Fix #332: Disable FAIL_ON_EMPTY_BEANS for NF 25.10.x

[drernie]

Summary

• Disable SerializationFeature.FAIL_ON_EMPTY_BEANS on the shared Jackson ObjectMapper so writeMapToPackage.toJson survives Nextflow 25.10.x configs containing dynamic process directive closures (e.g. cpus = { task.attempt * 2 }) that transitively pull in the script binding's SecretsLoader$1 field.
• Add a regression test in QuiltProductTest that nests an anonymous-class object inside the config map and confirms toJson does not throw.
• Add make bump [LEVEL=patch|minor|major] (default patch) backed by wf/bump-version.sh, which rewrites version in build.gradle and commits.
• Bump to 1.0.1, pre-publish nf-quilt/dest-1.0.1 to udp-spec, update CHANGELOG.

Closes #332.

Test plan

• ./gradlew check passes (test + jacoco coverage gate)
• Verified the new regression test fails on main's ObjectMapper and passes with FAIL_ON_EMPTY_BEANS disabled
• make pkg-test WRITE_BUCKET=udp-spec published nf-quilt/dest-1.0.1 successfully

🤖 Generated with Claude Code

Greptile Summary

This PR fixes a serialization crash introduced in Nextflow 25.10.x where dynamic process directive closures (e.g. cpus = { task.attempt * 2 }) transitively pull in SecretsLoader$1 — an anonymous inner class with no bean properties — causing Jackson to throw when toJson is called. The fix disables SerializationFeature.FAIL_ON_EMPTY_BEANS on the shared ObjectMapper, accompanied by a targeted regression test, a make bump convenience target, and a version bump to 1.0.1.

Confidence Score: 4/5

Safe to merge; the core fix is minimal and correct, with only a trivial style issue in the new shell script.

All P2-only findings — the sole issue is an unescaped dot in the sed regex inside bump-version.sh, which is extremely unlikely to cause a false match in practice. The main bug fix and regression test are correct and well-scoped.

wf/bump-version.sh (minor sed escaping issue on line 29)

Important Files Changed

Filename	Overview
src/main/groovy/nextflow/quilt/QuiltProduct.groovy	Adds .disable(SerializationFeature.FAIL_ON_EMPTY_BEANS) to the shared ObjectMapper — correct targeted fix for NF 25.10.x closure serialization failure.
src/test/groovy/nextflow/quilt/QuiltProductTest.groovy	Adds regression test verifying toJson handles anonymous inner classes without throwing; assertion and Spock structure are correct.
wf/bump-version.sh	New version-bump helper script; minor: version string used unescaped as a sed regex, so dots act as wildcards (unlikely to cause real problems but not strictly correct).
Makefile	Adds bump phony target delegating to wf/bump-version.sh with configurable LEVEL; straightforward and correct.
build.gradle	Version bump from 1.0.0 to 1.0.1 — matches CHANGELOG and PR intent.
CHANGELOG.md	1.0.1 release notes added with accurate description of the fix and new make bump target.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A["NF 25.10.x config map\n(contains dynamic closures)"] --> B["QuiltProduct.writeMapToPackage"]
    B --> C["toJson(map)"]
    C --> D["OBJECT_WRITER.writeValueAsString(value)"]
    D --> E{FAIL_ON_EMPTY_BEANS?}
    E -- "enabled (main)" --> F["JsonMappingException\nSecretsLoader$1 has no properties"]
    E -- "disabled (this PR)" --> G["Serializes empty bean as {}"]
    G --> H["JSON string written to package"]

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_{Reviews (1): Last reviewed commit: "Update CHANGELOG for 1.0.1" | Re-trigger Greptile}

Greptile also left 1 inline comment on this PR.

[greptile-apps]

Unescaped dots in sed regex pattern

${OLD} (e.g. 1.0.1) is inserted directly into a sed regex, where . is a wildcard matching any character. In practice the surrounding single-quote context makes a false match extremely unlikely, but it is safer to escape the dots so the pattern is anchored to literal version strings.

Suggested change

	sed -i.bak "s/^version = '${OLD}'\$/version = '${NEW}'/" "$FILE"
	sed -i.bak "s/^version = '${OLD//./\\.}'\$/version = '${NEW}'/" "$FILE"