Release 1.0.0 (#323)

[drernie]

Summary

First release published to the Nextflow Plugin Registry. Bumps the plugin version to 1.0.0, consolidating the unpublished 0.9.2 intermediate into the registry-migration release.

This is the final PR in the migration tracked by #323. It bundles three previously-merged PRs:

• Fix Jackson OffsetDateTime serialization for Nextflow 24.10+ (#321) #322 — Jackson OffsetDateTime serialization fix for Nextflow 24.10+
• Migrate to new Nextflow plugin build system (#323) #324 — Migrate to the new io.nextflow.nextflow-plugin Gradle build system
• Docs + restore JaCoCo coverage gate (#323) #327 — Docs refresh + restore JaCoCo 70% line-coverage gate

Changes

• build.gradle: version = '0.9.2' -> '1.0.0'
• CHANGELOG.md: rename [0.9.2] section to [1.0.0] and add note about Nextflow Plugin Registry as the publishing channel
• README-DEV.md: bump example nf-quilt@0.9.2 references to @1.0.0

The dest-1.0.0 test package has been pre-published to s3://udp-spec so QuiltPkgTest > should confirm contents of dest URI passes in CI.

Post-merge manual steps (human)

The actual registry publish is intentionally NOT automated in this PR:

1. git tag 1.0.0 && git push origin 1.0.0
2. export NPR_API_KEY=... && ./gradlew releasePlugin
3. Verify the plugin appears on https://registry.nextflow.io
4. Close Nextflow version mismatches? #321 with the registry URL

Test plan

• ./gradlew test passes
• ./gradlew check passes (JaCoCo gate satisfied)
• ./gradlew packagePlugin produces build/distributions/nf-quilt-1.0.0.zip
• make pkg-test WRITE_BUCKET=udp-spec published nf-quilt/dest-1.0.0 to udp-spec
• CI green

Closes #323
Closes #321

🤖 Generated with Claude Code

Greptile Summary

This PR bumps the plugin version from 0.9.2 to 1.0.0 across build.gradle, CHANGELOG.md, and README-DEV.md in preparation for the first publish to the Nextflow Plugin Registry. All 0.9.2 references have been consistently updated and no stale occurrences remain in the repository.

Confidence Score: 4/5

Safe to merge — changes are purely a version bump with no functional code modifications.

Only P2 finding (stale comment in build.gradle); no logic, security, or correctness issues present.

No files require special attention beyond the minor stale comment in build.gradle line 17.

Important Files Changed

Filename	Overview
build.gradle	Version bumped from 0.9.2 to 1.0.0; stale "until the 1.0.0 release" comment left in place (P2)
CHANGELOG.md	Section heading renamed from [0.9.2] to [1.0.0]; registry publication note prepended — no issues found
README-DEV.md	Four nf-quilt version references updated from 0.9.2 to 1.0.0 in example commands — no issues found

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A["build.gradle\nversion = '1.0.0'"] --> B["./gradlew packagePlugin\nnf-quilt-1.0.0.zip"]
    B --> C["git tag 1.0.0\ngit push origin 1.0.0"]
    C --> D["./gradlew releasePlugin\nNPR_API_KEY set"]
    D --> E["Nextflow Plugin Registry\nregistry.nextflow.io"]
    F["CHANGELOG.md\n1.0.0 section"] -.-> B
    G["README-DEV.md\nnf-quilt at 1.0.0"] -.-> E

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_{Reviews (1): Last reviewed commit: "Release 1.0.0" | Re-trigger Greptile}

Greptile also left 1 inline comment on this PR.

[greptile-apps]

Stale comment now that 1.0.0 has shipped

The inline comment "Keep in sync with any references in CHANGELOG / README until the 1.0.0 release" refers to a milestone that this PR itself completes. The guidance no longer applies and the phrase could confuse future contributors who bump the version again.

Suggested change

	// Keep in sync with any references in CHANGELOG / README until the 1.0.0 release.
	// Plugin version: bump here to release a new version.

[drernie]

Fixed — dropped the stale pre-1.0 sync comment.

[github-actions]

🦙 MegaLinter status: ✅ SUCCESS

Descriptor	Linter	Files	Fixed	Errors	Warnings	Elapsed time
✅ MARKDOWN	markdown-link-check	2		0	0	2.82s
✅ MARKDOWN	markdown-table-formatter	2	1	0	0	0.18s
✅ REPOSITORY	checkov	yes		no	no	12.0s
✅ REPOSITORY	git_diff	yes		no	no	0.01s
✅ REPOSITORY	grype	yes		no	no	31.65s
✅ REPOSITORY	secretlint	yes		no	no	0.47s
✅ REPOSITORY	syft	yes		no	no	1.1s
✅ REPOSITORY	trivy	yes		no	no	8.14s
✅ REPOSITORY	trivy-sbom	yes		no	no	0.08s
✅ REPOSITORY	trufflehog	yes		no	no	2.26s

See detailed report in MegaLinter reports
Set VALIDATE_ALL_CODEBASE: true in mega-linter.yml to validate all sources, not only the diff