build: Use nextflow gradle plugin #26
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edmundmiller
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bentsherman
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Apr 10, 2025
build.gradle
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| sourceSets { | ||
| main { | ||
| groovy { | ||
| srcDirs = ['src/main/groovy'] | ||
| } | ||
| resources { | ||
| srcDirs = ['src/main/resources'] | ||
| } | ||
| } | ||
| test { | ||
| groovy { | ||
| srcDirs = ['src/test/groovy'] | ||
| } | ||
| } | ||
| } |
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I think this can be removed
bentsherman
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Apr 10, 2025
build.gradle
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| // Replace commons-logging with jcl-over-slf4j | ||
| implementation 'org.slf4j:jcl-over-slf4j:2.0.7' |
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I think this can be removed
bentsherman
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Apr 10, 2025
build.gradle
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| testImplementation ("org.apache.groovy:groovy-test:4.0.23") { exclude group: 'org.apache.groovy' } | ||
| testImplementation ("cglib:cglib-nodep:3.3.0") | ||
| testImplementation ("org.objenesis:objenesis:3.1") | ||
| testImplementation ("org.spockframework:spock-core:2.3-groovy-4.0") { exclude group: 'org.apache.groovy'; exclude group: 'net.bytebuddy' } | ||
| testImplementation ('org.spockframework:spock-junit4:2.3-groovy-4.0') { exclude group: 'org.apache.groovy'; exclude group: 'net.bytebuddy' } | ||
| testImplementation ('com.google.jimfs:jimfs:1.1') | ||
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| testImplementation(testFixtures("io.nextflow:nextflow:$nextflowVersion")) | ||
| testImplementation(testFixtures("io.nextflow:nf-commons:$nextflowVersion")) | ||
| // Add back Nextflow test dependencies | ||
| testImplementation "io.nextflow:nextflow:${nextflowPlugin.nextflowVersion}" | ||
| testImplementation(testFixtures("io.nextflow:nextflow:${nextflowPlugin.nextflowVersion}")) | ||
| testImplementation(testFixtures("io.nextflow:nf-commons:${nextflowPlugin.nextflowVersion}")) |
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I think all of this can be removed
bentsherman
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Apr 10, 2025
build.gradle
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| configurations { | ||
| // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sub:exclude_transitive_dependencies | ||
| runtimeClasspath.exclude group: 'org.slf4j', module: 'slf4j-api' | ||
| } |
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I think this can be removed
bentsherman
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Apr 10, 2025
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| // AWS Athena dependencies setup - migrated from the original build.gradle | ||
| apply plugin: 'de.undercouch.download' |
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This can be moved to the plugins block at the top
bentsherman
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Apr 10, 2025
settings.gradle
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| // For the Nextflow plugin Gradle plugin | ||
| pluginManagement { | ||
| repositories { | ||
| mavenLocal() | ||
| gradlePluginPortal() | ||
| } | ||
| } |
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This should not be needed anymore since the nextflow gradle plugin was published to Maven Central
pditommaso
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Apr 10, 2025
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Worth to resume this now that the registry is avail |
Signed-off-by: Edmund Miller <[email protected]>
- Remove unnecessary sourceSets configuration per @bentsherman feedback - Remove explicit test dependencies (handled by plugin) - Remove SLF4J and runtime classpath exclusions - Simplify settings.gradle (remove pluginManagement block) - Keep only essential database dependencies and Athena tasks - Update to latest Nextflow Gradle plugin v1.0.0-beta.6 - Maintain full functionality while reducing complexity All tests pass and plugin builds/installs successfully. Co-authored-by: Ben Sherman <[email protected]> Signed-off-by: Edmund Miller <[email protected]>
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This pull request refactors the build and plugin management system for the project, simplifying the
Makefile, removing the root-levelplugins/build.gradle, and updating Gradle settings for plugin management. The changes streamline how plugins are built, tested, installed, and released, and shift plugin configuration to a more modern Gradle setup.Follows https://www.nextflow.io/docs/latest/guides/migrate-plugin.html