Fix Jackson OffsetDateTime serialization for Nextflow 24.10+ (#321) (#322)

## 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
- [x] 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`
- [x] `start`/`complete` in `workflow.json` are ISO-8601 strings (e.g.
`2026-04-29T08:09:29.334938-07:00`), not epoch decimals
- [x] 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](https://claude.com/claude-code)

<!-- greptile_comment -->

<h3>Greptile Summary</h3>

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.

<h3>Confidence Score: 5/5</h3>

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.

<h3>Important Files Changed</h3>

| 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. |

</details>

<h3>Sequence Diagram</h3>

```mermaid
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
```

<sub>Reviews (3): Last reviewed commit: ["address PR review
feedback"](50c071d)
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---------

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: drernie

CHANGELOG.md

@@ -1,9 +1,12 @@
 # Changelog
 
-## [0.9.2] 2025-05-XX
+## [0.9.2] 2026-04-29
 
 - Use "package" as default prefix
 - Modernize main*.nf files
+- Fix Jackson serialization of `java.time.OffsetDateTime` from Nextflow 24.10+ workflow metadata (#321)
+- Restore working test input package (replace deleted `nf-core-gallery` with `udp-spec/nf-quilt/source`)
+- Remove `wf/main.gallery.nf` (referenced the deleted `nf-core-gallery` bucket)
 
 ## [0.9.1] 2024-12-24
 

README-DEV.md

@@ -15,7 +15,7 @@ From the command-line, do, e.g.:
 
 ```bash
 export LOG4J_DEBUG=true  # for verbose logging
-export VERSION=0.9.1
+export VERSION=0.9.2
 export NXF_PLUGINS_TEST_REPOSITORY=https://github.com/quiltdata/nf-quilt/releases/download/$(VERSION)/nf-quilt-$(VERSION)-meta.json
 nextflow run main.nf -plugins nf-quilt@$(VERSION)
 ```

build.gradle

@@ -101,6 +101,7 @@ allprojects {
         // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sec:module_replacement
         implementation "org.${groovySource}.groovy:groovy-all:$groovyVersion"
         implementation 'com.fasterxml.jackson.core:jackson-databind:2.19.0'
+        implementation 'com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.19.0'
         implementation 'com.upplication:s3fs:2.2.2'
 
         modules {

main.nf

@@ -2,8 +2,7 @@
 /* groovylint-disable CompileStatic */
 
 nextflow.enable.dsl = 2
-params.hash =  '90527238d0e2ebc9e1ba98265e5f79440b557697fed3f0d29ec95942cbb4e4e0'
-params.input = "quilt+s3://nf-core-gallery#package=test/observer@${params.hash}&catalog=demo.quiltdata.com"
+params.input = 'quilt+s3://udp-spec#package=nf-quilt/source@c4e44f6932'
 params.outdir = '/var/tmp'
 
 process transfer {

plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy

@@ -17,6 +17,8 @@ package nextflow.quilt
 
 import com.fasterxml.jackson.databind.ObjectMapper
 import com.fasterxml.jackson.databind.ObjectWriter
+import com.fasterxml.jackson.databind.SerializationFeature
+import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule
 import nextflow.quilt.jep.QuiltPackage
 import nextflow.quilt.jep.QuiltParser
 import nextflow.quilt.nio.QuiltPath
@@ -97,6 +99,8 @@ ${nextflow}
     ]
 
     private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
+        .registerModule(new JavaTimeModule())
+        .disable(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS)
     private static final ObjectWriter OBJECT_WRITER = OBJECT_MAPPER.writerWithDefaultPrettyPrinter()
     static String toJson(Object value) {
         String result = OBJECT_WRITER.writeValueAsString(value)

plugins/nf-quilt/src/resources/META-INF/MANIFEST.MF

@@ -1,7 +1,7 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.quilt.QuiltPlugin
 Plugin-Id: nf-quilt
-Plugin-Version: 0.9.1
+Plugin-Version: 0.9.2
 Plugin-Provider: Quilt Data
 Plugin-Requires: >=24.10.0
 

plugins/nf-quilt/src/test/nextflow/quilt/QuiltProductTest.groovy

@@ -28,6 +28,8 @@ import nextflow.quilt.jep.QuiltPackage
 import java.nio.file.Files
 import java.nio.file.Path
 import java.nio.file.Paths
+import java.time.OffsetDateTime
+import java.time.ZoneOffset
 import groovy.transform.CompileDynamic
 import spock.lang.Ignore
 import spock.lang.IgnoreIf
@@ -95,6 +97,23 @@ class QuiltProductTest extends QuiltSpecification {
         product.displayName().replace('%2f', '/') == testURI
     }
 
+    void 'toJson serializes OffsetDateTime as ISO-8601 string'() {
+        // Regression test for #321: Nextflow 24.10+ returns OffsetDateTime
+        // for workflow start/complete; without JavaTimeModule + disabling
+        // WRITE_DATES_AS_TIMESTAMPS, Jackson would either throw or emit
+        // a numeric epoch like 1.735040400E9.
+        given:
+        OffsetDateTime when = OffsetDateTime.of(2026, 1, 2, 3, 4, 5, 0, ZoneOffset.UTC)
+        Map map = [start: when, complete: when]
+
+        when:
+        String json = QuiltProduct.toJson(map)
+
+        then:
+        json.contains('"2026-01-02T03:04:05Z"')
+        !(json =~ /"start"\s*:\s*[0-9]/)
+    }
+
     void 'should generate solid string for timestamp from now'() {
         when:
         def now = QuiltProduct.now()