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build: Use nextflow gradle plugin #26

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@edmundmiller edmundmiller force-pushed the nextflow-plugin-gradle branch from 57e06ee to eacccc7 Compare April 10, 2025 15:01
Comment on lines +31 to 45
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

Comment on lines +64 to +65
// 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

Comment on lines 74 to +84
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')

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

Comment on lines +87 to +90
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

Comment on lines +131 to +132
// 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

Comment on lines +1 to +7
// 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

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Please keep this on hold, until we don't have a pre-production plugin and registry

@edmundmiller edmundmiller marked this pull request as draft April 16, 2025 18:02
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3 participants