-29T08:09:29.334938-07:00"
    OM-->>QP: JSON string (ISO-8601)
    QP->>PKG: writeMapToPackage(workflow.json)
    PKG-->>NF: Package published with metadata

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[github-actions]

🦙 MegaLinter status: ✅ SUCCESS

Descriptor	Linter	Files	Fixed	Errors	Warnings	Elapsed time
✅ MARKDOWN	markdown-link-check	2		0	0	2.6s
✅ MARKDOWN	markdown-table-formatter	2	0	0	0	0.14s
✅ REPOSITORY	checkov	yes		no	no	9.99s
✅ REPOSITORY	git_diff	yes		no	no	0.0s
✅ REPOSITORY	grype	yes		no	no	38.06s
✅ REPOSITORY	secretlint	yes		no	no	0.43s
✅ REPOSITORY	syft	yes		no	no	1.13s
✅ REPOSITORY	trivy	yes		no	no	4.92s
✅ REPOSITORY	trivy-sbom	yes		no	no	0.08s
✅ REPOSITORY	trufflehog	yes		no	no	2.27s

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[drernie]

@greptileai

[Copilot]

Pull request overview

Fixes JSON serialization of Nextflow 24.10+ workflow metadata containing java.time.OffsetDateTime, ensuring config.json, params.json, and workflow.json are written correctly by the nf-quilt plugin.

Changes:

• Register Jackson JavaTimeModule and disable timestamp serialization on the shared ObjectMapper.
• Add jackson-datatype-jsr310:2.19.0 to match the existing Jackson databind version.
• Bump plugin version to 0.9.2, update changelog, and refresh the example main.nf input package.

Reviewed changes

Copilot reviewed 4 out of 5 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
plugins/nf-quilt/src/resources/META-INF/MANIFEST.MF	Bumps plugin version to 0.9.2.
plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy	Configures Jackson for Java time types to prevent OffsetDateTime serialization failures.
build.gradle	Adds jackson-datatype-jsr310 dependency for Java time support.
main.nf	Updates example/test input package URI.
CHANGELOG.md	Records the release notes for the serialization fix and input package change.

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[drernie]

@greptile-apps