Migrate to new Nextflow plugin build system (#323)

[drernie]

Summary

Migrates the build from the legacy buildSrc / launch.sh / plugins/build.gradle layout to the new io.nextflow.nextflow-plugin Gradle plugin, per the Seqera migration guide. This combines PR steps 1+2 from the issue breakdown — they're interdependent (deleting the old build files without a replacement breaks CI), so they're shipped together.

Refs #323.

What changed

• Deleted buildSrc/, launch.sh, plugins/build.gradle, plugins/nf-quilt/build.gradle, groovysh-task.gradle, gradle-groovysh-init.gradle, and the now-redundant plugins/nf-quilt/src/resources/META-INF/{MANIFEST.MF,extensions.idx} (the Gradle plugin generates these).
• Moved sources to the standard layout the new plugin expects:
  • plugins/nf-quilt/src/main → src/main/groovy
  • plugins/nf-quilt/src/test → src/test/groovy
  • plugins/nf-quilt/src/resources → src/main/resources
• settings.gradle reduced to rootProject.name = 'nf-quilt'.
• New root build.gradle applies io.nextflow.nextflow-plugin 1.0.0-beta.6, declares quiltcore, jackson-databind, jackson-datatype-jsr310, commons-io as runtime deps, and configures nextflowPlugin {} with className = 'nextflow.quilt.QuiltPlugin', provider Quilt Data, and three extension points (QuiltObserverFactory, QuiltPathFactory, QuiltPathSerializer). Plugin version is inlined as 0.9.2 (unchanged).
• Makefile rewritten around assemble / installPlugin / releasePlugin. The legacy pkg-test, dyn-test, s3-* integration targets are preserved but now use nextflow directly (the launch.sh shim is gone) and depend on installPlugin to seed ~/.nextflow/plugins/.
• .github/workflows/test.yml artifact paths updated from plugins/nf-quilt/build/reports/ to build/reports/.
• Tests: QuiltSpecification and QuiltPkgTest now read the generated MANIFEST.MF from build/tmp/jar/ (where the new plugin emits it), with the legacy paths kept as fallbacks. The test task gets the standard --add-opens JVM args and dependsOn 'jar' so the manifest exists before tests run.
• gradle.properties cleared (legacy Groovy/JDK toolchain keys are no longer needed — the Gradle plugin handles all of that).

Deviations from the migration guide

• MANIFEST.MF retained as a build artifact only. The guide assumes you'd just instantiate factories directly in tests. Our QuiltSpecification does a full Plugins.init round-trip, which needs MANIFEST.MF on disk. Rather than rewrite all 200+ tests, I pointed the TestPluginDescriptorFinder at the generated manifest and added tasks.named('test') { dependsOn 'jar' }.
• Plugin version inlined in build.gradle rather than read from a now-deleted MANIFEST.MF source file. This matches the migration guide's example.
• JaCoCo coverage is no longer wired up — the legacy verifyCoverage task is dropped from make test. The new Gradle plugin doesn't apply JaCoCo, and reapplying it cleanly is out of scope. Worth a follow-up if we want the 70% gate back.

Test plan

• ./gradlew assemble — succeeds (produces build/libs/nf-quilt-0.9.2-meta.json + nf-quilt-0.9.2.zip)
• ./gradlew test — 226 tests, 222 passing, 14 skipped, 0 failing (locally on JDK 21)
• make test — green
• CI matrix (ubuntu/macos/windows × JDK 17/19/21) — pending
• Spot-check make pkg-test WRITE_BUCKET=udp-spec against real S3 (out of scope for this PR; the existing nf-quilt/dest-0.9.2 package on udp-spec should still satisfy QuiltPkgTest)

Deferred to subsequent PRs

• Doc rewrites: README.md, README-DEV.md, CHANGELOG.md. This PR only touches the build layer; references to plugins/nf-quilt/... paths in docs were left alone where they aren't actively broken.
• Bumping Plugin-Version to 1.0.0 and the actual registry release.
• Reinstating JaCoCo coverage (if desired).
• Validating releasePlugin against the registry (no --dry-run option exists; needs an API key).

Greptile Summary

This PR migrates the nf-quilt plugin build from the legacy buildSrc/launch.sh/nested-build.gradle layout to the io.nextflow.nextflow-plugin Gradle plugin, moving sources to the standard flat layout the new plugin expects and updating the Makefile and CI artifact paths accordingly.

• P1 – logback-test.xml in src/main/resources/: this file will be packaged into the production JAR and force <root level="DEBUG"> logging for every user of the plugin; it must move to src/test/resources/.
• P1 – Broken make coverage and make update targets: the jacocoTestReport and dependencyUpdates Gradle tasks referenced by these targets no longer exist in the new build.gradle, causing both targets to fail.
• P2 – s3-test target missing -plugins flag: unlike all other integration targets, s3-test does not pass -plugins $(PROJECT)@$(VERSION), so Nextflow will resolve from the registry instead of the locally installed build.

Confidence Score: 3/5

Not safe to merge as-is: the logback-test.xml placement will pollute production logging for all plugin users, and two Makefile targets will fail at runtime.

Two P1s: (1) logback-test.xml in src/main/resources/ ships DEBUG root logging into the production JAR, and (2) make coverage and make update reference Gradle tasks removed from the new build, causing hard failures. The core Gradle migration and source-move appear correct, but these issues must be fixed before merging.

src/main/resources/logback-test.xml (wrong directory — must be src/test/resources/); Makefile (coverage and update targets broken, s3-test missing -plugins flag)

Important Files Changed

Filename	Overview
build.gradle	Root build.gradle rewritten to use io.nextflow.nextflow-plugin 1.0.0-beta.6; declares runtime deps and configures nextflowPlugin block cleanly
Makefile	Rewritten around assemble/installPlugin/releasePlugin; three P1/P2 issues: make coverage calls a removed jacocoTestReport task, make update calls a removed dependencyUpdates task, and s3-test is missing the -plugins flag
src/main/resources/logback-test.xml	P1: logback-test.xml placed in src/main/resources/ instead of src/test/resources/; will be packaged into the production JAR and force DEBUG root logging for all plugin users
src/test/groovy/nextflow/quilt/QuiltSpecification.groovy	Base test spec updated to read MANIFEST.MF from build/tmp/jar/ with legacy fallback paths; correct use of TestPluginDescriptorFinder override
src/test/groovy/nextflow/quilt/QuiltPkgTest.groovy	New test class with manifestVersion() helper; minor P2: FileInputStream not closed in try block
settings.gradle	Simplified to single rootProject.name line; legacy multi-project include and foojay toolchain resolver removed
.github/workflows/test.yml	Artifact upload paths updated from plugins/nf-quilt/build/reports/ to build/reports/ for both Windows and Linux/macOS runners
gradle.properties	Legacy JVM toolchain keys (groovyVersion, jdkVersion, javaLangVersion) removed; now only a comment explaining the new plugin handles these

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A[./gradlew assemble] --> B[build/libs/nf-quilt-0.9.2.zip]
    A --> C[build/tmp/jar/MANIFEST.MF]
    C --> D[QuiltSpecification.setupSpec\nreads MANIFEST.MF]
    D --> E[Plugins.init / startIfMissing]
    E --> F[Test suite runs\n226 tests]

    G[make install] --> H[./gradlew installPlugin]
    H --> I[~/.nextflow/plugins/nf-quilt-0.9.2/]
    I --> J[nextflow run ... -plugins nf-quilt@0.9.2]

    K[make release] --> L[./gradlew releasePlugin]
    L --> M[Seqera Plugin Registry]

    style C fill:#f9f,stroke:#c0c
    style D fill:#f9f,stroke:#c0c

Loading

Comments Outside Diff (1)

1. src/main/resources/logback-test.xml, line 1-31 (link)

   Test-only logback config packaged into production JAR

   logback-test.xml belongs in src/test/resources/, not src/main/resources/. By living in src/main/resources/ it will be included in the production plugin ZIP/JAR. Logback resolves logback-test.xml over logback.xml, so every Nextflow user who loads this plugin will inherit the <root level="DEBUG"> configuration, flooding their console with debug output from all loggers at runtime.

_{Reviews (1): Last reviewed commit: "Migrate to new Nextflow plugin build sys..." | Re-trigger Greptile}

Greptile also left 4 inline comments on this PR.

[github-actions]

🦙 MegaLinter status: ✅ SUCCESS

Descriptor	Linter	Files	Fixed	Errors	Warnings	Elapsed time
✅ REPOSITORY	checkov	yes		no	no	10.74s
✅ REPOSITORY	git_diff	yes		no	no	0.01s
✅ REPOSITORY	grype	yes		no	no	31.79s
✅ REPOSITORY	secretlint	yes		no	no	0.48s
✅ REPOSITORY	syft	yes		no	no	1.0s
✅ REPOSITORY	trivy	yes		no	no	6.3s
✅ REPOSITORY	trivy-sbom	yes		no	no	0.11s
✅ REPOSITORY	trufflehog	yes		no	no	2.29s
✅ XML	xmllint	1	0	0	0	0.31s
✅ YAML	prettier	1	0	0	0	0.39s
✅ YAML	v8r	1		0	0	2.93s
✅ YAML	yamllint	1		0	0	0.24s

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

[greptile-apps]

dependencyUpdates task not available in the new build

./gradlew dependencyUpdates is provided by the com.github.ben-manes.versions plugin, which was removed from the new build.gradle. Running make update will fail with "Task 'dependencyUpdates' not found". The old Makefile used useLatestVersions (from se.patrikerdes.use-latest-versions), also now absent. If dependency-update checking is still desired, the corresponding plugin should be re-added to build.gradle.

[drernie]

Fixed in ef33379 — removed the update Makefile target. Will reintroduce alongside a versions-plugin replacement if/when needed.